Size and Carbon Content of Sub-seafloor Microbial Cells at Landsort Deep, Baltic Sea

PubMed Central

Braun, Stefan; Morono, Yuki; Littmann, Sten; Kuypers, Marcel; Aslan, Hüsnü; Dong, Mingdong; Jørgensen, Bo B.; Lomstein, Bente Aa.

2016-01-01

The discovery of a microbial ecosystem in ocean sediments has evoked interest in life under extreme energy limitation and its role in global element cycling. However, fundamental parameters such as the size and the amount of biomass of sub-seafloor microbial cells are poorly constrained. Here we determined the volume and the carbon content of microbial cells from a marine sediment drill core retrieved by the Integrated Ocean Drilling Program (IODP), Expedition 347, at Landsort Deep, Baltic Sea. To determine their shape and volume, cells were separated from the sediment matrix by multi-layer density centrifugation and visualized via epifluorescence microscopy (FM) and scanning electron microscopy (SEM). Total cell-carbon was calculated from amino acid-carbon, which was analyzed by high-performance liquid chromatography (HPLC) after cells had been purified by fluorescence-activated cell sorting (FACS). The majority of microbial cells in the sediment have coccoid or slightly elongated morphology. From the sediment surface to the deepest investigated sample (~60 m below the seafloor), the cell volume of both coccoid and elongated cells decreased by an order of magnitude from ~0.05 to 0.005 μm3. The cell-specific carbon content was 19–31 fg C cell−1, which is at the lower end of previous estimates that were used for global estimates of microbial biomass. The cell-specific carbon density increased with sediment depth from about 200 to 1000 fg C μm−3, suggesting that cells decrease their water content and grow small cell sizes as adaptation to the long-term subsistence at very low energy availability in the deep biosphere. We present for the first time depth-related data on the cell volume and carbon content of sedimentary microbial cells buried down to 60 m below the seafloor. Our data enable estimates of volume- and biomass-specific cellular rates of energy metabolism in the deep biosphere and will improve global estimates of microbial biomass. PMID:27630628

Effect of red blood cells on the growth of Porphyromonas endodontalis and microbial community development.

PubMed

Zerr, M A; Cox, C D; Johnson, W T; Drake, D R

1998-04-01

Establishment of a microbial community in the root canal system depends on numerous factors, of which nutrient availability may be one of the most important. We hypothesized that the presence of red blood cells or hemoglobin in this environment could cause shifts in microbial composition of communities, resulting in organisms such as Porphyromonas endodontalis becoming more dominant. An in vitro model system using mixed, batch cultures was performed with the bacteria P. endodontalis, Fusobacterium nucleatum, Peptostreptococcus micros and Campylobacter rectus. Bacteria were cultured in media with or without the addition of washed red blood cells, hemoglobin, or serum. Cyclic growth studies revealed that P. endodontalis was lost from the community of organisms after three cycles. However, inclusion of red blood cells resulted in establishment of this organism. Moreover, red blood cells added to pure cultures of P. endodontalis substantially enhanced growth and protected the organisms from oxygen. We conclude that the presence of red blood cells could result in shifts of microbial communities of organisms within the root canal system.

Thousands of Viral Populations Recovered from Peatland Soil Metagenomes Reveal Viral Impacts on Carbon Cycling in Thawing Permafrost

NASA Astrophysics Data System (ADS)

Emerson, J. B.; Brum, J. R.; Roux, S.; Bolduc, B.; Woodcroft, B. J.; Singleton, C. M.; Boyd, J. A.; Hodgkins, S. B.; Wilson, R.; Trubl, G. G.; Jang, H. B.; Crill, P. M.; Chanton, J.; Saleska, S. R.; Rich, V. I.; Tyson, G. W.; Sullivan, M. B.

2016-12-01

Methane and carbon dioxide emissions, which are under significant microbial control, provide positive feedbacks to climate change in thawing permafrost peatlands. Although viruses in marine systems have been shown to impact microbial ecology and biogeochemical cycling through host cell lysis, horizontal gene transfer, and auxiliary metabolic gene expression, viral ecology in permafrost and other soils remains virtually unstudied due to methodological challenges. Here, we identified viral sequences in 208 assembled bulk soil metagenomes derived from a permafrost thaw gradient in Stordalen Mire, northern Sweden, from 2010-2012. 2,048 viral populations were recovered, which genome- and network-based classification revealed to be largely novel, increasing known viral genera globally by 40%. Ecologically, viral communities differed significantly across the thaw gradient and by soil depth. Co-occurring microbial community composition, soil moisture, and pH were predictors of viral community composition, indicative of biological and biogeochemical feedbacks as permafrost thaws. Host prediction—achieved through clustered regularly interspaced short palindromic repeats (CRISPRs), tetranucleotide frequency patterns, and other sequence similarities to binned microbial population genomes—was able to link 38% of the viral populations to a microbial host. 5% of the implicated hosts were archaea, predominantly methanogens and ammonia-oxidizing Nitrososphaera, 45% were Acidobacteria or Verrucomicrobia (mostly predicted heterotrophic complex carbon degraders), and 21% were Proteobacteria, including methane oxidizers. Recovered viral genome fragments also contained auxiliary metabolic genes involved in carbon and nitrogen cycling. Together, these data reveal multiple levels of previously unknown viral contributions to biogeochemical cycling, including to carbon gas emissions, in peatland soils undergoing and contributing to climate change. This work represents a significant step towards understanding viral roles in microbially-mediated biogeochemical cycling in soil.

Geomicrobiology of subglacial meltwater samples from Store Landgletscher and Russell Glacier, West Greenland

NASA Astrophysics Data System (ADS)

Cameron, K. A.; Dieser, M.; Choquette, K.; Christner, B. C.; Hagedorn, B.; Harrold, Z.; Liu, L.; Sletten, R. S.; Junge, K.

2012-12-01

The melting of the Greenland Ice Sheet provides direct connections between atmospheric, supraglacial and subglacial environments. The intraglacial hydrological pathways that result are believed to accommodate the microbial colonization of subglacial environments; however, little is known about the abundance, diversity and activity of microorganisms within these niches. The Greenland Ice Sheet (1.7 million square kilometers) and its associated surpaglacial and subglacial ecosystems may contribute significantly to biogeochemical cycling processes. We analyzed subglacial microbial assemblages in subglacial outflows, near Thule and Kangerlussuaq, West Greenland. The investigative approach included correlating microbial diversity, inferred function, abundance, melt water chemistry, O-18 water isotope ratios, alkalinity and sediment load. Using Illumina sequencing, bacterial small subunit ribosomal RNA hypervariable regions have been targeted and amplified from both extracted DNA and reverse transcribed rRNA. Over 3 billion sequence reads have been generated to create a comprehensive diversity profile. Total abundances ranged from 2.24E+04 to 1.58E+06 cells mL-1. In comparison, the total abundance of supraglacial early season snow samples ranged from 3.35E+02 to 2.8E+04 cells mL-1. 65 % of samples incubated with cyano ditoyl tetrazolium chloride (CTC), used to identify actively respiring cells, contained CTC-positive cells. On average, these cells represented 1.9 % of the estimated total abundance (1.86E+02 to 2.19E+03 CTC positive cells mL-1; 1.39E+03 cells mL-1 standard deviation); comparative to those measured in temperate freshwater lakes. The overarching objective of our research is to provide data that indicates the role of microbial communities, associated with ice sheets, in elemental cycling and in the release of biomass and nutrients to the surrounding marine biome.

Systems Level Dissection of Anaerobic Methane Cycling: Quantitative Measurements of Single Cell Ecophysiology, Genetic Mechanisms, and Microbial Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orphan, Victoria; Tyson, Gene; Meile, Christof

The global biological CH4 cycle is largely controlled through coordinated and often intimate microbial interactions between archaea and bacteria, the majority of which are still unknown or have been only cursorily identified. Members of the methanotrophic archaea, aka ‘ANME’, are believed to play a major role in the cycling of methane in anoxic environments coupled to sulfate, nitrate, and possibly iron and manganese oxides, frequently forming diverse physical and metabolic partnerships with a range of bacteria. The thermodynamic challenges overcome by the ANME and their bacterial partners and corresponding slow rates of growth are common characteristics in anaerobic ecosystems, and,more » in stark contrast to most cultured microorganisms, this type of energy and resource limited microbial lifestyle is likely the norm in the environment. While we have gained an in-depth systems level understanding of fast-growing, energy-replete microorganisms, comparatively little is known about the dynamics of cell respiration, growth, protein turnover, gene expression, and energy storage in the slow-growing microbial majority. These fundamental properties, combined with the observed metabolic and symbiotic versatility of methanotrophic ANME, make these cooperative microbial systems a relevant (albeit challenging) system to study and for which to develop and optimize culture-independent methodologies, which enable a systems-level understanding of microbial interactions and metabolic networks. We used an integrative systems biology approach to study anaerobic sediment microcosms and methane-oxidizing bioreactors and expanded our understanding of the methanotrophic ANME archaea, their interactions with physically-associated bacteria, ecophysiological characteristics, and underlying genetic basis for cooperative microbial methane-oxidation linked with different terminal electron acceptors. Our approach is inherently multi-disciplinary and multi-scaled, combining transcriptional and proteomic analyses with high resolution microscopy techniques, and stable isotopic and chemical analyses that span community level ‘omics investigations (cm scale) to interspecies consortia (µm scale), to the individual cell and its subcellular components (nm scale). We have organized our methodological approach into three broad categories, RNA-based, Protein-targeted and Geochemical, each encompassing a range of scales, with many techniques and resulting datasets that are highly complementary with one another, and together, offer a unique systems-level perspective of methane-based microbial interactions.« less

Fibrous polyaniline@manganese oxide nanocomposites as supercapacitor electrode materials and cathode catalysts for improved power production in microbial fuel cells.

PubMed

Ansari, Sajid Ali; Parveen, Nazish; Han, Thi Hiep; Ansari, Mohammad Omaish; Cho, Moo Hwan

2016-04-07

Fibrous Pani-MnO2 nanocomposite were prepared using a one-step and scalable in situ chemical oxidative polymerization method. The formation, structural and morphological properties were investigated using a range of characterization techniques. The electrochemical capacitive behavior of the fibrous Pani-MnO2 nanocomposite was examined by cyclic voltammetry and galvanostatic charge-discharge measurements using a three-electrode experimental setup in an aqueous electrolyte. The fibrous Pani-MnO2 nanocomposite achieved high capacitance (525 F g(-1) at a current density of 2 A g(-1)) and excellent cycling stability of 76.9% after 1000 cycles at 10 A g(-1). Furthermore, the microbial fuel cell constructed with the fibrous Pani-MnO2 cathode catalyst showed an improved power density of 0.0588 W m(-2), which was higher than that of pure Pani and carbon paper, respectively. The improved electrochemical supercapacitive performance and cathode catalyst performance in microbial fuel cells were attributed mainly to the synergistic effect of Pani and MnO2 in fibrous Pani-MnO2, which provides high surface area for the electrode/electrolyte contact as well as electronic conductive channels and exhibits pseudocapacitance behavior.

Watch Out for the “Living Dead”: Cell-Free Enzymes and Their Fate

PubMed Central

Baltar, Federico

2018-01-01

Microbes are the engines driving biogeochemical cycles. Microbial extracellular enzymatic activities (EEAs) are the “gatekeepers” of the carbon cycle. The total EEA is the sum of cell-bound (i.e., cell-attached), and dissolved (i.e., cell-free) enzyme activities. Cell-free enzymes make up a substantial proportion (up to 100%) of the total marine EEA. Although we are learning more about how microbial diversity and function (including total EEA) will be affected by environmental changes, little is known about what factors control the importance of the abundant cell-free enzymes. Since cell-attached EEAs are linked to the cell, their fate will likely be linked to the factors controlling the cell’s fate. In contrast, cell-free enzymes belong to a kind of “living dead” realm because they are not attached to a living cell but still are able to perform their function away from the cell; and as such, the factors controlling their activity and fate might differ from those affecting cell-attached enzymes. This article aims to place cell-free EEA into the wider context of hydrolysis of organic matter, deal with recent studies assessing what controls the production, activity and lifetime of cell-free EEA, and what their fate might be in response to environmental stressors. This perspective article advocates the need to go “beyond the living things,” studying the response of cells/organisms to different stressors, but also to study cell-free enzymes, in order to fully constrain the future and evolution of marine biogeochemical cycles. PMID:29354095

Effect of temperature and cycle length on microbial competition in PHB-producing sequencing batch reactor.

PubMed

Jiang, Yang; Marang, Leonie; Kleerebezem, Robbert; Muyzer, Gerard; van Loosdrecht, Mark C M

2011-05-01

The impact of temperature and cycle length on microbial competition between polyhydroxybutyrate (PHB)-producing populations enriched in feast-famine sequencing batch reactors (SBRs) was investigated at temperatures of 20 °C and 30 °C, and in a cycle length range of 1-18 h. In this study, the microbial community structure of the PHB-producing enrichments was found to be strongly dependent on temperature, but not on cycle length. Zoogloea and Plasticicumulans acidivorans dominated the SBRs operated at 20 °C and 30 °C, respectively. Both enrichments accumulated PHB more than 75% of cell dry weight. Short-term temperature change experiments revealed that P. acidivorans was more temperature sensitive as compared with Zoogloea. This is particularly true for the PHB degradation, resulting in incomplete PHB degradation in P. acidivorans at 20 °C. Incomplete PHB degradation limited biomass growth and allowed Zoogloea to outcompete P. acidivorans. The PHB content at the end of the feast phase correlated well with the cycle length at a constant solid retention time (SRT). These results suggest that to establish enrichment with the capacity to store a high fraction of PHB, the number of cycles per SRT should be minimized independent of the temperature.

Use of pressure cycling technology for cell lysis and recovery of bacterial and fungal communities from soil

USDA-ARS?s Scientific Manuscript database

Current molecular methodologies, specifically DNA-based approaches, provide access to previously hidden soil biodiversity and are routinely employed in environmental studies of microbial ecology. Selection of cell lysis methodology is critical to community analyses due to the inability of any singul...

Restriction Endonucleases from Invasive Neisseria gonorrhoeae Cause Double-Strand Breaks and Distort Mitosis in Epithelial Cells during Infection

PubMed Central

Weyler, Linda; Engelbrecht, Mattias; Mata Forsberg, Manuel; Brehwens, Karl; Vare, Daniel; Vielfort, Katarina; Wojcik, Andrzej; Aro, Helena

2014-01-01

The host epithelium is both a barrier against, and the target for microbial infections. Maintaining regulated cell growth ensures an intact protective layer towards microbial-induced cellular damage. Neisseria gonorrhoeae infections disrupt host cell cycle regulation machinery and the infection causes DNA double strand breaks that delay progression through the G2/M phase. We show that intracellular gonococci upregulate and release restriction endonucleases that enter the nucleus and damage human chromosomal DNA. Bacterial lysates containing restriction endonucleases were able to fragment genomic DNA as detected by PFGE. Lysates were also microinjected into the cytoplasm of cells in interphase and after 20 h, DNA double strand breaks were identified by 53BP1 staining. In addition, by using live-cell microscopy and NHS-ester stained live gonococci we visualized the subcellular location of the bacteria upon mitosis. Infected cells show dysregulation of the spindle assembly checkpoint proteins MAD1 and MAD2, impaired and prolonged M-phase, nuclear swelling, micronuclei formation and chromosomal instability. These data highlight basic molecular functions of how gonococcal infections affect host cell cycle regulation, cause DNA double strand breaks and predispose cellular malignancies. PMID:25460012

Restriction endonucleases from invasive Neisseria gonorrhoeae cause double-strand breaks and distort mitosis in epithelial cells during infection.

PubMed

Weyler, Linda; Engelbrecht, Mattias; Mata Forsberg, Manuel; Brehwens, Karl; Vare, Daniel; Vielfort, Katarina; Wojcik, Andrzej; Aro, Helena

2014-01-01

The host epithelium is both a barrier against, and the target for microbial infections. Maintaining regulated cell growth ensures an intact protective layer towards microbial-induced cellular damage. Neisseria gonorrhoeae infections disrupt host cell cycle regulation machinery and the infection causes DNA double strand breaks that delay progression through the G2/M phase. We show that intracellular gonococci upregulate and release restriction endonucleases that enter the nucleus and damage human chromosomal DNA. Bacterial lysates containing restriction endonucleases were able to fragment genomic DNA as detected by PFGE. Lysates were also microinjected into the cytoplasm of cells in interphase and after 20 h, DNA double strand breaks were identified by 53BP1 staining. In addition, by using live-cell microscopy and NHS-ester stained live gonococci we visualized the subcellular location of the bacteria upon mitosis. Infected cells show dysregulation of the spindle assembly checkpoint proteins MAD1 and MAD2, impaired and prolonged M-phase, nuclear swelling, micronuclei formation and chromosomal instability. These data highlight basic molecular functions of how gonococcal infections affect host cell cycle regulation, cause DNA double strand breaks and predispose cellular malignancies.

Microbial Influences on Trace Metal Cycling in a Meromictic Lake, Fayetteville Green Lake, NY

NASA Astrophysics Data System (ADS)

Zerkle, A. L.; House, C.; Kump, L.

2002-12-01

Microorganisms can exist in aquatic environments at very high cell densities of up to 1011 cells/L, and can accumulate significant quantities of trace metals. Bacteria actively take up bioactive trace metals, including Fe, Zn, Mn, Co, Ni, Cu, and Mo, which function as catalytic centers in metalloproteins and metal-activated enzymes involved in virtually all cellular functions. In addition, bacteria may catalyze the release of trace metals from inorganic substrates by processes such as the reduction of iron and manganese oxides, suggesting that trace metal distributions within a natural environment dominated by microbial processes may be controlled primarily by microbial ecology. Fayetteville Green Lake (FGL), NY, is a permanently stratified meromictic lake that has a well-oxygenated surface water mass (mixolimnion) overlying a relatively stagnant, anoxic deep water mass (monimolimnion). A chemocline separates the water masses at around 20m depth, where oxygen concentrations decrease and sulfate and methane concentrations increase. In addition, previous studies have indicated that trace metals such as V, Cr, Co, Mn, and Fe reach elevated concentrations at the chemocline. Using fluorescent in situ hybridization (FISH) of FGL samples from depths of up to 40m with bacterial and archaeal probes, we have shown that fluctuating redox conditions within the FGL water column correlate with significant variations in the composition and distribution of microbial populations with depth. The mixolimnion is dominated by Eubacteria, with increasing concentrations of Archaea in the lower anoxic zone. Increases in microbial cell densities coincide with increases in trace metals at the chemocline, suggesting microbial activity may be responsible for trace metal release at this boundary. 16S rRNA PCR cloning techniques are currently being used to identify dominant microbial populations at various levels within the FGL water column. Future studies will focus on the potential for these dominant microorganisms to influence trace metal cycling and bioavailability in the FGL water column.

Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex

PubMed Central

Kubo, Yusuke; Hoshino, Tatsuhiko; Sakai, Sanae; Arnold, Gail L.; Case, David H.; Lever, Mark A.; Morita, Sumito; Nakamura, Ko-ichi

2018-01-01

Microbial life inhabiting subseafloor sediments plays an important role in Earth’s carbon cycle. However, the impact of geodynamic processes on the distributions and carbon-cycling activities of subseafloor life remains poorly constrained. We explore a submarine mud volcano of the Nankai accretionary complex by drilling down to 200 m below the summit. Stable isotopic compositions of water and carbon compounds, including clumped methane isotopologues, suggest that ~90% of methane is microbially produced at 16° to 30°C and 300 to 900 m below seafloor, corresponding to the basin bottom, where fluids in the accretionary prism are supplied via megasplay faults. Radiotracer experiments showed that relatively small microbial populations in deep mud volcano sediments (102 to 103 cells cm−3) include highly active hydrogenotrophic methanogens and acetogens. Our findings indicate that subduction-associated fluid migration has stimulated microbial activity in the mud reservoir and that mud volcanoes may contribute more substantially to the methane budget than previously estimated. PMID:29928689

Radioisotope tracer studies of inorganic carbon and Ca in microbially derived CaCO3

USGS Publications Warehouse

Yates, Kimberly K.; Robbins, Lisa L.

1999-01-01

Microbial calcification significantly impacts the cycling and deposition of inorganic carbon. This research employs 45Ca and 14C techniques as radioisotopic tracers to examine the role of cellular cycling of Ca2+ and inorganic carbon in CaCO3 precipitation by the unicellular green alga Nannochloris atomus. Implications of the effects of these physiological aspects on CaCO3 precipitation and the effects of microbial calcification on CaCO3 δ13C ratios are discussed. Results from pulse/chase experiments indicate that intracellular Ca2+ is incorporated into extracellular CaCO3. Intracellular inorganic carbon leaks from cells within 10 to 12 s after injection of unlabelled NaHCO3, providing a source of inorganic carbon for extracellular CaCO3. Cellular expulsion of calcium plays a key role in increasing the CaCO3 saturation state at the site of calcification. The δ13C ratios of microbial carbonates may vary depending on the amount of photorespiratory CO2 incorporated.

Microbial iron redox cycling in a circumneutral-pH groundwater seep.

PubMed

Blöthe, Marco; Roden, Eric E

2009-01-01

The potential for microbially mediated redox cycling of iron (Fe) in a circumneutral-pH groundwater seep in north central Alabama was studied. Incubation of freshly collected seep material under anoxic conditions with acetate-lactate or H(2) as an electron donor revealed the potential for rapid Fe(III) oxide reduction (ca. 700 to 2,000 micromol liter(-1) day(-1)). Fe(III) reduction at lower but significant rates took place in unamended controls (ca. 300 micromol liter(-1) day(-1)). Culture-based enumerations (most probable numbers [MPNs]) revealed significant numbers (10(2) to 10(6) cells ml(-1)) of organic carbon- and H(2)-oxidizing dissimilatory Fe(III)-reducing microorganisms. Three isolates with the ability to reduce Fe(III) oxides by dissimilatory or fermentative metabolism were obtained (Geobacter sp. strain IST-3, Shewanella sp. strain IST-21, and Bacillus sp. strain IST-38). MPN analysis also revealed the presence of microaerophilic Fe(II)-oxidizing microorganisms (10(3) to 10(5) cells ml(-1)). A 16S rRNA gene library from the iron seep was dominated by representatives of the Betaproteobacteria including Gallionella, Leptothrix, and Comamonas species. Aerobic Fe(II)-oxidizing Comamonas sp. strain IST-3 was isolated. The 16S rRNA gene sequence of this organism is 100% similar to the type strain of the betaproteobacterium Comamonas testosteroni (M11224). Testing of the type strain showed no Fe(II) oxidation. Collectively our results suggest that active microbial Fe redox cycling occurred within this habitat and support previous conceptual models for how microbial Fe oxidation and reduction can be coupled in surface and subsurface sedimentary environments.

Winter survival of microbial contaminants in soil: an in situ verification.

PubMed

Bucci, Antonio; Allocca, Vincenzo; Naclerio, Gino; Capobianco, Giovanni; Divino, Fabio; Fiorillo, Francesco; Celico, Fulvio

2015-01-01

The aim of the research was to evaluate, at site scale, the influence of freezing and freeze/thaw cycles on the survival of faecal coliforms and faecal enterococci in soil, in a climate change perspective. Before the winter period and during grazing, viable cells of faecal coliforms and faecal enterococci were detected only in the first 10 cm below ground, while, after the winter period and before the new seasonal grazing, a lower number of viable cells of both faecal indicators was detected only in some of the investigated soil profiles, and within the first 5 cm. Taking into consideration the results of specific investigations, we hypothesise that the non-uniform spatial distribution of grass roots within the studied soil can play an important role in influencing this phenomenon, while several abiotic factors do not play any significant role. Taking into account the local trend in the increase of air temperature, a different distribution of microbial pollution over time is expected in spring waters, in future climate scenarios. The progressive increase in air temperature will cause a progressive decrease in freeze/thaw cycles at higher altitudes, minimising cold shocks on microbial cells, and causing spring water pollution also during winter. Copyright © 2014. Published by Elsevier B.V.

Interferon-inducible effector mechanisms in cell-autonomous immunity

PubMed Central

MacMicking, John D.

2014-01-01

Interferons (IFNs) induce the expression of hundreds of genes as part of an elaborate antimicrobial programme designed to combat infection in all nucleated cells — a process termed cell-autonomous immunity. As described in this Review, recent genomic and subgenomic analyses have begun to assign functional properties to novel IFN-inducible effector proteins that restrict bacteria, protozoa and viruses in different subcellular compartments and at different stages of the pathogen life cycle. Several newly described host defence factors also participate in canonical oxidative and autophagic pathways by spatially coordinating their activities to enhance microbial killing. Together, these IFN-induced effector networks help to confer vertebrate host resistance to a vast and complex microbial world. PMID:22531325

The possible interplanetary transfer of microbes: assessing the viability of Deinococcus spp. under the ISS Environmental conditions for performing exposure experiments of microbes in the Tanpopo mission.

PubMed

Kawaguchi, Yuko; Yang, Yinjie; Kawashiri, Narutoshi; Shiraishi, Keisuke; Takasu, Masako; Narumi, Issay; Satoh, Katsuya; Hashimoto, Hirofumi; Nakagawa, Kazumichi; Tanigawa, Yoshiaki; Momoki, Yoh-Hei; Tanabe, Maiko; Sugino, Tomohiro; Takahashi, Yuta; Shimizu, Yasuyuki; Yoshida, Satoshi; Kobayashi, Kensei; Yokobori, Shin-Ichi; Yamagishi, Akihiko

2013-10-01

To investigate the possible interplanetary transfer of life, numerous exposure experiments have been carried out on various microbes in space since the 1960s. In the Tanpopo mission, we have proposed to carry out experiments on capture and space exposure of microbes at the Exposure Facility of the Japanese Experimental Module of the International Space Station (ISS). Microbial candidates for the exposure experiments in space include Deinococcus spp.: Deinococcus radiodurans, D. aerius and D. aetherius. In this paper, we have examined the survivability of Deinococcus spp. under the environmental conditions in ISS in orbit (i.e., long exposure to heavy-ion beams, temperature cycles, vacuum and UV irradiation). A One-year dose of heavy-ion beam irradiation did not affect the viability of Deinococcus spp. within the detection limit. Vacuum (10(-1) Pa) also had little effect on the cell viability. Experiments to test the effects of changes in temperature from 80 °C to -80 °C in 90 min (± 80 °C/90 min cycle) or from 60 °C to -60 °C in 90 min (± 60 °C/90 min cycle) on cell viability revealed that the survival rate decreased severely by the ± 80 °C/90 min temperature cycle. Exposure of various thicknesses of deinococcal cell aggregates to UV radiation (172 nm and 254 nm, respectively) revealed that a few hundred micrometer thick aggregate of deinococcal cells would be able to withstand the solar UV radiation on ISS for 1 year. We concluded that aggregated deinococcal cells will survive the yearlong exposure experiments. We propose that microbial cells can aggregate as an ark for the interplanetary transfer of microbes, and we named it 'massapanspermia'.

Microbial fuel cell as a biocapacitor by using pseudo-capacitive anode materials

NASA Astrophysics Data System (ADS)

Lv, Zhisheng; Xie, Daohai; Li, Fusheng; Hu, Yun; Wei, Chaohai; Feng, Chunhua

2014-01-01

Here, we report that the microbial fuel cell (MFC) containing pseudo-capacitive anode materials such as polypyrrole (PPy)/9,10-anthraquinone-2-sulfonic acid sodium salt (AQS) composite films and RuO2 nanoparticles can function as a biocapacitor, able to store bioelectrons generated from microbial oxidation of substrate and release the accumulated charge upon requirement. Influences of the specific capacitance of the PPy/AQS- and RuO2-modified carbon felt anodes on the extent of accumulated charge are examined. Results show that increasing anode capacitance is responsible for the increases in the amount of electrons stored and released, and thereby leading to more energy stored and average power dissipated. The long-term charging-discharging tests indicate that the RuO2-modified biocapacitor with a specific capacitance of 3.74 F cm-2 exhibits 6% loss in the amount of released charge over 10 cycles for one-month operation, and 40% loss over 60 cycles for six-month operation. Our findings suggest that the MFC anode incorporating pseudo-capacitive materials shows potential for storing energy from waste organic matter and releasing in a short time of high power to the electronic device.

A Microbial Avenue to Cell Cycle Control in the Plant Superkingdom[C][W][OPEN

PubMed Central

Tulin, Frej; Cross, Frederick R.

2014-01-01

Research in yeast and animals has resulted in a well-supported consensus model for eukaryotic cell cycle control. The fit of this model to early diverging eukaryotes, such as the plant kingdom, remains unclear. Using the green alga Chlamydomonas reinhardtii, we developed an efficient pipeline, incorporating robotics, semiautomated image analysis, and deep sequencing, to molecularly identify >50 genes, mostly conserved in higher plants, specifically required for cell division but not cell growth. Mutated genes include the cyclin-dependent kinases CDKA (resembling yeast and animal Cdk1) and the plant-specific CDKB. The Chlamydomonas cell cycle consists of a long G1 during which cells can grow >10-fold, followed by multiple rapid cycles of DNA replication and segregation. CDKA and CDKB execute nonoverlapping functions: CDKA promotes transition between G1 and entry into the division cycle, while CDKB is essential specifically for spindle formation and nuclear division, but not for DNA replication, once CDKA-dependent initiation has occurred. The anaphase-promoting complex is required for similar steps in the Chlamydomonas cell cycle as in Opisthokonts; however, the spindle assembly checkpoint, which targets the APC in Opisthokonts, appears severely attenuated in Chlamydomonas, based on analysis of mutants affecting microtubule function. This approach allows unbiased integration of the consensus cell cycle control model with innovations specific to the plant lineage. PMID:25336509

Survival of microbial isolates from clouds toward simulated atmospheric stress factors

NASA Astrophysics Data System (ADS)

Joly, Muriel; Amato, Pierre; Sancelme, Martine; Vinatier, Virginie; Abrantes, Magali; Deguillaume, Laurent; Delort, Anne-Marie

2015-09-01

In the atmosphere, airborne microbial cells are exposed to conditions that are thought to affect their survival. Here, we investigated the survival of 5 microorganisms among the most represented in the cultivable community of clouds (4 bacteria affiliated to Pseudomonas, Sphingomonas and Arthrobacter and 1 yeast of Dioszegia) after exposition to different atmospheric factors generally considered stressful for cells: artificial solar light (10 h), oxidant (hydrogen peroxide: 0-1 mM for 90 min), osmotic shocks (0.1-2.5 M NaCl) and freeze-thaw cycles (6 cycles of 5 °C/-40 °C). Each condition was applied separately to cell suspensions, and survival rates were examined by culture. Survival was highly strain and stress dependent, with no relationship with pigmentation or ice nucleation activity. In all strains, solar light had no or mitigated influence, and exposition to H2O2 at the concentration measured in cloud water only slightly impacted viability (>70% of the cells survived). The strain Sphingomonas sp. was particularly impacted by osmotic shocks while repeated freeze-thaw was particularly damaging for Arthrobacter and Pseudomonas species. Overall, our results tend to indicate that in the atmosphere, the most stringent selection factors on living organisms are probably freeze-thaw and condensation/evaporation (osmotic shocks) cycles, whereas the impacts of oxidants and of solar light are limited.

Variations in microbial carbon sources and cycling in the deep continental subsurface

NASA Astrophysics Data System (ADS)

Simkus, Danielle N.; Slater, Greg F.; Lollar, Barbara Sherwood; Wilkie, Kenna; Kieft, Thomas L.; Magnabosco, Cara; Lau, Maggie C. Y.; Pullin, Michael J.; Hendrickson, Sarah B.; Wommack, K. Eric; Sakowski, Eric G.; van Heerden, Esta; Kuloyo, Olukayode; Linage, Borja; Borgonie, Gaetan; Onstott, Tullis C.

2016-01-01

Deep continental subsurface fracture water systems, ranging from 1.1 to 3.3 km below land surface (kmbls), were investigated to characterize the indigenous microorganisms and elucidate microbial carbon sources and their cycling. Analysis of phospholipid fatty acid (PLFA) abundances and direct cell counts detected varying biomass that was not correlated with depth. Compound-specific carbon isotope analyses (δ13C and Δ14C) of the phospholipid fatty acids (PLFAs) and carbon substrates combined with genomic analyses did identify, however, distinct carbon sources and cycles between the two depth ranges studied. In the shallower boreholes at circa 1 kmbls, isotopic evidence indicated microbial incorporation of biogenic CH4 by the in situ microbial community. At the shallowest site, 1.05 kmbls in Driefontein mine, this process clearly dominated the isotopic signal. At slightly deeper depths, 1.34 kmbls in Beatrix mine, the isotopic data indicated the incorporation of both biogenic CH4 and dissolved inorganic carbon (DIC) derived from CH4 oxidation. In both of these cases, molecular genetic analysis indicated that methanogenic and methanotrophic organisms together comprised a small component (<5%) of the microbial community. Thus, it appears that a relatively minor component of the prokaryotic community is supporting a much larger overall bacterial community in these samples. In the samples collected from >3 kmbls in Tau Tona mine (TT107, TT109 Bh2), the CH4 had an isotopic signature suggesting a predominantly abiogenic origin with minor inputs from microbial methanogenesis. In these samples, the isotopic enrichments (δ13C and Δ14C) of the PLFAs relative to CH4 were consistent with little incorporation of CH4 into the biomass. The most 13C-enriched PLFAs were observed in TT107 where the dominant CO2-fixation pathway was the acetyl-CoA pathway by non-acetogenic bacteria. The differences in the δ13C of the PLFAs and the DIC and DOC for TT109 Bh2 were ∼-24‰ and 0‰, respectively. The dominant CO2-fixation pathways were 3-HP/4-HB cycle > acetyl-CoA pathway > reductive pentose phosphate cycle.

Paleobiological Perspectives on Early Microbial Evolution

PubMed Central

Knoll, Andrew H.

2015-01-01

Microfossils, stromatolites, and chemical biosignatures indicate that Earth became a biological planet more than 3.5 billion years ago, making most of life's history microbial. Proterozoic rocks preserve a rich record of cyanobacteria, including derived forms that differentiate multiple cell types. Stromatolites, in turn, show that microbial communities covered the seafloor from tidal flats to the base of the photic zone. The Archean record is more challenging to interpret, particularly on the question of cyanobacterial antiquity, which remains to be resolved. In the late Neoproterozoic Era, increasing oxygen and radiating eukaryotes altered the biosphere, with planktonic algae gaining ecological prominence in the water column, whereas seaweeds and, eventually, animals spread across shallow seafloors. From a microbial perspective, however, animals, algae, and, later, plants simply provided new opportunities for diversification, and, to this day, microbial metabolisms remain the only essential components of biogeochemical cycles. PMID:26134315

Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

NASA Astrophysics Data System (ADS)

Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

2014-12-01

Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake

PubMed Central

Li, Wei; Podar, Mircea

2016-01-01

ABSTRACT The McMurdo Dry Valleys (MCM) of southern Victoria Land, Antarctica, harbor numerous ice-covered bodies of water that provide year-round liquid water oases for isolated food webs dominated by the microbial loop. Single-cell microbial eukaryotes (protists) occupy major trophic positions within this truncated food web, ranging from primary producers (e.g., chlorophytes, haptophytes, and cryptophytes) to tertiary predators (e.g., ciliates, dinoflagellates, and choanoflagellates). To advance the understanding of MCM protist ecology and the roles of MCM protists in nutrient and energy cycling, we investigated potential metabolic strategies and microbial interactions of key MCM protists isolated from a well-described lake (Lake Bonney). Fluorescence-activated cell sorting (FACS) of enrichment cultures, combined with single amplified genome/amplicon sequencing and fluorescence microscopy, revealed that MCM protists possess diverse potential metabolic capabilities and interactions. Two metabolically distinct bacterial clades (Flavobacteria and Methylobacteriaceae) were independently associated with two key MCM lake microalgae (Isochrysis and Chlamydomonas, respectively). We also report on the discovery of two heterotrophic nanoflagellates belonging to the Stramenopila supergroup, one of which lives as a parasite of Chlamydomonas, a dominate primary producer in the shallow, nutrient-poor layers of the lake. IMPORTANCE Single-cell eukaryotes called protists play critical roles in the cycling of organic matter in aquatic environments. In the ice-covered lakes of Antarctica, protists play key roles in the aquatic food web, providing the majority of organic carbon to the rest of the food web (photosynthetic protists) and acting as the major consumers at the top of the food web (predatory protists). In this study, we utilized a combination of techniques (microscopy, cell sorting, and genomic analysis) to describe the trophic abilities of Antarctic lake protists and their potential interactions with other microbes. Our work reveals that Antarctic lake protists rely on metabolic versatility for their energy and nutrient requirements in this unique and isolated environment. PMID:27084010

Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake.

PubMed

Li, Wei; Podar, Mircea; Morgan-Kiss, Rachael M

2016-06-15

The McMurdo Dry Valleys (MCM) of southern Victoria Land, Antarctica, harbor numerous ice-covered bodies of water that provide year-round liquid water oases for isolated food webs dominated by the microbial loop. Single-cell microbial eukaryotes (protists) occupy major trophic positions within this truncated food web, ranging from primary producers (e.g., chlorophytes, haptophytes, and cryptophytes) to tertiary predators (e.g., ciliates, dinoflagellates, and choanoflagellates). To advance the understanding of MCM protist ecology and the roles of MCM protists in nutrient and energy cycling, we investigated potential metabolic strategies and microbial interactions of key MCM protists isolated from a well-described lake (Lake Bonney). Fluorescence-activated cell sorting (FACS) of enrichment cultures, combined with single amplified genome/amplicon sequencing and fluorescence microscopy, revealed that MCM protists possess diverse potential metabolic capabilities and interactions. Two metabolically distinct bacterial clades (Flavobacteria and Methylobacteriaceae) were independently associated with two key MCM lake microalgae (Isochrysis and Chlamydomonas, respectively). We also report on the discovery of two heterotrophic nanoflagellates belonging to the Stramenopila supergroup, one of which lives as a parasite of Chlamydomonas, a dominate primary producer in the shallow, nutrient-poor layers of the lake. Single-cell eukaryotes called protists play critical roles in the cycling of organic matter in aquatic environments. In the ice-covered lakes of Antarctica, protists play key roles in the aquatic food web, providing the majority of organic carbon to the rest of the food web (photosynthetic protists) and acting as the major consumers at the top of the food web (predatory protists). In this study, we utilized a combination of techniques (microscopy, cell sorting, and genomic analysis) to describe the trophic abilities of Antarctic lake protists and their potential interactions with other microbes. Our work reveals that Antarctic lake protists rely on metabolic versatility for their energy and nutrient requirements in this unique and isolated environment. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Wei; Podar, Mircea; Morgan-Kiss, Rachael M.

The McMurdo Dry Valleys (MCM) of southern Victoria Land, Antarctica, harbor numerous ice-covered bodies of water that provide year-round liquid water oases for isolated food webs dominated by the microbial loop. Single-cell microbial eukaryotes (protists) occupy major trophic positions within this truncated food web, ranging from primary producers (e.g., chlorophytes, haptophytes, and cryptophytes) to tertiary predators (e.g., ciliates, dinoflagellates, and choanoflagellates). To advance the understanding of MCM protist ecology and the roles of MCM protists in nutrient and energy cycling, we investigated potential metabolic strategies and microbial interactions of key MCM protists isolated from a well-described lake (Lake Bonney). Fluorescence-activatedmore » cell sorting (FACS) of enrichment cultures, combined with single amplified genome/amplicon sequencing and fluorescence microscopy, revealed that MCM protists possess diverse potential metabolic capabilities and interactions. Two metabolically distinct bacterial clades (FlavobacteriaandMethylobacteriaceae) were independently associated with two key MCM lake microalgae (IsochrysisandChlamydomonas, respectively). We also report on the discovery of two heterotrophic nanoflagellates belonging to the Stramenopila supergroup, one of which lives as a parasite ofChlamydomonas, a dominate primary producer in the shallow, nutrient-poor layers of the lake. Single-cell eukaryotes called protists play critical roles in the cycling of organic matter in aquatic environments. In the ice-covered lakes of Antarctica, protists play key roles in the aquatic food web, providing the majority of organic carbon to the rest of the food web (photosynthetic protists) and acting as the major consumers at the top of the food web (predatory protists). In this study, we utilized a combination of techniques (microscopy, cell sorting, and genomic analysis) to describe the trophic abilities of Antarctic lake protists and their potential interactions with other microbes. Ultimately, our work reveals that Antarctic lake protists rely on metabolic versatility for their energy and nutrient requirements in this unique and isolated environment.« less

Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake

DOE PAGES

Li, Wei; Podar, Mircea; Morgan-Kiss, Rachael M.

2016-04-15

The McMurdo Dry Valleys (MCM) of southern Victoria Land, Antarctica, harbor numerous ice-covered bodies of water that provide year-round liquid water oases for isolated food webs dominated by the microbial loop. Single-cell microbial eukaryotes (protists) occupy major trophic positions within this truncated food web, ranging from primary producers (e.g., chlorophytes, haptophytes, and cryptophytes) to tertiary predators (e.g., ciliates, dinoflagellates, and choanoflagellates). To advance the understanding of MCM protist ecology and the roles of MCM protists in nutrient and energy cycling, we investigated potential metabolic strategies and microbial interactions of key MCM protists isolated from a well-described lake (Lake Bonney). Fluorescence-activatedmore » cell sorting (FACS) of enrichment cultures, combined with single amplified genome/amplicon sequencing and fluorescence microscopy, revealed that MCM protists possess diverse potential metabolic capabilities and interactions. Two metabolically distinct bacterial clades (FlavobacteriaandMethylobacteriaceae) were independently associated with two key MCM lake microalgae (IsochrysisandChlamydomonas, respectively). We also report on the discovery of two heterotrophic nanoflagellates belonging to the Stramenopila supergroup, one of which lives as a parasite ofChlamydomonas, a dominate primary producer in the shallow, nutrient-poor layers of the lake. Single-cell eukaryotes called protists play critical roles in the cycling of organic matter in aquatic environments. In the ice-covered lakes of Antarctica, protists play key roles in the aquatic food web, providing the majority of organic carbon to the rest of the food web (photosynthetic protists) and acting as the major consumers at the top of the food web (predatory protists). In this study, we utilized a combination of techniques (microscopy, cell sorting, and genomic analysis) to describe the trophic abilities of Antarctic lake protists and their potential interactions with other microbes. Ultimately, our work reveals that Antarctic lake protists rely on metabolic versatility for their energy and nutrient requirements in this unique and isolated environment.« less

A new method for water desalination using microbial desalination cells.

PubMed

Cao, Xiaoxin; Huang, Xia; Liang, Peng; Xiao, Kang; Zhou, Yingjun; Zhang, Xiaoyuan; Logan, Bruce E

2009-09-15

Current water desalination techniques are energy intensive and some use membranes operated at high pressures. It is shown here that water desalination can be accomplished without electrical energy input or high water pressure by using a source of organic matter as the fuel to desalinate water. A microbial fuel cell was modified by placing two membranes between the anode and cathode, creating a middle chamber for water desalination between the membranes. An anion exchange membrane was placed adjacent to the anode, and a cation exchange membrane was positioned next to the cathode. When current was produced by bacteria on the anode, ionic species in the middle chamber were transferred into the two electrode chambers, desalinating the water in the middle chamber. Proof-of-concept experiments for this approach, using what we call a microbial desalination cell (MDC), was demonstrated using water at different initial salt concentrations (5, 20, and 35 g/L) with acetate used as the substrate for the bacteria. The MDC produced a maximum of 2 W/m2 (31 W/m3) while at the same time removing about 90% of the salt in a single desalination cycle. As the salt was removed from the middle chamber the ohmic resistance of the MDC (measured using electrochemical impedance spectroscopy) increased from 25 Omega to 970 Omega at the end of the cycle. This increased resistance was reflected by a continuous decrease in the voltage produced over the cycle. These results demonstrate for the first time the possibility for a new method for water desalination and power production that uses only a source of biodegradable organic matter and bacteria.

Design of a microbial fuel cell and its transition to microbial electrolytic cell for hydrogen production by electrohydrogenesis.

PubMed

Gupta, Pratima; Parkhey, Piyush; Joshi, Komal; Mahilkar, Anjali

2013-10-01

Anaerobic bacteria were isolated from industrial wastewater and soil samples and tested for exoelectrogenic activity by current production in double chambered microbial fuel cell (MFC), which was further transitioned into a single chambered microbial electrolytic cell to test hydrogen production by electrohydrogenesis. Of all the cultures, the isolate from industrial water sample showed the maximum values for current = 0.161 mA, current density = 108.57 mA/m2 and power density = 48.85 mW/m2 with graphite electrode. Maximum voltage across the cell, however, was reported by the isolate from sewage water sample (506 mv) with copper as electrode. Tap water with KMnO4 was the best cathodic electrolyte as the highest values for all the measured MFC parameters were reported with it. Once the exoelectrogenic activity of the isolates was confirmed by current production, these were tested for hydrogen production in a single chambered microbial electrolytic cell (MEC) modified from the MFC. Hydrogen production was reported positive from co-culture of isolates of both the water samples and co-culture of one soil and one water sample. The maximum rate and yield of hydrogen production was 0.18 m3H2/m3/d and 3.2 mol H2/mol glucose respectively with total hydrogen production of 42.4 mL and energy recovery of 57.4%. Cumulative hydrogen production for a five day cycle of MEC operation was 0.16 m3H2/m3/d.

Electricity generation and wastewater treatment of oil refinery in microbial fuel cells using Pseudomonas putida.

PubMed

Majumder, Dip; Maity, Jyoti Prakash; Tseng, Min-Jen; Nimje, Vanita Roshan; Chen, Hau-Ren; Chen, Chien-Cheng; Chang, Young-Fo; Yang, Tsui-Chu; Chen, Chen-Yen

2014-09-22

Microbial fuel cells (MFCs) represent a novel platform for treating wastewater and at the same time generating electricity. Using Pseudomonas putida (BCRC 1059), a wild-type bacterium, we demonstrated that the refinery wastewater could be treated and also generate electric current in an air-cathode chamber over four-batch cycles for 63 cumulative days. Our study indicated that the oil refinery wastewater containing 2213 mg/L (ppm) chemical oxygen demand (COD) could be used as a substrate for electricity generation in the reactor of the MFC. A maximum voltage of 355 mV was obtained with the highest power density of 0.005 mW/cm² in the third cycle with a maximum current density of 0.015 mA/cm² in regard to the external resistor of 1000 Ω. A maximum coulombic efficiency of 6 × 10⁻²% was obtained in the fourth cycle. The removal efficiency of the COD reached 30% as a function of time. Electron transfer mechanism was studied using cyclic voltammetry, which indicated the presence of a soluble electron shuttle in the reactor. Our study demonstrated that oil refinery wastewater could be used as a substrate for electricity generation.

Electricity Generation and Wastewater Treatment of Oil Refinery in Microbial Fuel Cells Using Pseudomonas putida

PubMed Central

Majumder, Dip; Maity, Jyoti Prakash; Tseng, Min-Jen; Nimje, Vanita Roshan; Chen, Hau-Ren; Chen, Chien-Cheng; Chang, Young-Fo; Yang, Tsui-Chu; Chen, Chen-Yen

2014-01-01

Microbial fuel cells (MFCs) represent a novel platform for treating wastewater and at the same time generating electricity. Using Pseudomonas putida (BCRC 1059), a wild-type bacterium, we demonstrated that the refinery wastewater could be treated and also generate electric current in an air-cathode chamber over four-batch cycles for 63 cumulative days. Our study indicated that the oil refinery wastewater containing 2213 mg/L (ppm) chemical oxygen demand (COD) could be used as a substrate for electricity generation in the reactor of the MFC. A maximum voltage of 355 mV was obtained with the highest power density of 0.005 mW/cm2 in the third cycle with a maximum current density of 0.015 mA/cm2 in regard to the external resistor of 1000 Ω. A maximum coulombic efficiency of 6 × 10−2% was obtained in the fourth cycle. The removal efficiency of the COD reached 30% as a function of time. Electron transfer mechanism was studied using cyclic voltammetry, which indicated the presence of a soluble electron shuttle in the reactor. Our study demonstrated that oil refinery wastewater could be used as a substrate for electricity generation. PMID:25247576

Linking environmental processes to the in situ functioning of microorganisms by high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission X-ray microscopy (STXM).

PubMed

Behrens, Sebastian; Kappler, Andreas; Obst, Martin

2012-11-01

Environmental microbiology research increasingly focuses on the single microbial cell as the defining entity that drives environmental processes. The interactions of individual microbial cells with each other, the environment and with higher organisms shape microbial communities and control the functioning of whole ecosystems. A single-cell view of microorganisms in their natural environment requires analytical tools that measure both cell function and chemical speciation at the submicrometre scale. Here we review the technical capabilities and limitations of high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission (soft) X-ray microscopy (STXM) and give examples of their applications. Whereas NanoSIMS can be combined with isotope-labelling, thereby localizing the distribution of cellular activities (e.g. carbon/nitrogen fixation/turnover), STXM provides information on the location and chemical speciation of metabolites and products of redox reactions. We propose the combined use of both techniques and discuss the technical challenges of their joint application. Both techniques have the potential to enhance our understanding of cellular mechanisms and activities that contribute to microbially mediated processes, such as the biogeochemical cycling of elements, the transformation of contaminants and the precipitation of mineral phases. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Nano-scale investigation of the association of microbial nitrogen residues with iron (hydr)oxides in a forest soil O-horizon

NASA Astrophysics Data System (ADS)

Keiluweit, Marco; Bougoure, Jeremy J.; Zeglin, Lydia H.; Myrold, David D.; Weber, Peter K.; Pett-Ridge, Jennifer; Kleber, Markus; Nico, Peter S.

2012-10-01

Amino sugars in fungal cell walls (such as chitin) represent an important source of nitrogen (N) in many forest soil ecosystems. Despite the importance of this material in soil nitrogen cycling, comparatively little is known about abiotic and biotic controls on and the timescale of its turnover. Part of the reason for this lack of information is the inaccessibility of these materials to classic bulk extraction methods. To address this issue, we used advanced visualization tools to examine transformation pathways of chitin-rich fungal cell wall residues as they interact with microorganisms, soil organic matter and mineral surfaces. Our goal was to document initial micro-scale dynamics of the incorporation of 13C- and 15N-labeled chitin into fungi-dominated microenvironments in O-horizons of old-growth forest soils. At the end of a 3-week incubation experiment, high-resolution secondary ion mass spectrometry imaging of hyphae-associated soil microstructures revealed a preferential association of 15N with Fe-rich particles. Synchrotron-based scanning transmission X-ray spectromicroscopy (STXM/NEXAFS) of the same samples showed that thin organic coatings on these soil microstructures are enriched in aliphatic C and amide N on Fe (hydr)oxides, suggesting a concentration of microbial lipids and proteins on these surfaces. A possible explanation for the results of our micro-scale investigation of chemical and spatial patterns is that amide N from chitinous fungal cell walls was assimilated by hyphae-associated bacteria, resynthesized into proteinaceous amide N, and subsequently concentrated onto Fe (hydr)oxide surfaces. If confirmed in other soil ecosystems, such rapid association of microbial N with hydroxylated Fe oxide surfaces may have important implications for mechanistic models of microbial cycling of C and N.

SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

NASA Astrophysics Data System (ADS)

Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

2015-10-01

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework designed to simulate microbial dynamics and biogeochemical cycling during initial ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The rationale for model development arises from decades of empirical observations in glacier forefields, and enables a quantitative and process focussed approach. Here, we provide a detailed description of SHIMMER, test its performance in two case study forefields: the Damma Glacier (Switzerland) and the Athabasca Glacier (Canada) and analyse sensitivity to identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Primary production is responsible for the initial build-up of labile substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter, and nitrogen fixation, are important in sustaining this productivity. The development and application of SHIMMER also highlights aspects of these systems that require further empirical research: quantifying nutrient budgets and biogeochemical rates, exploring seasonality and microbial growth and cell death. This will lead to increased understanding of how glacier forefields contribute to global biogeochemical cycling and climate under future ice retreat.

Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change

PubMed Central

Nazaries, Loïc; Pan, Yao; Bodrossy, Levente; Baggs, Elizabeth M.; Millard, Peter; Murrell, J. Colin

2013-01-01

Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles. PMID:23624469

Neisseria meningitidis causes cell cycle arrest of human brain microvascular endothelial cells at S phase via p21 and cyclin G2.

PubMed

Oosthuysen, Wilhelm F; Mueller, Tobias; Dittrich, Marcus T; Schubert-Unkmeir, Alexandra

2016-01-01

Microbial pathogens have developed several mechanisms to modulate and interfere with host cell cycle progression. In this study, we analysed the effect of the human pathogen Neisseria meningitidis on cell cycle in a brain endothelial cell line as well as in primary brain endothelial cells. We found that N.  Meningitidis causes an accumulation of cells in the S phase early at 3 and at 24 h post-infection that was paralleled by a decrease of cells in G2/M phase. Importantly, the outer membrane proteins of the colony opacity-associated (Opa) protein family as well as the Opc protein proved to trigger the accumulation of cells in the S phase. A focused cell cycle reverse transcription quantitative polymerase chain reaction-based array and integrated network analysis revealed changes in the abundance of several cell cycle regulatory mRNAs, including the cell cycle inhibitors p21(WAF1/CIP1) and cyclin G2. These alterations were reflected in changes in protein expression levels and/or relocalization in N. meningitidis-infected cells. Moreover, an increase in p21(WAF1/CIP1) expression was found to be p53 independent. Genetic ablation of p21(WAF1/CIP1) and cyclin G2 abrogated N. meningitidis-induced S phase accumulation. Finally, by measuring the levels of the biomarker 8-hydroxydeoxyguanosine and phosphorylation of the histone variant H2AX, we provide evidence that N. meningitidis induces oxidative DNA damage in infected cells. © 2015 John Wiley & Sons Ltd.

Spies and Bloggers: New Synthetic Biology Tools to Understand Microbial Processes in Soils and Sediments

NASA Astrophysics Data System (ADS)

Masiello, C. A.; Silberg, J. J.; Cheng, H. Y.; Del Valle, I.; Fulk, E. M.; Gao, X.; Bennett, G. N.

2017-12-01

Microbes can be programmed through synthetic biology to report on their behavior, informing researchers when their environment has triggered changes in their gene expression (e.g. in response to shifts in O2 or H2O), or when they have participated in a specific step of an elemental cycle (e.g. denitrification). This use of synthetic biology has the potential to significantly improve our understanding of microbes' roles in elemental and water cycling, because it allows reporting on the environment from the perspective of a microbe, matching the measurement scale exactly to the scale that a microbe experiences. However, synthetic microbes have not yet seen wide use in soil and sediment laboratory experiments because synthetic organisms typically report by fluorescing, making their signals difficult to detect outside the petri dish. We are developing a new suite of microbial programs that report instead by releasing easily-detected gases, allowing the real-time, noninvasive monitoring of behaviors in sediments and soils. Microbial biosensors can, in theory, be programmed to detect dynamic processes that contribute to a wide range of geobiological processes, including C cycling (biofilm production, methanogenesis, and synthesis of extracellular enzymes that degrade organic matter), N cycling (expression of enzymes that underlie different steps of the N cycle) and potentially S cycling. We will provide an overview of the potential uses of gas-reporting biosensors in soil and sediment lab experiments, and will report the development of the systematics of these sensors. Successful development of gas biosensors for laboratory use will require addressing issues including: engineering the intensity and selectivity of microbial gas production to maximize the signal to noise ratio; normalizing the gas reporter signal to cell population size, managing gas diffusion effects on signal shape; and developing multiple gases that can be used in parallel.

Electron harvest and treatment of amendment free municipal wastewater using microbial anodes: A case study

NASA Astrophysics Data System (ADS)

Rosa, Luis F. M.; Koch, Christin; Korth, Benjamin; Harnisch, Falk

2017-07-01

Microbial electrochemical technologies (METs) and especially microbial fuel cells (MFCs) are considered to allow energy harvest from the fuel wastewater during its treatment. However, the majority of studies use either "artificial" wastewater, amended wastewater, (i.e. with addition of chemicals), or pre-enriched microbial anodes. As these strategies might not be transferable to large scale, this study uses exclusively amendment free municipal wastewater as inoculum and sole carbon and energy source. It is shown that electrons can be harvested, at maximum current densities of 0.01 mA cm-2. In weekly cycles using batch systems (with 90 cm2 L-1 anode surface) only a minor fraction (<10%) of the available charge from COD-removal was turned into electricity by a highly diverse anodic microbial community. This performance is below those achieved by pre-enriched anodes or in amended wastewater studies, illustrating the need for more fundamental, application relevant studies.

Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

PubMed

Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

2016-06-15

The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Gold-FISH: A correlative approach to microscopic imaging of single microbial cells in environmental samples

NASA Astrophysics Data System (ADS)

Schmidt, Hannes; Seki, David; Woebken, Dagmar; Eickhorst, Thilo

2017-04-01

Fluorescence in situ hybridization (FISH) is routinely used for the phylogenetic identification, detection, and quantification of single microbial cells environmental microbiology. Oligonucleotide probes that match the 16S rRNA sequence of target organisms are generally applied and the resulting signals are visualized via fluorescence microscopy. Consequently, the detection of the microbial cells of interest is limited by the resolution and the sensitivity of light microscopy where objects smaller than 0.2 µm can hardly be represented. Visualizing microbial cells at magnifications beyond light microscopy, however, can provide information on the composition and potential complexity of microbial habitats - the actual sites of nutrient cycling in soil and sediments. We present a recently developed technique that combines (1) the phylogenetic identification and detection of individual microorganisms by epifluorescence microscopy, with (2) the in situ localization of gold-labelled target cells on an ultrastructural level by SEM. Based on 16S rRNA targeted in situ hybridization combined with catalyzed reporter deposition, a streptavidin conjugate labeled with a fluorescent dye and nanogold particles is introduced into whole microbial cells. A two-step visualization process including an autometallographic enhancement of nanogold particles then allows for either fluorescence or electron microscopy, or a correlative application thereof. We will present applications of the Gold-FISH protocol to samples of marine sediments, agricultural soils, and plant roots. The detection and enumeration of bacterial cells in soil and sediment samples was comparable to CARD-FISH applications via fluorescence microscopy. Examples of microbe-surface interaction analysis will be presented on the basis of bacteria colonizing the rhizoplane of rice roots. In principle, Gold-FISH can be performed on any material to give a snapshot of microbe-surface interactions and provides a promising tool for the acquisition of correlative information on microorganisms within their respective habitats.

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

PubMed Central

Rajala, Pauliina; Bomberg, Malin

2017-01-01

Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions. PMID:28367144

Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

USGS Publications Warehouse

Aiello, I.W.; Bekins, B.A.

2010-01-01

The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

Convergent development of anodic bacterial communities in microbial fuel cells.

PubMed

Yates, Matthew D; Kiely, Patrick D; Call, Douglas F; Rismani-Yazdi, Hamid; Bibby, Kyle; Peccia, Jordan; Regan, John M; Logan, Bruce E

2012-11-01

Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. The bog-inoculated MFCs initially produced higher power densities than the wastewater-inoculated MFCs, but after 20 cycles all MFCs on average converged to similar voltages (470±20 mV) and maximum power densities (590±170 mW m(-2)). The power output from replicate bog-inoculated MFCs was not significantly different, but one wastewater-inoculated MFC (UAJA3 (UAJA, University Area Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel electrophoresis profiling showed a stable exoelectrogenic biofilm community in all samples after 11 cycles. After 16 cycles the predominance of Geobacter spp. in anode communities was identified using 16S rRNA gene clone libraries (58±10%), fluorescent in-situ hybridization (FISH) (63±6%) and pyrosequencing (81±4%). While the clone library analysis for the underperforming UAJA3 had a significantly lower percentage of Geobacter spp. sequences (36%), suggesting that a predominance of this microbe was needed for convergent power densities, the lower percentage of this species was not verified by FISH or pyrosequencing analyses. These results show that the predominance of Geobacter spp. in acetate-fed systems was consistent with good MFC performance and independent of the inoculum source.

Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production

PubMed Central

Xiang, Ruidong; McNally, Jody; Rowe, Suzanne; Jonker, Arjan; Pinares-Patino, Cesar S.; Oddy, V. Hutton; Vercoe, Phil E.; McEwan, John C.; Dalrymple, Brian P.

2016-01-01

Ruminants obtain nutrients from microbial fermentation of plant material, primarily in their rumen, a multilayered forestomach. How the different layers of the rumen wall respond to diet and influence microbial fermentation, and how these process are regulated, is not well understood. Gene expression correlation networks were constructed from full thickness rumen wall transcriptomes of 24 sheep fed two different amounts and qualities of a forage and measured for methane production. The network contained two major negatively correlated gene sub-networks predominantly representing the epithelial and muscle layers of the rumen wall. Within the epithelium sub-network gene clusters representing lipid/oxo-acid metabolism, general metabolism and proliferating and differentiating cells were identified. The expression of cell cycle and metabolic genes was positively correlated with dry matter intake, ruminal short chain fatty acid concentrations and methane production. A weak correlation between lipid/oxo-acid metabolism genes and methane yield was observed. Feed consumption level explained the majority of gene expression variation, particularly for the cell cycle genes. Many known stratified epithelium transcription factors had significantly enriched targets in the epithelial gene clusters. The expression patterns of the transcription factors and their targets in proliferating and differentiating skin is mirrored in the rumen, suggesting conservation of regulatory systems. PMID:27966600

Final Technical Report: Viral Infection of Subsurface Microorganisms and Metal/Radionuclide Transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Karrie A.; Bender, Kelly S.; Li, Yusong

Microbially mediated metabolisms have been identified as a significant factor either directly or indirectly impacting the fate and transport of heavy metal/radionuclide contaminants. To date microorganisms have been isolated from contaminated environments. Examination of annotated finished genome sequences of many of these subsurface isolates from DOE sites, revealed evidence of prior viral infection. To date the role that viruses play influencing microbial mortality and the resulting community structure which directly influences biogeochemical cycling in soils and sedimentary environments remains poorly understood. The objective of this exploratory study was to investigate the role of viral infection of subsurface bacteria and themore » formation of contaminant-bearing viral particles. This objective was approached by examining the following working hypotheses: (i) subsurface microorganisms are susceptible to viral infections by the indigenous subsurface viral community, and (ii) viral surfaces will adsorb heavy metals and radionuclides. Our results have addressed basic research needed to accomplish the BER Long Term Measure to provide sufficient scientific understanding such that DOE sites would be able to incorporate coupled physical, chemical and biological processes into decision making for environmental remediation or natural attenuation and long-term stewardship by establishing viral-microbial relationships on the subsequent fate and transport of heavy metals and radionuclides. Here we demonstrated that viruses play a significant role in microbial mortality and community structure in terrestrial subsurface sedimentary systems. The production of viral-like particles within subsurface sediments in response to biostimulation with dissolved organic carbon and a terminal electron acceptor resulted in the production of viral-like particles. Organic carbon alone did not result in significant viral production and required the addition of a terminal electron acceptor (nitrate), indicating that nutrients are not limiting viral production, but rather substrates that can be converted into energy for host metabolism. Our results also revealed that cell abundance was not correlated to the mineralization of organic carbon, but rather viruses were positively correlated with carbon mineralization. This is a result of viral-mediated cell lysis and demonstrates that viruses are sensitive indicators of microbial activity. Viruses as an indicator of microbial activity was not unique to batch culture studies as results obtained from an in situ field experiment conducted at the DOE Old Rifle Field site. This study revealed that viral abundance increased in response to the injection of oxygenated groundwater and influx of dissolved organic carbon whereas cell abundance changes were minimal. However, the extent to which viral-mediated cell lysis alters organic matter pools subsequently influencing microbial community structure and biogeochemical function remains a critical question in subsurface biogeochemical cycling. The production of significant numbers of viruses in groundwater has implications for nanoparticulate metal as well as carbon transport in groundwater. We have demonstrated that the virus surface is reactive and will adsorb heavy metals. Thus viruses can promote colloidal contaminant mobility. Interestingly, the presence of heavy metals has a positive effect on infectivity of the phage, increasing phage infection which could lead to further production of viruses. Together, the results indicate that the sorption of metals to the surface of viruses could not only contribute to nanoparticulate metal as well as carbon transport but could also enhance infectivity further contributing to cell lysis which could subsequently influence biogeochemical cycling. As more viruses infect host microbial populations the high concentration of metals would enhance infection, resulting in cell lysis, and decreasing the metabolically active host population while yielding greater numbers of viruses capable of transporting contaminats. Additional studies will be necessary to further establish the potential relationship(s) between viruses, cells, carbon, and metals/radionuclides to provide sufficient scientific understanding to incorporate coupled physical, chemical, and biological processes into agent based and reactive transport models.« less

Mineralogical impact on long-term patterns of soil nitrogen and phosphorus enzyme activities

NASA Astrophysics Data System (ADS)

Mikutta, Robert; Turner, Stephanie; Meyer-Stüve, Sandra; Guggenberger, Georg; Dohrmann, Reiner; Schippers, Axel

2014-05-01

Soil chronosequences provide a unique opportunity to study microbial activity over time in mineralogical diverse soils of different ages. The main objective of this study was to test the effect of mineralogical properties, nutrient and organic matter availability over whole soil pro-files on the abundance and activity of the microbial communities. We focused on microbio-logical processes involved in nitrogen and phosphorus cycling at the 120,000-year Franz Josef soil chronosequence. Microbial abundances (microbial biomass and total cell counts) and enzyme activities (protease, urease, aminopeptidase, and phosphatase) were determined and related to nutrient contents and mineralogical soil properties. Both, microbial abundances and enzyme activities decreased with soil depth at all sites. In the organic layers, microbial biomass and the activities of N-hydrolyzing enzymes showed their maximum at the intermediate-aged sites, corresponding to a high aboveground biomass. In contrast, the phosphatase activity increased with site age. The activities of N-hydrolyzing enzymes were positively correlated with total carbon and nitrogen contents, whereas the phosphatase activity was negatively correlated with the phosphorus content. In the mineral soil, the enzyme activities were generally low, thus reflecting the presence of strongly sorbing minerals. Sub-strate-normalized enzyme activities correlated negatively to clay content as well as poorly crystalline Al and Fe oxyhydroxides, supporting the view that the evolution of reactive sec-ondary mineral phases alters the activity of the microbial communities by constraining sub-strate availability. Our data suggest a strong mineralogical influence on nutrient cycling par-ticularly in subsoil environments.

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

PubMed Central

Qi, Qi; Zhao, Mengxin; Wang, Shiping; Ma, Xingyu; Wang, Yuxuan; Gao, Ying; Lin, Qiaoyan; Li, Xiangzhen; Gu, Baohua; Li, Guoxue; Zhou, Jizhong; Yang, Yunfeng

2017-01-01

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures. PMID:28659870

Outlook for benefits of sediment microbial fuel cells with two bio‐electrodes

PubMed Central

De Schamphelaire, Liesje; Rabaey, Korneel; Boeckx, Pascal; Boon, Nico; Verstraete, Willy

2008-01-01

Summary The benefits of sediment microbial fuel cells (SMFCs) go beyond energy generation for low‐power applications. Aside from producing electrical energy, SMFCs can enhance the oxidation of reduced compounds at the anode, thus bringing about the removal of excessive or unwanted reducing equivalents from submerged soils. Moreover, an SMFC could be applied to control redox‐dependent processes in sediment layers. Several cathodic reactions that may drive these sediment oxidation reactions are examined. Special attention is given to two biologically mediated cathodic reactions, respectively employing an oxygen reduction and a manganese cycle. Both reactions imply a low cost and a high electrode potential and are of interest for reactor‐type MFCs as well as for SMFCs. PMID:21261866

Anaerobic Redox Cycling of Iron by Freshwater Sediment Microorganisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Karrie A.; Urrutia, Matilde M.; Churchill, Perry F.

2006-01-01

The potential for microbially-mediated anaerobic redox cycling of iron (Fe) was examined in a first-generation enrichment culture of freshwater wetland sediment microorganisms. MPN enumerations revealed the presence of significant populations of Fe(III)-reducing (ca. 108 cells mL-1) and Fe(II)-oxidizing, nitrate-reducing organisms (ca. 105 cells mL-1) in the sediment used to inoculate the enrichment cultures. Nitrate reduction commenced immediately following inoculation of acetate-containing (ca. 1 mM) medium with a small quantity (1% vol/vol) of wetland sediment, and resulted in the transient accumulation of NO2- and production of a mixture of end-products including NH4+. Fe(III) oxide (high surface area goethite) reduction took placemore » - after NO3- was depleted and continued until all the acetate was utilized. Addition of NO3 after Fe(III) reduction ceased resulted in the immediate oxidation of Fe(II) coupled to reduction of + NO3-to NH4 . No significant NO2- accumulation was observed during nitrate-dependent Fe(II) oxidation. No Fe(II) oxidation occurred in pasteurized controls. Microbial community structure in the enrichment was monitored by DGGE analysis of PCR amplified 16s rDNA and RT-PCR amplified 16S rRNA, as well as by construction of 16S rDNA clone libraries for four different time points during the experiment. Strong similarities in dominant members of the microbial community were observed in the Fe(III) reduction and nitrate-dependent Fe(II) oxidation phases of the experiment, specifically the common presence of organisms closely related (= 95% sequence similarity) to the genera Geobacter and Dechloromonas. These results indicate that the wetland sediments contained organisms such as Geobacter sp. which are capable of both + dissimilatory Fe(III) reduction and oxidation of Fe(II) with reduction of NO3-reduction to NH4 . Our findings suggest that microbially-catalyzed nitrate-dependent Fe(II) oxidation has the potential to contribute to a dynamic anaerobic Fe redox cycle in freshwater sediments.« less

Strategies for merging microbial fuel cell technologies in water desalination processes: Start-up protocol and desalination efficiency assessment

NASA Astrophysics Data System (ADS)

Borjas, Zulema; Esteve-Núñez, Abraham; Ortiz, Juan Manuel

2017-07-01

Microbial Desalination Cells constitute an innovative technology where microbial fuel cell and electrodialysis merge in the same device for obtaining fresh water from saline water with no energy-associated cost for the user. In this work, an anodic biofilm of the electroactive bacteria Geobacter sulfurreducens was able to efficiently convert the acetate present in synthetic waste water into electric current (j = 0.32 mA cm-2) able to desalinate water. .Moreover, we implemented an efficient start-up protocol where desalination up to 90% occurred in a desalination cycle (water production:0.308 L m-2 h-1, initial salinity: 9 mS cm-1, final salinity: <1 mS cm-1) using a filter press-based MDC prototype without any energy supply (excluding peristaltic pump energy). This start-up protocol is not only optimized for time but also simplifies operational procedures making it a more feasible strategy for future scaling-up of MDCs either as a single process or as a pre-treatment method combined with other well established desalination technologies such as reverse osmosis (RO) or reverse electrodialysis.

Microbial responses to microgravity and other low-shear environments.

PubMed

Nickerson, Cheryl A; Ott, C Mark; Wilson, James W; Ramamurthy, Rajee; Pierson, Duane L

2004-06-01

Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.

Microbial Responses to Microgravity and Other Low-Shear Environments

NASA Technical Reports Server (NTRS)

Nickerson, Cheryl A.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; Pierson, Duane L.

2004-01-01

Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.

Seasonality in ocean microbial communities.

PubMed

Giovannoni, Stephen J; Vergin, Kevin L

2012-02-10

Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

Microbial Iron(II) Oxidation in Littoral Freshwater Lake Sediment: The Potential for Competition between Phototrophic vs. Nitrate-Reducing Iron(II)-Oxidizers

PubMed Central

Melton, E. D.; Schmidt, C.; Kappler, A.

2012-01-01

The distribution of neutrophilic microbial iron oxidation is mainly determined by local gradients of oxygen, light, nitrate and ferrous iron. In the anoxic top part of littoral freshwater lake sediment, nitrate-reducing and phototrophic Fe(II)-oxidizers compete for the same e− donor; reduced iron. It is not yet understood how these microbes co-exist in the sediment and what role they play in the Fe cycle. We show that both metabolic types of anaerobic Fe(II)-oxidizing microorganisms are present in the same sediment layer directly beneath the oxic-anoxic sediment interface. The photoferrotrophic most probable number counted 3.4·105 cells·g−1 and the autotrophic and mixotrophic nitrate-reducing Fe(II)-oxidizers totaled 1.8·104 and 4.5·104 cells·g−1 dry weight sediment, respectively. To distinguish between the two microbial Fe(II) oxidation processes and assess their individual contribution to the sedimentary Fe cycle, littoral lake sediment was incubated in microcosm experiments. Nitrate-reducing Fe(II)-oxidizing bacteria exhibited a higher maximum Fe(II) oxidation rate per cell, in both pure cultures and microcosms, than photoferrotrophs. In microcosms, photoferrotrophs instantly started oxidizing Fe(II), whilst nitrate-reducing Fe(II)-oxidizers showed a significant lag-phase during which they probably use organics as e− donor before initiating Fe(II) oxidation. This suggests that they will be outcompeted by phototrophic Fe(II)-oxidizers during optimal light conditions; as phototrophs deplete Fe(II) before nitrate-reducing Fe(II)-oxidizers start Fe(II) oxidation. Thus, the co-existence of the two anaerobic Fe(II)-oxidizers may be possible due to a niche space separation in time by the day-night cycle, where nitrate-reducing Fe(II)-oxidizers oxidize Fe(II) during darkness and phototrophs play a dominant role in Fe(II) oxidation during daylight. Furthermore, metabolic flexibility of Fe(II)-oxidizing microbes may play a paramount role in the conservation of the sedimentary Fe cycle. PMID:22666221

Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events

PubMed Central

Mooshammer, Maria; Hofhansl, Florian; Frank, Alexander H.; Wanek, Wolfgang; Hämmerle, Ieda; Leitner, Sonja; Schnecker, Jörg; Wild, Birgit; Watzka, Margarete; Keiblinger, Katharina M.; Zechmeister-Boltenstern, Sophie; Richter, Andreas

2017-01-01

Predicted changes in the intensity and frequency of climate extremes urge a better mechanistic understanding of the stress response of microbially mediated carbon (C) and nutrient cycling processes. We analyzed the resistance and resilience of microbial C, nitrogen (N), and phosphorus (P) cycling processes and microbial community composition in decomposing plant litter to transient, but severe, temperature disturbances, namely, freeze-thaw and heat. Disturbances led temporarily to a more rapid cycling of C and N but caused a down-regulation of P cycling. In contrast to the fast recovery of the initially stimulated C and N processes, we found a slow recovery of P mineralization rates, which was not accompanied by significant changes in community composition. The functional and structural responses to the two distinct temperature disturbances were markedly similar, suggesting that direct negative physical effects and costs associated with the stress response were comparable. Moreover, the stress response of extracellular enzyme activities, but not that of intracellular microbial processes (for example, respiration or N mineralization), was dependent on the nutrient content of the resource through its effect on microbial physiology and community composition. Our laboratory study provides novel insights into the mechanisms of microbial functional stress responses that can serve as a basis for field studies and, in particular, illustrates the need for a closer integration of microbial C-N-P interactions into climate extremes research. PMID:28508070

Characterization of a microbial fuel cell with reticulated carbon foam electrodes.

PubMed

Lepage, Guillaume; Albernaz, Fabio Ovenhausen; Perrier, Gérard; Merlin, Gérard

2012-11-01

A microbial fuel cell with open-pore reticulated vitreous carbon electrodes is studied to assess the suitability of this material in a batch mode, in the perspective of flow-through reactors for wastewater treatment with electricity generation. The cell shows good stability and fair robustness in regards to substrate cycles. A power density of 40 W/m(3) is reached. The cell efficiency is mainly limited by cathodic transfers, representing 85% of the global overpotential in open circuit. Through impedance spectrocopy, equivalent circuit modeling reveals the complex nature of the bioelectrochemical phenomena. The global electrical behavior of the cell seems to result in the addition of three anodic and two cathodic distinct phenomena. On the cathode side, the Warburg element in the model is related to the diffusion of oxygen. Warburg resistance and time are respectively 2.99 kΩ cm(2) and 16.4s, similar to those published elsewhere. Copyright © 2012 Elsevier Ltd. All rights reserved.

Experimental evolution of multicellularity using microbial pseudo-organisms.

PubMed

Queller, David C; Strassmann, Joan E

2013-02-23

In a major evolutionary transition to a new level of organization, internal conflicts must be controlled before the transition can truly be successful. One such transition is that from single cells to multicellularity. Conflicts among cells in multicellular organisms can be greatly reduced if they consist of genetically identical clones. However, mutations to cheaters that experience one round of within-individual selection could still be a problem, particularly for certain life cycles. We propose an experimental evolution method to investigate this issue, using micro-organisms to construct multicellular pseudo-organisms, which can be evolved under different artificial life cycles. These experiments can be used to test the importance of various life cycle features in maintaining cooperation. They include structured reproduction, in which small propagule size reduces within-individual genetic variation. They also include structured growth, which increases local relatedness within individual bodies. Our method provides a novel way to test how different life cycles favour cooperation, even for life cycles that do not exist.

Using Deep UV Raman Spectroscopy to Identify In Situ Microbial Activity

NASA Astrophysics Data System (ADS)

Sapers, H. M.; Wanger, G.; Amend, J.; Orphan, V. J.; Bhartia, R.

2017-12-01

Microbial communities living in close association with lithic substrates play a critical role in biogeochemical cycles. Understanding the interactions between microorganisms and their abiotic substrates requires knowledge of microbial activity. Identifying active cells adhered to complex environmental substrates, especially in low biomass systems, remains a challenge. Stable isotope probing (SIP) provides a means to trace microbial activity in environmental systems. Active members of the community take up labeled substrates and incorporate the labels into biomolecules that can be detected through downstream analyses. Here we show for the first time that Deep UV (248 nm) Raman spectroscopy can differentiate microbial cells labeled with stable isotopes. Previous studies have used Raman spectroscopy with a 532 nm source to identify active bacterial cells by measuring a Raman shift between peaks corresponding to amino acids incorporating 13C compared to controls. However, excitation at 532 nm precludes detection on complex substrates due to high autofluorescence of native minerals. Excitation in the DUV range offers non-destructive imaging on mineral surfaces - retaining critical contextual information. We prepared cultures of E. coli grown in 50 atom% 13C glucose spotted onto Al wafers to test the ability of DUV Raman spectroscopy to differentiate labeled and unlabeled cells. For the first time, we are able to demonstrate a distinct and repeatable shift between cells grown in labeled media and unlabeled media when imaged on Al wafers with DUV Raman spectroscopy. The Raman spectra are dominated by the characteristic Raman bands of guanine. The dominant marker peak for guanine attributed to N7-C8 and C8-N9 ring stretching and C8-H in-plane bending, is visible at 1480 cm-1 in the unlabeled cells and is blue-shifted by 20 wavenumbers to 1461 cm-1 in the labeled cells. The ability of DUV Raman to effectively identify regions containing cells that have incorporated isotopic labels will allow in situ detection of metabolically-targeted active community members on complex natural substrates providing a crucial link between microbial activity and environmental context.

Differential Nutrient Limitation of Soil Microbial Biomass and Metabolic Quotients (qCO2): Is There a Biological Stoichiometry of Soil Microbes?

PubMed Central

Hartman, Wyatt H.; Richardson, Curtis J.

2013-01-01

Background Variation in microbial metabolism poses one of the greatest current uncertainties in models of global carbon cycling, and is particularly poorly understood in soils. Biological Stoichiometry theory describes biochemical mechanisms linking metabolic rates with variation in the elemental composition of cells and organisms, and has been widely observed in animals, plants, and plankton. However, this theory has not been widely tested in microbes, which are considered to have fixed ratios of major elements in soils. Methodology/Principal Findings To determine whether Biological Stoichiometry underlies patterns of soil microbial metabolism, we compiled published data on microbial biomass carbon (C), nitrogen (N), and phosphorus (P) pools in soils spanning the global range of climate, vegetation, and land use types. We compared element ratios in microbial biomass pools to the metabolic quotient qCO2 (respiration per unit biomass), where soil C mineralization was simultaneously measured in controlled incubations. Although microbial C, N, and P stoichiometry appeared to follow somewhat constrained allometric relationships at the global scale, we found significant variation in the C∶N∶P ratios of soil microbes across land use and habitat types, and size-dependent scaling of microbial C∶N and C∶P (but not N∶P) ratios. Microbial stoichiometry and metabolic quotients were also weakly correlated as suggested by Biological Stoichiometry theory. Importantly, we found that while soil microbial biomass appeared constrained by soil N availability, microbial metabolic rates (qCO2) were most strongly associated with inorganic P availability. Conclusions/Significance Our findings appear consistent with the model of cellular metabolism described by Biological Stoichiometry theory, where biomass is limited by N needed to build proteins, but rates of protein synthesis are limited by the high P demands of ribosomes. Incorporation of these physiological processes may improve models of carbon cycling and understanding of the effects of nutrient availability on soil C turnover across terrestrial and wetland habitats. PMID:23526933

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world.

Effect of pre-acclimation of granular activated carbon on microbial electrolysis cell startup and performance.

PubMed

LaBarge, Nicole; Yilmazel, Yasemin Dilsad; Hong, Pei-Ying; Logan, Bruce E

2017-02-01

Microbial electrolysis cells (MECs) can generate methane by fixing carbon dioxide without using expensive catalysts, but the impact of acclimation procedures on subsequent performance has not been investigated. Granular activated carbon (GAC) was used to pre-enrich electrotrophic methanogenic communities, as GAC has been shown to stimulate direct transfer of electrons between different microbial species. MEC startup times using pre-acclimated GAC were improved compared to controls (without pre-acclimation or without GAC), and after three fed batch cycles methane generation rates were similar (P>0.4) for GAC acclimated to hydrogen (22±9.3nmolcm -3 d -1 ), methanol (25±9.7nmolcm -3 d -1 ), and a volatile fatty acid (VFA) mix (22±11nmolcm -3 d -1 ). However, MECs started with GAC but no pre-acclimation had lower methane generation rates (13±4.1nmolcm -3 d -1 ), and MECs without GAC had the lowest rates (0.7±0.8nmolcm -3 d -1 after cycle 2). Microbes previously found in methanogenic MECs, or previously shown to be capable of exocellular electron transfer, were enriched on the GAC. Pre-acclimation using GAC is therefore a simple approach to enrich electroactive communities, improve methane generation rates, and decrease startup times in MECs. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of Nutrient Enrichment on Microbial Communities and Carbon Cycling in Wetland Soils

NASA Astrophysics Data System (ADS)

Hartman, W.; Neubauer, S. C.; Richardson, C. J.

2013-12-01

Soil microbial communities are responsible for catalyzing biogeochemical transformations underlying critical wetland functions, including cycling of carbon (C) and nutrients, and emissions of greenhouse gasses (GHG). Alteration of nutrient availability in wetland soils may commonly occur as the result of anthropogenic impacts including runoff from human land uses in uplands, alteration of hydrology, and atmospheric deposition. However, the impacts of altered nutrient availability on microbial communities and carbon cycling in wetland soils are poorly understood. To assess these impacts, soil microbial communities and carbon cycling were determined in replicate experimental nutrient addition plots (control, +N, +P, +NP) across several wetland types, including pocosin peat bogs (NC), freshwater tidal marshes (GA), and tidal salt marshes (SC). Microbial communities were determined by pyrosequencing (Roche 454) extracted soil DNA, targeting both bacteria (16S rDNA) and fungi (LSU) at a depth of ca. 1000 sequences per plot. Wetland carbon cycling was evaluated using static chambers to determine soil GHG fluxes, and plant inclusion chambers were used to determine ecosystem C cycling. Soil bacterial communities responded to nutrient addition treatments in freshwater and tidal marshes, while fungal communities did not respond to treatments in any of our sites. We also compared microbial communities to continuous biogeochemical variables in soil, and found that bacterial community composition was correlated only with the content and availability of soil phosphorus, while fungi responded to phosphorus stoichiometry and soil pH. Surprisingly, we did not find a significant effect of our nutrient addition treatments on most metrics of carbon cycling. However, we did find that several metrics of soil carbon cycling appeared much more related to soil phosphorus than to nitrogen or soil carbon pools. Finally, while overall microbial community composition was weakly correlated with soil carbon cycling, our work did identify a small number of individual taxonomic groups that were more strongly correlated with soil CO2 flux. These results suggest that a small number of microbial groups may potentially serve as keystone taxa (and functional indicators), which simple community fingerprinting approaches may overlook. Our results also demonstrate strong effects of soil phosphorus availability on both microbial communities and soil carbon cycling, even in wetland types traditionally considered to be nitrogen limited.

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qi, Qi; Zhao, Mengxin; Wang, Shiping

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. Themore » range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.« less

CO2 – Intrinsic Product, Essential Substrate, and Regulatory Trigger of Microbial and Mammalian Production Processes

PubMed Central

Blombach, Bastian; Takors, Ralf

2015-01-01

Carbon dioxide formation mirrors the final carbon oxidation steps of aerobic metabolism in microbial and mammalian cells. As a consequence, CO2/HCO3− dissociation equilibria arise in fermenters by the growing culture. Anaplerotic reactions make use of the abundant CO2/HCO3− levels for refueling citric acid cycle demands and for enabling oxaloacetate-derived products. At the same time, CO2 is released manifold in metabolic reactions via decarboxylation activity. The levels of extracellular CO2/HCO3− depend on cellular activities and physical constraints such as hydrostatic pressures, aeration, and the efficiency of mixing in large-scale bioreactors. Besides, local CO2/HCO3− levels might also act as metabolic inhibitors or transcriptional effectors triggering regulatory events inside the cells. This review gives an overview about fundamental physicochemical properties of CO2/HCO3− in microbial and mammalian cultures effecting cellular physiology, production processes, metabolic activity, and transcriptional regulation. PMID:26284242

Microbial biosynthesis and secretion of l-malic acid and its applications.

PubMed

Chi, Zhe; Wang, Zhi-Peng; Wang, Guang-Yuan; Khan, Ibrar; Chi, Zhen-Ming

2016-01-01

l-Malic acid has many uses in food, beverage, pharmaceutical, chemical and medical industries. It can be produced by one-step fermentation, enzymatic transformation of fumaric acid to l-malate and acid hydrolysis of polymalic acid. However, the process for one-step fermentation is preferred as it has many advantages over any other process. The pathways of l-malic acid biosynthesis in microorganisms are partially clear and three metabolic pathways including non-oxidative pathway, oxidative pathway and glyoxylate cycle for the production of l-malic acid from glucose have been identified. Usually, high levels of l-malate are produced under the nitrogen starvation conditions, l-malate, as a calcium salt, is secreted from microbial cells and CaCO3 can play an important role in calcium malate biosynthesis and regulation. However, it is still unclear how it is secreted into the medium. To enhance l-malate biosynthesis and secretion by microbial cells, it is very important to study the mechanisms of l-malic acid biosynthesis and secretion at enzymatic and molecular levels.

Comparative study on power generation of dual-cathode microbial fuel cell according to polarization methods.

PubMed

Lee, Kang-yu; Ryu, Wyan-seuk; Cho, Sung-il; Lim, Kyeong-ho

2015-11-01

Microbial fuel cells (MFCs) exist in various forms depending on the type of pollutant to be removed and the expected performance. Dual-cathode MFCs, with their simple structure, are capable of removing both organic matter and nitrogen. Moreover, various methods are available for the collection of polarization data, which can be used to calculate the maximum power density, an important factor of MFCs. Many researchers prefer the method of varying the external resistance in a single-cycle due to the short measurement time and high accuracy. This study compared power densities of dual-cathode MFCs in a single-cycle with values calculated over multi-cycles to determine the optimal polarization method. External resistance was varied from high to low and vice versa in the single-cycle, to calculate power density. External resistance was organized in descending order with initial start-up at open circuit voltage (OCV), and then it was organized in descending order again after the initial start-up at 1000 Ω. As a result, power density was underestimated at the anoxic cathode when the external resistance was varied from low to high, and overestimated at the aerobic cathode and anoxic cathode when external resistance at OCV was reduced following initial start-up. In calculating the power densities of dual-cathode MFCs, this paper recommends the method of gradually reducing the external resistance after initial start-up with high external resistance. Copyright © 2015 Elsevier Ltd. All rights reserved.

Divergence in plant and microbial allocation strategies explains continental patterns in microbial allocation and biogeochemical fluxes.

PubMed

Averill, Colin

2014-10-01

Allocation trade-offs shape ecological and biogeochemical phenomena at local to global scale. Plant allocation strategies drive major changes in ecosystem carbon cycling. Microbial allocation to enzymes that decompose carbon vs. organic nutrients may similarly affect ecosystem carbon cycling. Current solutions to this allocation problem prioritise stoichiometric tradeoffs implemented in plant ecology. These solutions may not maximise microbial growth and fitness under all conditions, because organic nutrients are also a significant carbon resource for microbes. I created multiple allocation frameworks and simulated microbial growth using a microbial explicit biogeochemical model. I demonstrate that prioritising stoichiometric trade-offs does not optimise microbial allocation, while exploiting organic nutrients as carbon resources does. Analysis of continental-scale enzyme data supports the allocation patterns predicted by this framework, and modelling suggests large deviations in soil C loss based on which strategy is implemented. Therefore, understanding microbial allocation strategies will likely improve our understanding of carbon cycling and climate. © 2014 John Wiley & Sons Ltd/CNRS.

Living together in biofilms: the microbial cell factory and its biotechnological implications.

PubMed

Berlanga, Mercedes; Guerrero, Ricardo

2016-10-01

In nature, bacteria alternate between two modes of growth: a unicellular life phase, in which the cells are free-swimming (planktonic), and a multicellular life phase, in which the cells are sessile and live in a biofilm, that can be defined as surface-associated microbial heterogeneous structures comprising different populations of microorganisms surrounded by a self-produced matrix that allows their attachment to inert or organic surfaces. While a unicellular life phase allows for bacterial dispersion and the colonization of new environments, biofilms allow sessile cells to live in a coordinated, more permanent manner that favors their proliferation. In this alternating cycle, bacteria accomplish two physiological transitions via differential gene expression: (i) from planktonic cells to sessile cells within a biofilm, and (ii) from sessile to detached, newly planktonic cells. Many of the innate characteristics of biofilm bacteria are of biotechnological interest, such as the synthesis of valuable compounds (e.g., surfactants, ethanol) and the enhancement/processing of certain foods (e.g., table olives). Understanding the ecology of biofilm formation will allow the design of systems that will facilitate making products of interest and improve their yields.

Bimodal electricity generation and aromatic compounds removal from purified terephthalic acid plant wastewater in a microbial fuel cell.

PubMed

Marashi, Seyed Kamran Foad; Kariminia, Hamid-Reza; Savizi, Iman Shahidi Pour

2013-02-01

Wastewater of purified terephthalic acid (PTA) from a petrochemical plant was examined in a membrane-less single chamber microbial fuel cell for the first time. Time course of voltage during the cell operation cycle had two steady phases, which refers to the fact that metabolism of microorganisms was shifted from highly to less biodegradable carbon sources. The produced power density was 31.8 mW m(-2) (normalized per cathode area) and the calculated coulombic efficiency was 2.05 % for a COD removal of 74 % during 21 days. The total removal rate of different pollutants in the PTA wastewater was observed in the following order: (acetic acid) > (benzoic acid) > (phthalic acid) > (terephthalic acid) > (p-toluic acid). The cyclic voltammetry results revealed that the electron transfer mechanism was dominated by mediators which were produced by bacteria.

Environmental Stress-mediated EPS Production Shape Microbial Activity on Various Hydrated Rough Surfaces

NASA Astrophysics Data System (ADS)

Wang, G.; Liu, L.; Chen, G.

2016-12-01

The complex environmental physical and chemical processes and interplay with the associating biological responses are keys to understanding the environmental microbiology ensconced in environmental remediation, water quality control, food safety, nutrient cycling, and etc., yet remain poorly understood. Using experimental micromodels, we study how environmental conditions (e.g., hydration fluctuation, nutrient limitation, pH variation, etc.) affect microbial extracellular polymeric substances (EPS) production and their configuration within various hydrated surfaces, and impacts on microbial motility, surface attachment, aggregation, and other bioremediation activities. To elucidate the potential mechanisms underlying the complex bio-physicochemical processes, we developed an individual-based and spatio-temporally resolved modeling platform that explicitly considers microscale aqueous-phase configuration and nutrient transport/diffusion and associated biophysical processes affecting individual microbial cell life history. We quantitatively explore the effects of the above microscale environmental processes on bio-physicochemical interactions affecting microbial growth, motility, surface attachment and aggregation, and shaping population interactions and functions. Simulation scenarios of microbial induced pollutant (e.g., roxarsone) biotransformation on various hydrated rough surfaces will also be present.

Microbially mediated transformations of phosphorus in the sea: new views of an old cycle.

PubMed

Karl, David M

2014-01-01

Phosphorus (P) is a required element for life. Its various chemical forms are found throughout the lithosphere and hydrosphere, where they are acted on by numerous abiotic and biotic processes collectively referred to as the P cycle. In the sea, microorganisms are primarily responsible for P assimilation and remineralization, including recently discovered P reduction-oxidation bioenergetic processes that add new complexity to the marine microbial P cycle. Human-induced enhancement of the global P cycle via mining of phosphate-bearing rock will likely influence the pace of P-cycle dynamics, especially in coastal marine habitats. The inextricable link between the P cycle and cycles of other bioelements predicts future impacts on, for example, nitrogen fixation and carbon dioxide sequestration. Additional laboratory and field research is required to build a comprehensive understanding of the marine microbial P cycle.

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

PubMed Central

Zhao, Mengxin; Xue, Kai; Wang, Feng; Liu, Shanshan; Bai, Shijie; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

2014-01-01

Despite microbes' key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling. PMID:24694714

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

PubMed Central

Wasmund, Kenneth; Mußmann, Marc

2017-01-01

Summary Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular‐ and ecosystem‐level processes. Sulfur‐transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate‐rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep‐subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. PMID:28419734

Integrated metagenomics and network analysis of soil microbial community of the forest timberline

PubMed Central

Ding, Junjun; Zhang, Yuguang; Deng, Ye; Cong, Jing; Lu, Hui; Sun, Xin; Yang, Caiyun; Yuan, Tong; Van Nostrand, Joy D.; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

2015-01-01

The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4+-N, NO3−-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift. PMID:25613225

Influence of Age, Reproductive Cycling Status, and Menstruation on the Vaginal Microbiome in Baboons (Papio anubis)

PubMed Central

UCHIHASHI, M.; BERGIN, I. L.; BASSIS, C. M.; HASHWAY, S. A.; CHAI, D.; BELL, J. D.

2015-01-01

The vaginal microbiome is believed to influence host health by providing protection from pathogens and influencing reproductive outcomes such as fertility and gestational length. In humans, age-associated declines in diversity of the vaginal microbiome occur in puberty and persist into adulthood. Additionally, menstruation has been associated with decreased microbial community stability. Adult female baboons, like other non-human primates (NHPs), have a different and highly diverse vaginal microbiome compared to that of humans, which is most commonly dominated by Lactobacillus spp. We evaluated the influence of age, reproductive cycling status (cycling vs. non-cycling) and menstruation on the vaginal microbiome of 38 wild-caught, captive female olive baboons (Papio anubis) by culture-independent sequencing of the V3–V5 region of the bacterial 16S rRNA gene. All baboons had highly diverse vaginal microbial communities. Adult baboons had significantly lower microbial diversity in comparison to subadult baboons, which was attributable to decreased relative abundance of minor taxa. No significant differences were detected based on cycling state or menstruation. Predictive metagenomic analysis showed uniformity in relative abundance of metabolic pathways regardless of age, cycle stage, or menstruation, indicating conservation of microbial community functions. This study suggests that selection of an optimal vaginal microbial community occurs at puberty. Since decreased diversity occurs in both baboons and humans at puberty, this may reflect a general strategy for selection of adult vaginal microbial communities. Comparative evaluation of vaginal microbial community development and composition may elucidate mechanisms of community formation and function that are conserved across host species or across microbial community types. These findings have implications for host health, evolutionary biology, and microbe-host ecosystems. PMID:25676781

Influence of age, reproductive cycling status, and menstruation on the vaginal microbiome in baboons (Papio anubis).

PubMed

Uchihashi, M; Bergin, I L; Bassis, C M; Hashway, S A; Chai, D; Bell, J D

2015-05-01

The vaginal microbiome is believed to influence host health by providing protection from pathogens and influencing reproductive outcomes such as fertility and gestational length. In humans, age-associated declines in diversity of the vaginal microbiome occur in puberty and persist into adulthood. Additionally, menstruation has been associated with decreased microbial community stability. Adult female baboons, like other non-human primates (NHPs), have a different and highly diverse vaginal microbiome compared to that of humans, which is most commonly dominated by Lactobacillus spp. We evaluated the influence of age, reproductive cycling status (cycling vs. non-cycling) and menstruation on the vaginal microbiome of 38 wild-caught, captive female olive baboons (Papio anubis) by culture-independent sequencing of the V3-V5 region of the bacterial 16S rRNA gene. All baboons had highly diverse vaginal microbial communities. Adult baboons had significantly lower microbial diversity in comparison to subadult baboons, which was attributable to decreased relative abundance of minor taxa. No significant differences were detected based on cycling state or menstruation. Predictive metagenomic analysis showed uniformity in relative abundance of metabolic pathways regardless of age, cycle stage, or menstruation, indicating conservation of microbial community functions. This study suggests that selection of an optimal vaginal microbial community occurs at puberty. Since decreased diversity occurs in both baboons and humans at puberty, this may reflect a general strategy for selection of adult vaginal microbial communities. Comparative evaluation of vaginal microbial community development and composition may elucidate mechanisms of community formation and function that are conserved across host species or across microbial community types. These findings have implications for host health, evolutionary biology, and microbe-host ecosystems. © 2015 Wiley Periodicals, Inc.

Turnover of microbial groups and cell components in soil: 13C analysis of cellular biomarkers

NASA Astrophysics Data System (ADS)

Gunina, Anna; Dippold, Michaela; Glaser, Bruno; Kuzyakov, Yakov

2017-01-01

Microorganisms regulate the carbon (C) cycle in soil, controlling the utilization and recycling of organic substances. To reveal the contribution of particular microbial groups to C utilization and turnover within the microbial cells, the fate of 13C-labelled glucose was studied under field conditions. Glucose-derived 13C was traced in cytosol, amino sugars and phospholipid fatty acid (PLFA) pools at intervals of 3, 10 and 50 days after glucose addition into the soil. 13C enrichment in PLFAs ( ˜ 1.5 % of PLFA C at day 3) was an order of magnitude greater than in cytosol, showing the importance of cell membranes for initial C utilization. The 13C enrichment in amino sugars of living microorganisms at day 3 accounted for 0.57 % of total C pool; as a result, we infer that the replacement of C in cell wall components is 3 times slower than that of cell membranes. The C turnover time in the cytosol (150 days) was 3 times longer than in PLFAs (47 days). Consequently, even though the cytosol pool has the fastest processing rates compared to other cellular compartments, intensive recycling of components here leads to a long C turnover time. Both PLFA and amino-sugar profiles indicated that bacteria dominated in glucose utilization. 13C enrichment decreased with time for bacterial cell membrane components, but it remained constant or even increased for filamentous microorganisms. 13C enrichment of muramic acid was the 3.5 times greater than for galactosamine, showing a more rapid turnover of bacterial cell wall components compared to fungal. Thus, bacteria utilize a greater proportion of low-molecular-weight organic substances, whereas filamentous microorganisms are responsible for further C transformations. Thus, tracing 13C in cellular compounds with contrasting turnover rates elucidated the role of microbial groups and their cellular compartments in C utilization and recycling in soil. The results also reflect that microbial C turnover is not restricted to the death or growth of new cells. Indeed, even within living cells, highly polymeric cell compounds are constantly replaced and renewed. This is especially important for assessing C fluxes in soil and the contribution of C from microbial residues to soil organic matter.

Microbial processing of carbon in hydrothermal systems (Invited)

NASA Astrophysics Data System (ADS)

LaRowe, D.; Amend, J. P.

2013-12-01

Microorganisms are known to be active in hydrothermal systems. They catalyze reactions that consume and produce carbon compounds as a result of their efforts to gain energy, grow and replace biomass. However, the rates of these processes, as well as the size of the active component of microbial populations, are poorly constrained in hydrothermal environments. In order to better characterize biogeochemical processes in these settings, a quantitative relationship between rates of microbial catalysis, energy supply and demand and population size is presented. Within this formulation, rates of biomass change are determined as a function of the proportion of catabolic power that is converted into biomass - either new microorganisms or the replacement of existing cell components - and the amount of energy that is required to synthesize biomass. The constraints that hydrothermal conditions place on power supply and demand are explicitly taken into account. The chemical composition, including the concentrations of organic compounds, of diffuse and focused flow hydrothermal fluids, hydrothermally influenced sediment pore water and fluids from the oceanic lithosphere are used in conjunction with cell count data and the model described above to constrain the rates of microbial processes that influence the carbon cycle in the Juan de Fuca hydrothermal system.

Stabilization of glucose-C in microbial cell membranes (PLFA) and cell walls (amino sugars) evaluated by 13C-labelling in a field experiment

NASA Astrophysics Data System (ADS)

Gunina, Anna; Kuzyakov, Yakov; Glaser, Bruno

2015-04-01

Microorganisms control carbon (C) cycle and strongly contribute to formation of soil organic matter. Strong differences in the turnover of microbial groups and cellular compounds complicate the assessment of their contribution to microbial food webs and C sequestration in soil in situ. The uptake and incorporation of 13C labeled glucose by microbial groups were traced during 50 days after the labeling under field conditions. 13C was analysed: i) in the cytosolic pool by chloroform fumigation extraction, ii) in cell membranes by phospholipid fatty acids (PLFA), iii) in cell walls by amino sugars, and iv) remaining in bulk soil. This allowed tracing C in microbial groups as well as cellular compounds. Mean residence times (MRT) of C in PLFA and the cytosol were 47 and 150 days, respectively. Such long cytosol MRT depends on its heterogeneous composition, which includes high and low molecular weight organics. Amino sugars were mainly originated from microbial residues and thus, observation periods higher than 1 year are required for estimation of their MRT. Relative 13C incorporation (13C portion in total pool C) was the highest for PLFAs (~1.5% at day 3), whereas 13C content of the cytosol and amino sugars was one and two orders of magnitude less, respectively. Relative 13C incorporation into amino sugars of living microorganisms showed only 0.57% on day 3. Therefore, the turnover of cell membrane components is two times faster than that of cell walls, even in living microorganisms. Both PLFAs and amino sugars showed that glucose C was preferentially used by bacteria. 13C incorporation into bacterial cell walls and membranes decreased with time, but increased or remained constant for fungi, reflecting faster turnover of bacteria than fungi. Consequently, bacteria contribute more to the decomposition of low molecular weight organics, whereas fungi consume bacterial products or necromass and contribute more to long-term C stabilisation. Thus, tracing of 13C in cellular compounds with contrasting turnover provides key information to C fluxes through the soil microbial food-web and elucidates the role of distinct groups as well as individual cellular compartments in SOM formation and C sequestration.

Increased resiliency and activity of microbial mediated carbon cycling enzymes in diversified bioenergy cropping systems

NASA Astrophysics Data System (ADS)

Upton, R.; Bach, E.; Hofmockel, K. S.

2017-12-01

Microbes are mediators of soil carbon (C) and are influenced in membership and activity by nitrogen (N) fertilization and inter-annual abiotic factors. Microbial communities and their extracellular enzyme activities (EEA) are important parameters that influence ecosystem C cycling properties and are often included in microbial explicit C cycling models. In an effort to generate model relevant, empirical findings, we investigated how both microbial community structure and C degrading enzyme activity are influenced by inter-annual variability and N inputs in bioenergy crops. Our study was performed at the Comparison of Biofuel Systems field-site from 2011 to 2014, in three bioenergy cropping systems, continuous corn (CC) and two restored prairies, both fertilized (FP) and unfertilized (P). We hypothesized microbial community structure would diverge during the prairie restoration, leading to changes in C cycling enzymes over time. Using a sequencing approach (16S and ITS) we determined the bacterial and fungal community structure response to the cropping system, fertilization, and inter-annual variability. Additionally, we used EEA of β-glucosidase, cellobiohydrolase, and β-xylosidase to determine inter-annual and ecosystem impacts on microbial activity. Our results show cropping system was a main effect for microbial community structure, with corn diverging from both prairies to be less diverse. Inter-annual changes showed that a drought occurring in 2012 significantly impacted microbial community structure in both the P and CC, decreasing microbial richness. However, FP increased in microbial richness, suggesting the application of N increased resiliency to drought. Similarly, the only year in which C cycling enzymes were impacted by ecosystem was 2012, with FP supporting higher potential enzymatic activity then CC and P. The highest EEA across all ecosystems occurred in 2014, suggesting the continued root biomass and litter build-up in this no till system provides increased C cycling activity. Our results showed that diverse cropping systems still benefit from N fertilization to confer resiliency to abiotic stress factors. Long-term studies for microbial mediation of soil C are necessary for modeling the impacts of restoration on SOC to assure inclusion of sustainability and resiliency.

Formation of resting cells by non-spore-forming microorganisms as a strategy of long-term survival in the environment

NASA Astrophysics Data System (ADS)

Mulyukin, Andrei L.; Soina, Vera S.; Demkina, Elena V.; Kozlova, Alla N.; Suzina, Natalia E.; Dmitriev, Vladimir V.; Duda, Vitalii I.; El'-Registan, Galina I.

2003-01-01

Non-spore-forming bacteria of the genera Micrococcus and Arthrobacter, including the isolates from permafrost sediments, were found to be able to form cystlike cells under special conditions. Cystlike cells maintained the viability during long-term storage (for up to several years), had undetectable respiratory activity and the elevated resistance to heating and other unfavorable conditions, possessed the specific fine structure and morphology, and were formed in the life cycles of the microorganism. These properties allow cystlike cells to be attributed to a new type of resting microbial forms. Furthermore, the distinctive feature of resting cystlike cells was their low P/S ratios and high Ca/K ratios in comparison to vegetative cells as shown by X-ray microanalysis. The experimentally obtained bacterial cystlike cells with thickened and laminated cell walls and altered texture of the cytoplasm were similar to the cells abundant in native microbial populations isolated from permafrost sediments and ancient soils of the Kolyma lowland (Siberia, Russia). Due to the inherent elevated resistance to adverse conditions and maintenance of viability for prolonged periods, resting cystlike cells are likely to ensure long-term survival of non-spore-forming bacteria in cold environments.

Streptomyces Exploration: Competition, Volatile Communication and New Bacterial Behaviours.

PubMed

Jones, Stephanie E; Elliot, Marie A

2017-07-01

Streptomyces bacteria are prolific producers of specialized metabolites, and have a well studied, complex life cycle. Recent work has revealed a new type of Streptomyces growth termed 'exploration' - so named for the ability of explorer cells to rapidly traverse solid surfaces. Streptomyces exploration is stimulated by fungal interactions, and is associated with the production of an alkaline volatile organic compound (VOC) capable of inducing exploration by other streptomycetes. Here, we examine Streptomyces exploration from the perspectives of interkingdom interactions, pH-induced morphological switches, and VOC-mediated communication. The phenotypic diversity that can be revealed through microbial interactions and VOC exposure is providing us with insight into novel modes of microbial development, and an opportunity to exploit VOCs to stimulate desired microbial behaviours. Copyright © 2017 Elsevier Ltd. All rights reserved.

Carbon availability structures microbial community composition and function in soil aggregate fractions

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.; Howe, A.

2014-12-01

Identifying the microbial metabolic pathways that most strongly influence ecosystem carbon (C) cycling requires a deeper understanding of the availability and accessibility of microbial substrates. A first step towards this goal is characterizing the relationships between microbial community function and soil C chemistry in a field context. For this perspective, soil aggregate fractions can be used as model systems that scale between microbe-substrate interactions and ecosystem C cycling and storage. The present study addresses how physicochemical variation among soil aggregate fractions influences the composition and functional potential of C cycling microbial communities. We report variation across soil aggregates using plot scale biological replicates from biofuel agroecosystems (fertilized, reconstructed, tallgrass prairie). Our results suggest that C and nitrogen (N) chemistry significantly differ among aggregate fractions. This leads to variation in microbial community composition, which was better characterized among aggregates than by using the whole soil. In fact by considering soil aggregation, we were able to characterize almost 2000 more taxa than whole soil alone, resulting in 65% greater community richness. Availability of C and N strongly influenced the composition of microbial communities among soil aggregate fractions. The normalized abundance of microbial functional guilds among aggregate fractions correlated with C and N chemistry, as did functional potential, measured by extracellular enzyme activity. Metagenomic results suggest that soil aggregate fractions select for functionally distinct microbial communities, which may significantly influence decomposition and soil C storage. Our study provides support for the premise that integration of soil aggregate chemistry, especially microaggregates that have greater microbial richness and occur at spatial scales relevant to microbial community functioning, may be necessary to understand the role of microbial communities on terrestrial C and N cycling.

Responses of benthic bacteria to experimental drying in sediments from Mediterranean temporary rivers.

PubMed

Amalfitano, Stefano; Fazi, Stefano; Zoppini, Annamaria; Barra Caracciolo, Anna; Grenni, Paola; Puddu, Alberto

2008-02-01

In the semiarid Mediterranean regions, water scarcity represents a common physiological stress for microbial communities residing in river sediments. However, the effect of drying has not yet adequately been evaluated when analyzing riverine microbiological processes. The bacterial community structure (abundance, biomass, composition) and functioning (carbon production, live cell percentage) were assessed during experimental desiccation in microcosms with sediments from different Mediterranean temporary rivers (Tagliamento, Krathis, Mulargia, Pardiela). Our results showed that the overall responses to drying of the bacterial community were independent from sediment origin and strictly related to water content. During desiccation, a prompt decline (up to 100%) of the initial bacterial carbon production was followed by a slower decrease in abundance and biomass, with an overall reduction of 74% and 78%, respectively. By the end of the experiment, live cells were still abundant but depressed in their main metabolic functions, thus resulting in a drastic increase in the community turnover time. Only 14% of the initial live cell biomass was available in dry sediments to immediately start the reactivation of the aquatic microbial food web after the arrival of new water. Community composition analysis showed a relative increase in alpha- and beta-Proteobacteria, when passing from wet to dry conditions. Our results suggest that the occurrence of drought events could affect carbon cycling through the freshwater microbial compartment, by temporarily limiting microbial mineralization and altering bacterial community structure.

Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Justice, Nicholas B; Pan, Chongle; Mueller, Ryan

Archaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition from Bacteria- to Archaea-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (pH 1.0,38 C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the class Thermoplasmata, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms,more » nanoarchaea comprise 10 to 25% of the community, based on fluorescent in situ hybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected 2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment of Ferroplasma and Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.« less

The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

PubMed

Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander

2017-08-01

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Facilitated extracellular electron transfer of Shewanella loihica PV-4 by antimony-doped tin oxide nanoparticles as active microelectrodes.

PubMed

Zhang, Xiaojian; Liu, Huan; Wang, Jinrong; Ren, Guangyuan; Xie, Beizhen; Liu, Hong; Zhu, Ying; Jiang, Lei

2015-11-28

Dissimilatory metal reducing bacteria are capable of extracellular electron transfer (EET) to insoluble metal oxides as external electron acceptors for their anaerobic respiration, which is recognized as an important energy-conversion process in natural and engineered environments, such as in mineral cycling, bioremediation, and microbial fuel/electrolysis cells. However, the low EET efficiency remains one of the major bottlenecks for its practical application. We report firstly that the microbial current generated by Shewanella loihica PV-4 (S. loihica PV-4) could be greatly improved that is up to ca. 115 fold, by adding antimony-doped tin oxide (ATO) nanoparticles in the electrochemical reactor. The results demonstrate that the biocompatible, electrically conductive ATO nanoparticles acted as active microelectrodes could facilitate the formation of a cells/ATO composite biofilm and the reduction of the outer membrane c-type cytochromes (OM c-Cyts) that are beneficial for the electron transfer from cells to electrode. Meanwhile, a synergistic effect between the participation of OM c-Cyts and the accelerated EET mediated by cell-secreted flavins may play an important role for the enhanced current generation in the presence of ATO nanoparticles. Moreover, it is worth noting that the TCA cycle in S. loihica PV-4 cells is activated by adding ATO nanoparticles, even if the potential is poised at +0.2 V, thereby also improving the EET process. The results presented here may provide a simple and effective strategy to boost the EET of S. loihica PV-4 cells, which is conducive to providing potential applications in bioelectrochemical systems.

Arsenic detoxification and evolution of trimethylarsine gas by a microbial arsenite S-adenosylmethionine methyltransferase

PubMed Central

Qin, Jie; Rosen, Barry P.; Zhang, Yang; Wang, Gejiao; Franke, Sylvia; Rensing, Christopher

2006-01-01

In this article, a mechanism of arsenite [As(III)]resistance through methylation and subsequent volatization is described. Heterologous expression of arsM from Rhodopseudomonas palustris was shown to confer As(III) resistance to an arsenic-sensitive strain of Escherichia coli. ArsM catalyzes the formation of a number of methylated intermediates from As(III), with trimethylarsine as the end product. The net result is loss of arsenic, from both the medium and the cells. Because ArsM homologues are widespread in nature, this microbial-mediated transformation is proposed to have an important impact on the global arsenic cycle. PMID:16452170

Impact of ocean phytoplankton diversity on phosphate uptake

PubMed Central

Lomas, Michael W.; Bonachela, Juan A.; Levin, Simon A.; Martiny, Adam C.

2014-01-01

We have a limited understanding of the consequences of variations in microbial biodiversity on ocean ecosystem functioning and global biogeochemical cycles. A core process is macronutrient uptake by microorganisms, as the uptake of nutrients controls ocean CO2 fixation rates in many regions. Here, we ask whether variations in ocean phytoplankton biodiversity lead to novel functional relationships between environmental variability and phosphate (Pi) uptake. We analyzed Pi uptake capabilities and cellular allocations among phytoplankton groups and the whole community throughout the extremely Pi-depleted western North Atlantic Ocean. Pi uptake capabilities of individual populations were well described by a classic uptake function but displayed adaptive differences in uptake capabilities that depend on cell size and nutrient availability. Using an eco-evolutionary model as well as observations of in situ uptake across the region, we confirmed that differences among populations lead to previously uncharacterized relationships between ambient Pi concentrations and uptake. Supported by novel theory, this work provides a robust empirical basis for describing and understanding assimilation of limiting nutrients in the oceans. Thus, it demonstrates that microbial biodiversity, beyond cell size, is important for understanding the global cycling of nutrients. PMID:25422472

Microbial interactions in the arsenic cycle: adoptive strategies and applications in environmental management.

PubMed

Dhuldhaj, Umesh Praveen; Yadav, Ishwar Chandra; Singh, Surendra; Sharma, Naveen Kumar

2013-01-01

Arsenic (As) is a nonessential element that is often present in plants and in other organisms. However, it is one of the most hazardous of toxic elements globally. In many parts of the world, arsenic contamination in groundwater is a serious and continuing threat to human health. Microbes play an important role in regulating the environmental fate of arsenic. Different microbial processes influence the biogeochemical cycling of arsenic in ways that affect the accumulation of different arsenic species in various ecosystem compartments. For example, in soil, there are bacteria that methylate arsenite to trimethylarsine gas, thereby releasing arsenic to the atmosphere.In marine ecosystems, microbes exist that can convert inorganic arsenicals to organic arsenicals (e.g., di- and tri-methylated arsenic derivatives, arsenocholine,arsenobetaine, arsenosugars, arsenolipids). The organo arsenicals are further metabolized to complete the arsenic cycle.Microbes have developed various strategies that enable them to tolerate arsenic and to survive in arsenic-rich environments. Such strategies include As exclusion from cells by establishing permeability barrier, intra- and extracellular sequestration,active efflux pumps, enzymatic reduction, and reduction in the sensitivity of cellular targets. These strategies are used either singly or in combination. In bacteria,the genes for arsenic resistance/detoxification are encoded by the arsenic resistance operons (ars operon).In this review, we have addressed and emphasized the impact of different microbial processes (e.g., arsenite oxidation, cytoplasmic arsenate reduction, respiratory arsenate reduction, arsenite methylation) on the arsenic cycle. Microbes are the only life forms reported to exist in heavy arsenic-contaminated environments. Therefore,an understanding of the strategies adopted by microbes to cope with arsenic stress is important in managing such arsenic-contaminated sites. Further future insights into the different microbial genes/proteins that are involved in arsenic resistance may also be useful for developing arsenic resistant crop plants.

Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth System Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Xiaofeng; Schimel, Joshua; Thornton, Peter E

2014-01-01

Microbial assimilation of soil organic carbon is one of the fundamental processes of global carbon cycling and it determines the magnitude of microbial biomass in soils. Mechanistic understanding of microbial assimilation of soil organic carbon and its controls is important for to improve Earth system models ability to simulate carbon-climate feedbacks. Although microbial assimilation of soil organic carbon is broadly considered to be an important parameter, it really comprises two separate physiological processes: one-time assimilation efficiency and time-dependent microbial maintenance energy. Representing of these two mechanisms is crucial to more accurately simulate carbon cycling in soils. In this study, amore » simple modeling framework was developed to evaluate the substrate and environmental controls on microbial assimilation of soil organic carbon using a new term: microbial annual active period (the length of microbes remaining active in one year). Substrate quality has a positive effect on microbial assimilation of soil organic carbon: higher substrate quality (lower C:N ratio) leads to higher ratio of microbial carbon to soil organic carbon and vice versa. Increases in microbial annual active period from zero stimulate microbial assimilation of soil organic carbon; however, when microbial annual active period is longer than an optimal threshold, increasing this period decreases microbial biomass. The simulated ratios of soil microbial biomass to soil organic carbon are reasonably consistent with a recently compiled global dataset at the biome-level. The modeling framework of microbial assimilation of soil organic carbon and its controls developed in this study offers an applicable ways to incorporate microbial contributions to the carbon cycling into Earth system models for simulating carbon-climate feedbacks and to explain global patterns of microbial biomass.« less

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.

PubMed

Cong, Jing; Liu, Xueduan; Lu, Hui; Xu, Han; Li, Yide; Deng, Ye; Li, Diqiang; Zhang, Yuguang

2015-08-20

Tropical rainforests cover over 50% of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology. Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure. Overall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.

Microbial extracellular enzymes in biogeochemical cycling of ecosystems.

PubMed

Luo, Ling; Meng, Han; Gu, Ji-Dong

2017-07-15

Extracellular enzymes, primarily produced by microorganisms, affect ecosystem processes because of their essential roles in degradation, transformation and mineralization of organic matter. Extracellular enzymes involved in the cycling of carbon (C), nitrogen (N) and phosphorus (P) have been widely investigated in many different ecosystems, and several enzymes have been recognized as key components in regulating C storage and nutrient cycling. In this review, it was the first time to summarize the specific extracellular enzymes related to C storage and nutrient cycling for better understanding the important role of microbial extracellular enzymes in biogeochemical cycling of ecosystems. Subsequently, ecoenzymatic stoichiometry - the relative ratio of extracellular enzyme, has been reviewed and further provided a new perspective for understanding biogeochemical cycling of ecosystems. Finally, the new insights of using microbial extracellular enzyme in indicating biogeochemical cycling and then protecting ecosystems have been suggested. Copyright © 2017 Elsevier Ltd. All rights reserved.

Subpopulation-proteomics in prokaryotic populations.

PubMed

Jahn, Michael; Seifert, Jana; von Bergen, Martin; Schmid, Andreas; Bühler, Bruno; Müller, Susann

2013-02-01

Clonal microbial cells do not behave in an identical manner and form subpopulations during cultivation. Besides varying micro-environmental conditions, cell inherent features like cell cycle dependent localization and concentration of regulatory proteins as well as epigenetic properties are well accepted mechanisms creating cell heterogeneity. Another suspected reason is molecular noise on the transcriptional and translational level. A promising tool to unravel reasons for cell heterogeneity is the combination of cell sorting and subpopulation proteomics. This review summarizes recent developments in prokaryotic single-cell analytics and provides a workflow for selection of single cells, low cell number mass spectrometry, and proteomics evaluation. This approach is useful for understanding the dependency of individual cell decisions on inherent protein profiles. Copyright © 2012 Elsevier Ltd. All rights reserved.

Effects of single-walled carbon nanotubes on soil microorganisms

NASA Astrophysics Data System (ADS)

Jin, L.; Chung, H.; Son, Y.

2011-12-01

Single-walled carbon nanotubes (SWCNTs) are novel materials that have the potential to be used in various commercial fields due to their unique physicochemical properties. As a result of commercial development of nanotechnology, SWCNTs may be discharged to the soil environment with unknown consequences. However, there are as yet no data in the scientific literature that demonstrate the effects of SWCNTs on microbial function in soils. Therefore, we aimed to determine the effects of SWCNTs on soil microbial activity through a 2-week incubation study on urban soils supplemented with different concentrations of SWCNTs ranging from 0 to 1000 μg CNT/g soil. Fluorometric test using fluorogenic substrates were employed for the measurement of several enzyme activities in soil samples. More specifically, we determined the changes in the activities of cellobiohydrolase, β-1,4-glucosidase, β-1,4-xylosidase, β-1,4-N-acetylglucosaminidase, L-leucine aminopeptidase and acid phosphatase which play important roles in the carbon, nitrogen, and phosphorus cycles in response to the addition of SWCNTs. We found that microbial enzyme activities decreased as the concentrations of SWCNT added increased. The lowest enzyme activities were observed under 1000 μg CNT/g soil. The overall pattern shows that enzyme activities decreased slightly in the first 2-3 days and increased in the later stage of the incubation. Our results suggest that relatively high concentrations of SWCNTs can inhibit microbial activities, and this may be due to microbial cell membrane damage caused by SWCNTs. However, further study needs to be conducted to determine the mechanism responsible for inhibitory effect of SWCNTs on soil microbial activity. It can be concluded that changes in the activities of extracellular enzymes can indicate the effect of SWCNTs on soil microorganisms and nutrient cycling.

Evidence for Direct Electron Transfer by a Gram-Positive Bacterium Isolated from a Microbial Fuel Cell▿†

PubMed Central

Wrighton, K. C.; Thrash, J. C.; Melnyk, R. A.; Bigi, J. P.; Byrne-Bailey, K. G.; Remis, J. P.; Schichnes, D.; Auer, M.; Chang, C. J.; Coates, J. D.

2011-01-01

Despite their importance in iron redox cycles and bioenergy production, the underlying physiological, genetic, and biochemical mechanisms of extracellular electron transfer by Gram-positive bacteria remain insufficiently understood. In this work, we investigated respiration by Thermincola potens strain JR, a Gram-positive isolate obtained from the anode surface of a microbial fuel cell, using insoluble electron acceptors. We found no evidence that soluble redox-active components were secreted into the surrounding medium on the basis of physiological experiments and cyclic voltammetry measurements. Confocal microscopy revealed highly stratified biofilms in which cells contacting the electrode surface were disproportionately viable relative to the rest of the biofilm. Furthermore, there was no correlation between biofilm thickness and power production, suggesting that cells in contact with the electrode were primarily responsible for current generation. These data, along with cryo-electron microscopy experiments, support contact-dependent electron transfer by T. potens strain JR from the cell membrane across the 37-nm cell envelope to the cell surface. Furthermore, we present physiological and genomic evidence that c-type cytochromes play a role in charge transfer across the Gram-positive bacterial cell envelope during metal reduction. PMID:21908627

Microbial ecology and biogeochemistry of continental Antarctic soils.

PubMed

Cowan, Don A; Makhalanyane, Thulani P; Dennis, Paul G; Hopkins, David W

2014-01-01

The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbor microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths) possess a genetic capacity for nitrogen and carbon cycling, polymer degradation, and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities.

Nitrogen Cycling Potential of a Grassland Litter Microbial Community

PubMed Central

Berlemont, Renaud; Martiny, Adam C.; Martiny, Jennifer B. H.

2015-01-01

Because microorganisms have different abilities to utilize nitrogen (N) through various assimilatory and dissimilatory pathways, microbial composition and diversity likely influence N cycling in an ecosystem. Terrestrial plant litter decomposition is often limited by N availability; however, little is known about the microorganisms involved in litter N cycling. In this study, we used metagenomics to characterize the potential N utilization of microbial communities in grassland plant litter. The frequencies of sequences associated with eight N cycling pathways differed by several orders of magnitude. Within a pathway, the distributions of these sequences among bacterial orders differed greatly. Many orders within the Actinobacteria and Proteobacteria appeared to be N cycling generalists, carrying genes from most (five or six) of the pathways. In contrast, orders from the Bacteroidetes were more specialized and carried genes for fewer (two or three) pathways. We also investigated how the abundance and composition of microbial N cycling genes differed over time and in response to two global change manipulations (drought and N addition). For many pathways, the abundance and composition of N cycling taxa differed over time, apparently reflecting precipitation patterns. In contrast to temporal variability, simulated global change had minor effects on N cycling potential. Overall, this study provides a blueprint for the genetic potential of N cycle processes in plant litter and a baseline for comparisons to other ecosystems. PMID:26231641

Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

NASA Astrophysics Data System (ADS)

Kim, Minsu; Or, Dani

2017-12-01

Biological soil crusts (biocrusts) are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment) under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

Linking Metabolism, Elemental Cycles, and Environmental Conditions in the Deep Biosphere: Growth of a Model Extremophile, Archaeoglobus fulgidus, Under High-Pressure Conditions

NASA Astrophysics Data System (ADS)

Oliver, G. C. M.; Cario, A.; Rogers, K. L.

2015-12-01

A majority of Earth's biosphere is hosted in subsurface environments where global-scale biogeochemical and energy cycles are driven by diverse microbial communities that operate on and are influenced by micro-scale environmental variables. While the subsurface hosts a variety of geochemical and geothermal conditions, elevated pressures are common to all subsurface ecosystems. Understanding how microbes adapt to and thrive in high-pressure environments is essential to linking microbial subsurface processes with global-scale cycles. Here we are using a model extremophile, Archaeoglobus fulgidus, to determine how elevated pressures affect the growth, metabolism, and physiology of subsurface microorganisms. A. fulgidus cycles carbon and sulfur via heterotrophic and autotrophic sulfate reduction in various high temperature and high-pressure niches including shallow marine vents, deep-sea hydrothermal vents, and deep oil reservoirs. Here we report the results of A. fulgidus growth experiments at optimum temperature, 83°C, and pressures up to 600 bars. Exponential growth was observed over the entire pressure range, though growth rates were diminished at 500 and 600 bars compared to ambient pressure experimental controls. At pressures up to 400 bars, cell density yields and growth rates were at least as high as ambient pressure controls. Elevated pressures and extended incubation times stimulated cell flocculation, a common stress response in this strain, and cellular morphology was affected at pressures exceeding 400 bars. These results suggest that A. fulgidus continues carbon, sulfur and energy cycling unaffected by elevated pressures up to 400 bars, representing a variety of subsurface environments. The ability of subsurface organisms to drive biogeochemical cycles at elevated pressures is a critical link between the surface and subsurface biospheres and understanding how species-scale processes operate under these conditions is a vital part of global-scale biogeochemical models.

Coassimilation of Organic Substrates via the Autotrophic 3-Hydroxypropionate Bi-Cycle in Chloroflexus aurantiacus▿†

PubMed Central

Zarzycki, Jan; Fuchs, Georg

2011-01-01

Chloroflexus aurantiacus is a facultative autotrophic green nonsulfur bacterium that grows phototrophically in thermal springs and forms microbial mats with cyanobacteria. Cyanobacteria produce glycolate during the day (photorespiration) and excrete fermentation products at night. C. aurantiacus uses the 3-hydroxypropionate bi-cycle for autotrophic carbon fixation. This pathway was thought to be also suited for the coassimilation of various organic substrates such as glycolate, acetate, propionate, 3-hydroxypropionate, lactate, butyrate, or succinate. To test this possibility, we added these compounds at a 5 mM concentration to autotrophically pregrown cells. Although the provided amounts of H2 and CO2 allowed continuing photoautotrophic growth, cells immediately consumed most substrates at rates equaling the rate of autotrophic carbon fixation. Using [14C]acetate, half of the labeled organic carbon was incorporated into cell mass. Our data suggest that C. aurantiacus uses the 3-hydroxypropionate bi-cycle, together with the glyoxylate cycle, to channel organic substrates into the central carbon metabolism. Enzyme activities of the 3-hydroxypropionate bi-cycle were marginally affected when cells were grown heterotrophically with such organic substrates. The 3-hydroxypropionate bi-cycle in Chloroflexi is unique and was likely fostered in an environment in which traces of organic compounds can be coassimilated. Other bacteria living under oligotrophic conditions acquired genes of a rudimentary 3-hydroxypropionate bi-cycle, possibly for the same purpose. Examples are Chloroherpeton thalassium, Erythrobacter sp. strain NAP-1, Nitrococcus mobilis, and marine gammaproteobacteria of the OM60/NOR5 clade such as Congregibacter litoralis. PMID:21764971

BTG interacts with retinoblastoma to control cell fate in Dictyostelium.

PubMed

Conte, Daniele; MacWilliams, Harry K; Ceccarelli, Adriano

2010-03-12

In the genesis of many tissues, a phase of cell proliferation is followed by cell cycle exit and terminal differentiation. The latter two processes overlap: genes involved in the cessation of growth may also be important in triggering differentiation. Though conceptually distinct, they are often causally related and functional interactions between the cell cycle machinery and cell fate control networks are fundamental to coordinate growth and differentiation. A switch from proliferation to differentiation may also be important in the life cycle of single-celled organisms, and genes which arose as regulators of microbial differentiation may be conserved in higher organisms. Studies in microorganisms may thus contribute to understanding the molecular links between cell cycle machinery and the determination of cell fate choice networks. Here we show that in the amoebozoan D. discoideum, an ortholog of the metazoan antiproliferative gene btg controls cell fate, and that this function is dependent on the presence of a second tumor suppressor ortholog, the retinoblastoma-like gene product. Specifically, we find that btg-overexpressing cells preferentially adopt a stalk cell (and, more particularly, an Anterior-Like Cell) fate. No btg-dependent preference for ALC fate is observed in cells in which the retinoblastoma-like gene has been genetically inactivated. Dictyostelium btg is the only example of non-metazoan member of the BTG family characterized so far, suggesting that a genetic interaction between btg and Rb predated the divergence between dictyostelids and metazoa. While the requirement for retinoblastoma function for BTG antiproliferative activity in metazoans is known, an interaction of these genes in the control of cell fate has not been previously documented. Involvement of a single pathway in the control of mutually exclusive processes may have relevant implication in the evolution of multicellularity.

A Terrestrial Single Chamber Microbial Fuel Cell-based Biosensor for Biochemical Oxygen Demand of Synthetic Rice Washed Wastewater

PubMed Central

Logroño, Washington; Guambo, Alex; Pérez, Mario; Kadier, Abudukeremu; Recalde, Celso

2016-01-01

Microbial fuel cells represent an innovative technology which allow simultaneous waste treatment, electricity production, and environmental monitoring. This study provides a preliminary investigation of the use of terrestrial Single chamber Microbial Fuel Cells (SMFCs) as biosensors. Three cells were created using Andean soil, each one for monitoring a BOD concentration of synthetic washed rice wastewater (SRWW) of 10, 100, and 200 mg/L for SMFC1, SMFC2 and SMFC3, respectively. The results showed transient, exponential, and steady stages in the SMFCs. The maximum open circuit voltage (OCV) peaks were reached during the elapsed time of the transient stages, according to the tested BOD concentrations. A good linearity between OCV and time was observed in the increasing stage. The average OCV in this stage increased independently of the tested concentrations. SMFC1 required less time than SMFC2 to reach the steady stage, suggesting the BOD concentration is an influencing factor in SMFCs, and SMFC3 did not reach it. The OCV ratios were between 40.6–58.8 mV and 18.2–32.9 mV for SMFC1 and SMFC2. The reproducibility of the SMFCs was observed in four and three cycles for SMFC1 and SMFC2, respectively. The presented SMFCs had a good response and reproducibility as biosensor devices, and could be an alternative for environmental monitoring. PMID:26784197

A Terrestrial Single Chamber Microbial Fuel Cell-based Biosensor for Biochemical Oxygen Demand of Synthetic Rice Washed Wastewater.

PubMed

Logroño, Washington; Guambo, Alex; Pérez, Mario; Kadier, Abudukeremu; Recalde, Celso

2016-01-15

Microbial fuel cells represent an innovative technology which allow simultaneous waste treatment, electricity production, and environmental monitoring. This study provides a preliminary investigation of the use of terrestrial Single chamber Microbial Fuel Cells (SMFCs) as biosensors. Three cells were created using Andean soil, each one for monitoring a BOD concentration of synthetic washed rice wastewater (SRWW) of 10, 100, and 200 mg/L for SMFC1, SMFC2 and SMFC3, respectively. The results showed transient, exponential, and steady stages in the SMFCs. The maximum open circuit voltage (OCV) peaks were reached during the elapsed time of the transient stages, according to the tested BOD concentrations. A good linearity between OCV and time was observed in the increasing stage. The average OCV in this stage increased independently of the tested concentrations. SMFC1 required less time than SMFC2 to reach the steady stage, suggesting the BOD concentration is an influencing factor in SMFCs, and SMFC3 did not reach it. The OCV ratios were between 40.6-58.8 mV and 18.2-32.9 mV for SMFC1 and SMFC2. The reproducibility of the SMFCs was observed in four and three cycles for SMFC1 and SMFC2, respectively. The presented SMFCs had a good response and reproducibility as biosensor devices, and could be an alternative for environmental monitoring.

Environmental controls on microbial abundance and activity on the greenland ice sheet: a multivariate analysis approach.

PubMed

Stibal, Marek; Telling, Jon; Cook, Joe; Mak, Ka Man; Hodson, Andy; Anesio, Alexandre M

2012-01-01

Microbes in supraglacial ecosystems have been proposed to be significant contributors to regional and possibly global carbon cycling, and quantifying the biogeochemical cycling of carbon in glacial ecosystems is of great significance for global carbon flow estimations. Here we present data on microbial abundance and productivity, collected along a transect across the ablation zone of the Greenland ice sheet (GrIS) in summer 2010. We analyse the relationships between the physical, chemical and biological variables using multivariate statistical analysis. Concentrations of debris-bound nutrients increased with distance from the ice sheet margin, as did both cell numbers and activity rates before reaching a peak (photosynthesis) or a plateau (respiration, abundance) between 10 and 20 km from the margin. The results of productivity measurements suggest an overall net autotrophy on the GrIS and support the proposed role of ice sheet ecosystems in carbon cycling as regional sinks of CO(2) and places of production of organic matter that can be a potential source of nutrients for downstream ecosystems. Principal component analysis based on chemical and biological data revealed three clusters of sites, corresponding to three 'glacier ecological zones', confirmed by a redundancy analysis (RDA) using physical data as predictors. RDA using data from the largest 'bare ice zone' showed that glacier surface slope, a proxy for melt water flow, accounted for most of the variation in the data. Variation in the chemical data was fully explainable by the determined physical variables. Abundance of phototrophic microbes and their proportion in the community were identified as significant controls of the carbon cycling-related microbial processes.

Microbial biomass as a significant source of soil organic matter

NASA Astrophysics Data System (ADS)

Miltner, Anja; Kindler, Reimo; Schweigert, Michael; Achtenhagen, Jan; Bombach, Petra; Fester, Thomas; Kästner, Matthias

2014-05-01

Soil organic matter (SOM) plays an important role for soil fertility and in the global carbon cycle. SOM management should be based on knowledge about the chemical composition as well as the spatial distribution of SOM and its individual components in soils. Both parameters strongly depend on the direct precursors of SOM. In the past, microbial biomass has been neglected as a potential source of SOM, mainly because of its small pool size. Recent studies, however, show that a substantial portion of SOM is derived from microbial biomass residues. We therefore investigated the fate of microbial biomass residues in soils by means of incubation experiments with 13C-labelled microbial biomass. For our studies, we selected model organisms representing the three types of soil microorganisms and their characteristic cell wall structures: Escherichia coli (a Gram-negative bacterium), Bacillus subtilis (a Gram-positive bacterium) and Laccaria bicolor (an ectomycorrhizal fungus). We labelled the organisms by growing them on 13C glucose and incubated them in soil. During incubation, we followed the mineralisation of the labelled C, its incorporation into microbial biomass, and its transformation to non-living SOM. We found that 50-65% of the microbial biomass C remained in the soil during incubation. However, only a small part remained in the microbial biomass, the majority was transformed to SOM. In particular, proteins seemed to be rather stable in our experiments. In addition, we used scanning electron microscopy to identify microbial residues in soils and, for comparison, in artificial groundwater microcosms. Scanning electron micrographs showed a low number of intact cells, but mainly fragments of about 200-500 nm size. Similar fragments were found in artificial groundwater microcosms where the only possible origin was microbial biomass residues. Based on the results obtained, we provide a mechanistic model which explains how microbial biomass residues are formed and stabilized in soils. This model also explains a number of chemical and physical properties of SOM such as the abundance and stability of microbial biomolecules, the low C/N ratio and the water repellency of SOM.

Photosynthesis and early Earth.

PubMed

Shih, Patrick M

2015-10-05

Life has been built on the evolution and innovation of microbial metabolisms. Even with our scant understanding of the full diversity of microbial life, it is clear that microbes have become integral components of the biogeochemical cycles that drive our planet. The antiquity of life further suggests that various microbial metabolisms have been core and essential to global elemental cycling for a majority of Earth's history. Copyright © 2015 Elsevier Ltd. All rights reserved.

Functionally Stable and Phylogenetically Diverse Microbial Enrichments from Microbial Fuel Cells during Wastewater Treatment

PubMed Central

Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M.; Nealson, Kenneth H.; Sekiguchi, Yuji; Gorby, Yuri A.; Bretschger, Orianna

2012-01-01

Microbial fuel cells (MFCs) are devices that exploit microorganisms as biocatalysts to recover energy from organic matter in the form of electricity. One of the goals of MFC research is to develop the technology for cost-effective wastewater treatment. However, before practical MFC applications are implemented it is important to gain fundamental knowledge about long-term system performance, reproducibility, and the formation and maintenance of functionally-stable microbial communities. Here we report findings from a MFC operated for over 300 days using only primary clarifier effluent collected from a municipal wastewater treatment plant as the microbial resource and substrate. The system was operated in a repeat-batch mode, where the reactor solution was replaced once every two weeks with new primary effluent that consisted of different microbial and chemical compositions with every batch exchange. The turbidity of the primary clarifier effluent solution notably decreased, and 97% of biological oxygen demand (BOD) was removed after an 8–13 day residence time for each batch cycle. On average, the limiting current density was 1000 mA/m2, the maximum power density was 13 mW/m2, and coulombic efficiency was 25%. Interestingly, the electrochemical performance and BOD removal rates were very reproducible throughout MFC operation regardless of the sample variability associated with each wastewater exchange. While MFC performance was very reproducible, the phylogenetic analyses of anode-associated electricity-generating biofilms showed that the microbial populations temporally fluctuated and maintained a high biodiversity throughout the year-long experiment. These results suggest that MFC communities are both self-selecting and self-optimizing, thereby able to develop and maintain functional stability regardless of fluctuations in carbon source(s) and regular introduction of microbial competitors. These results contribute significantly toward the practical application of MFC systems for long-term wastewater treatment as well as demonstrating MFC technology as a useful device to enrich for functionally stable microbial populations. PMID:22347379

Lipids as paleomarkers to constrain the marine nitrogen cycle

PubMed Central

Rush, Darci

2017-01-01

Summary Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction‐oxidation transformations of bio‐available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio‐available nitrogen species. As most microorganisms are soft‐bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically‐important cycle, and provides examples of biomarker applications in the geological past. PMID:28142226

Polar Marine Microorganisms and Climate Change.

PubMed

Verde, C; Giordano, D; Bellas, C M; di Prisco, G; Anesio, A M

2016-01-01

The large diversity of marine microorganisms harboured by oceans plays an important role in planet sustainability by driving globally important biogeochemical cycles; all primary and most secondary production in the oceans is performed by microorganisms. The largest part of the planet is covered by cold environments; consequently, cold-adapted microorganisms have crucial functional roles in globally important environmental processes and biogeochemical cycles cold-adapted extremophiles are a remarkable model to shed light on the molecular basis of survival at low temperature. The indigenous populations of Antarctic and Arctic microorganisms are endowed with genetic and physiological traits that allow them to live and effectively compete at the temperatures prevailing in polar regions. Some genes, e.g. glycosyltransferases and glycosylsynthetases involved in the architecture of the cell wall, may have been acquired/retained during evolution of polar strains or lost in tropical strains. This present work focusses on temperature and its role in shaping microbial adaptations; however, in assessing the impacts of climate changes on microbial diversity and biogeochemical cycles in polar oceans, it should not be forgotten that physiological studies need to include the interaction of temperature with other abiotic and biotic factors. © 2016 Elsevier Ltd All rights reserved.

Jellyfish extract induces apoptotic cell death through the p38 pathway and cell cycle arrest in chronic myelogenous leukemia K562 cells

PubMed Central

Kwak, Choong-Hwan; Abekura, Fukushi; Park, Jun-Young; Park, Nam Gyu; Chang, Young-Chae; Lee, Young-Choon; Chung, Tae-Wook; Ha, Ki-Tae; Son, Jong-Keun

2017-01-01

Jellyfish species are widely distributed in the world’s oceans, and their population is rapidly increasing. Jellyfish extracts have several biological functions, such as cytotoxic, anti-microbial, and antioxidant activities in cells and organisms. However, the anti-cancer effect of Jellyfish extract has not yet been examined. We used chronic myelogenous leukemia K562 cells to evaluate the mechanisms of anti-cancer activity of hexane extracts from Nomura’s jellyfish in vitro. In this study, jellyfish are subjected to hexane extraction, and the extract is shown to have an anticancer effect on chronic myelogenous leukemia K562 cells. Interestingly, the present results show that jellyfish hexane extract (Jellyfish-HE) induces apoptosis in a dose- and time-dependent manner. To identify the mechanism(s) underlying Jellyfish-HE-induced apoptosis in K562 cells, we examined the effects of Jellyfish-HE on activation of caspase and mitogen-activated protein kinases (MAPKs), which are responsible for cell cycle progression. Induction of apoptosis by Jellyfish-HE occurred through the activation of caspases-3,-8 and -9 and phosphorylation of p38. Jellyfish-HE-induced apoptosis was blocked by a caspase inhibitor, Z-VAD. Moreover, during apoptosis in K562 cells, p38 MAPK was inhibited by pretreatment with SB203580, an inhibitor of p38. SB203580 blocked jellyfish-HE-induced apoptosis. Additionally, Jellyfish-HE markedly arrests the cell cycle in the G0/G1 phase. Therefore, taken together, the results imply that the anti-cancer activity of Jellyfish-HE may be mediated apoptosis by induction of caspases and activation of MAPK, especially phosphorylation of p38, and cell cycle arrest at the Go/G1 phase in K562 cells. PMID:28133573

Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland.

PubMed

Yang, Yunfeng; Wu, Linwei; Lin, Qiaoyan; Yuan, Mengting; Xu, Depeng; Yu, Hao; Hu, Yigang; Duan, Jichuang; Li, Xiangzhen; He, Zhili; Xue, Kai; van Nostrand, Joy; Wang, Shiping; Zhou, Jizhong

2013-02-01

Microbes play key roles in various biogeochemical processes, including carbon (C) and nitrogen (N) cycling. However, changes of microbial community at the functional gene level by livestock grazing, which is a global land-use activity, remain unclear. Here we use a functional gene array, GeoChip 4.0, to examine the effects of free livestock grazing on the microbial community at an experimental site of Tibet, a region known to be very sensitive to anthropogenic perturbation and global warming. Our results showed that grazing changed microbial community functional structure, in addition to aboveground vegetation and soil geochemical properties. Further statistical tests showed that microbial community functional structures were closely correlated with environmental variables, and variations in microbial community functional structures were mainly controlled by aboveground vegetation, soil C/N ratio, and NH4 (+) -N. In-depth examination of N cycling genes showed that abundances of N mineralization and nitrification genes were increased at grazed sites, but denitrification and N-reduction genes were decreased, suggesting that functional potentials of relevant bioprocesses were changed. Meanwhile, abundances of genes involved in methane cycling, C fixation, and degradation were decreased, which might be caused by vegetation removal and hence decrease in litter accumulation at grazed sites. In contrast, abundances of virulence, stress, and antibiotics resistance genes were increased because of the presence of livestock. In conclusion, these results indicated that soil microbial community functional structure was very sensitive to the impact of livestock grazing and revealed microbial functional potentials in regulating soil N and C cycling, supporting the necessity to include microbial components in evaluating the consequence of land-use and/or climate changes. © 2012 Blackwell Publishing Ltd.

Nitrogen cycle in microbial mats: completely unknown?

NASA Astrophysics Data System (ADS)

Coban, O.; Bebout, B.

2015-12-01

Microbial mats are thought to have originated around 3.7 billion years ago, most likely in the areas around submarine hydrothermal vents, which supplied a source of energy in the form of reduced chemical species from the Earth's interior. Active hydrothermal vents are also believed to exist on Jupiter's moon Europa, Saturn's moon Enceladus, and on Mars, earlier in that planet's history. Microbial mats have been an important force in the maintenance of Earth's ecosystems and the first photosynthesis was also originated there. Microbial mats are believed to exhibit most, if not all, biogeochemical processes that exist in aquatic ecosystems, due to the presence of different physiological groups of microorganisms therein. While most microbially mediated biogeochemical transformations have been shown to occur within microbial mats, the nitrogen cycle in the microbial mats has received very little study in spite of the fact that nitrogen usually limits growth in marine environments. We will present the first results in the determination of a complete nitrogen budget for a photosynthetic microbial mat. Both in situ sources and sinks of nitrogen in photosynthetic microbial mats are being measured using stable isotope techniques. Our work has a particular focus on recently described, but poorly understood, processes, e.g., anammox and dissimilatory nitrate reduction, and an emphasis on understanding the role that nitrogen cycling may play in generating biogenic nitrogen isotopic signatures and biomarker molecules. Measurements of environmental controls on nitrogen cycling should offer insight into the nature of co-evolution of these microbial communities and their planets of origin. Identifying the spatial (microscale) as well as temporal (diel and seasonal) distribution of nitrogen transformations, e.g., rates of nitrification and denitrification, within mats, particularly with respect to the distribution of photosynthetically-produced oxygen, is anticipated. The results of this research, the first results of which will be presented here, will help us to improve our understanding of the cycle of the element most responsible for limiting the production of biomass on Earth and improved an ability to use stable isotopes of nitrogen, and nitrogen containing compounds, in our search for life elsewhere.

Effects of Land Use Change on C-N cycling: Microbes Matter.

NASA Astrophysics Data System (ADS)

Hofmockel, K.

2012-12-01

Large swaths of the terrestrial landscape have been altered by human actions on Earth's biophysical systems, resulting in the homogenization of Earth's biota, while simultaneously increasing greenhouse gases and reactive nitrogen (N). This is especially poignant in grasslands that have been largely replaced by managed agricultural systems with substantial N inputs, or by unmanaged grasslands that are dominated by exotic species. Impacted ecosystems may be important for global C models, because they comprise a major portion of the global land area, terrestrial NPP and the world's soil C stocks. This research investigates how anthropogenic changes in plant community composition and agricultural management systems influence the composition and function of microbial communities that mediate key aspects of belowground C and N cycling and storage. Data from agroecology and grassland climate change experiments are used to illustrate how microbial responses can have important implications for large scale coupling of C and N cycles. In this study exotic plant species significantly decreased root inputs, causing shifts in microbial community composition, including both specific taxa and functional guilds of bacteria. By contrast, climate change (precipitation manipulation) caused functional responses (increased carbon and phosphorus cycling) that were not detected in the microbial community composition. Mycorrhizal fungi in managed systems were responsive to both root biomass and nitrogen inputs, significantly altering hydrolytic enzyme activity and aggregate turnover. Collectively small-scale processes can alter the ecosystem biogeochemical cycles. Together theses results suggest that linking microbial communities to coupled C-N cycles may have important implications for terrestrial C cycling feedbacks that are an integral part of the anthropocene era.

Deep-Sea Microbes: Linking Biogeochemical Rates to -Omics Approaches

NASA Astrophysics Data System (ADS)

Herndl, G. J.; Sintes, E.; Bayer, B.; Bergauer, K.; Amano, C.; Hansman, R.; Garcia, J.; Reinthaler, T.

2016-02-01

Over the past decade substantial progress has been made in determining deep ocean microbial activity and resolving some of the enigmas in understanding the deep ocean carbon flux. Also, metagenomics approaches have shed light onto the dark ocean's microbes but linking -omics approaches to biogeochemical rate measurements are generally rare in microbial oceanography and even more so for the deep ocean. In this presentation, we will show by combining metagenomics, -proteomics and biogeochemical rate measurements on the bulk and single-cell level that deep-sea microbes exhibit characteristics of generalists with a large genome repertoire, versatile in utilizing substrate as revealed by metaproteomics. This is in striking contrast with the apparently rather uniform dissolved organic matter pool in the deep ocean. Combining the different -omics approaches with metabolic rate measurements, we will highlight some major inconsistencies and enigmas in our understanding of the carbon cycling and microbial food web structure in the dark ocean.

Ménage à trois in the human gut: interactions between host, bacteria and phages.

PubMed

Mirzaei, Mohammadali Khan; Maurice, Corinne F

2017-07-01

The human gut is host to one of the densest microbial communities known, the gut microbiota, which contains bacteria, archaea, viruses, fungi and other microbial eukaryotes. Bacteriophages in the gut are largely unexplored, despite their potential to regulate bacterial communities and thus human health. In addition to helping us understand gut homeostasis, applying an ecological perspective to the study of bacterial and phage communities in the gut will help us to understand how this microbial system functions. For example, temporal studies of bacteria, phages and host immune cells in the gut during health and disease could provide key information about disease development and inform therapeutic treatments, whereas understanding the regulation of the replication cycles of phages could help harness the gut microbiota to improve disease outcomes. As the most abundant biological entities in our gut, we must consider bacteriophages in our pursuit of personalized medicine.

Efficient anaerobic transformation of raw wheat straw by a robust cow rumen-derived microbial consortium.

PubMed

Lazuka, Adèle; Auer, Lucas; Bozonnet, Sophie; Morgavi, Diego P; O'Donohue, Michael; Hernandez-Raquet, Guillermina

2015-11-01

A rumen-derived microbial consortium was enriched on raw wheat straw as sole carbon source in a sequential batch-reactor (SBR) process under strict mesophilic anaerobic conditions. After five cycles of enrichment the procedure enabled to select a stable and efficient lignocellulolytic microbial consortium, mainly constituted by members of Firmicutes and Bacteroidetes phyla. The enriched community, designed rumen-wheat straw-derived consortium (RWS) efficiently hydrolyzed lignocellulosic biomass, degrading 55.5% w/w of raw wheat straw over 15days at 35°C and accumulating carboxylates as main products. Cellulolytic and hemicellulolytic activities, mainly detected on the cell bound fraction, were produced in the earlier steps of degradation, their production being correlated with the maximal lignocellulose degradation rates. Overall, these results demonstrate the potential of RWS to convert unpretreated lignocellulosic substrates into useful chemicals. Copyright © 2015 Elsevier Ltd. All rights reserved.

Where microorganisms meet rocks in the Earth's Critical Zone

NASA Astrophysics Data System (ADS)

Akob, D. M.; Küsel, K.

2011-03-01

The Earth's Critical Zone (CZ) is the critical, outer shell of the Earth that provides an arena for the interplay of diverse physical, chemical, and biological processes that are fundamental for sustaining life. As microbes are the principle drivers of biogeochemical cycles, it is necessary to understand the biodiversity of the CZ unseen majority and their impact on life-sustaining processes. This review aims to summarize the factors controlling where microbes (prokaryotes and micro-eukaryotes) live within the CZ and what is known to date about their diversity and function. Microbes live in all regions of the CZ down to 5 km depth, but due to changing habitat complexity, e.g., variability in pore spaces, water, oxygen, and nutrients, their functional role changes with depth. The abundance of prokaryotes and micro-eukaryotes decreases from a maximum of 1010 or 107 cells g soil-1 up to eight orders of magnitude with depth. Symbiotic mycorrhizal fungi and free-living decomposers are best understood in soil habitats, where they are up to 103 cells g soil-1. However, little is known about their identity and impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that these organisms are either limited in space or nutrients or unable to cope with oxygen limitations. Since deep regions of the CZ are limited in the recent input of photosynthesis-derived carbon, microbes are dependent on deposited organic material or on chemolithoautotrophic metabolism that allows for the establishment of a complete food chain independent from the surface. However, the energy flux available might only allow cell growth over tens to thousands of years. The recent development of "omics" technologies has provided microbial ecologists with methods to link the composition and function of in situ microbial communities. We should expect new metabolic discoveries as we have a closer look utilizing a polyphasic approach into the microbial communities of the CZ. Thus, future work is still needed to link microbial biodiversity to the exact role of microbes in weathering and geochemical cycling in the CZ, especially in subsurface habitats.

The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling

PubMed Central

Lindemann, Stephen R.; Moran, James J.; Stegen, James C.; Renslow, Ryan S.; Hutchison, Janine R.; Cole, Jessica K.; Dohnalkova, Alice C.; Tremblay, Julien; Singh, Kanwar; Malfatti, Stephanie A.; Chen, Feng; Tringe, Susannah G.; Beyenal, Haluk; Fredrickson, James K.

2013-01-01

Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg2+ and SO2−4) and irradiation over the annual cycle. We examined spatiotemporal variation in the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function. PMID:24312082

The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington. Community Structural Responses to Seasonal Cycling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindemann, Stephen R.; Moran, James J.; Stegen, James C.

2013-11-13

Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg 2+ and SO 2 -4) and irradiation over the annual cycle. We examined spatiotemporal variation inmore » the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function.« less

Butyrate induces apoptosis by activating PDC and inhibiting complex I through SIRT3 inactivation.

PubMed

Xu, Sha; Liu, Cai-Xia; Xu, Wei; Huang, Lei; Zhao, Jian-Yuan; Zhao, Shi-Min

2017-01-01

The underlying anticancer effects of butyrate, an end-product of the intestinal microbial fermentation of dietary fiber, remain elusive. Here, we report that butyrate promotes cancer cell apoptosis by acting as a SIRT3 inhibitor. Butyrate inhibits SIRT3 both in cultured cells and in vitro . Butyrate-induced PDHA1 hyperacetylation relieves the inhibitory phosphorylation of PDHA1 at serine 293, thereby activating an influx of glycolytic intermediates into the tricarboxylic acid (TCA) cycle and reversing the Warburg effect. Meanwhile, butyrate-induced hyperacetylation inactivates complex I of the electron transfer chain and prevents the utilization of TCA cycle intermediates. These metabolic stresses promote apoptosis in hyperglycolytic cancer cells, such as HCT116 p53 -/- cells. SIRT3 deacetylates both PDHA1 and complex I. Genetic ablation of Sirt3 in mouse hepatocytes abrogated the ability of butyrate to induce apoptosis. Our results identify a butyrate-mediated anti-tumor mechanism and indicate that the combined activation of PDC and inhibition of complex I is a novel tumor treatment strategy.

Unveiling Microbial Carbon Cycling Processes in Key U.S. Soils using ''Omics''

DOE Office of Scientific and Technical Information (OSTI.GOV)

Myrold, David D.; Bottomely, Peter J.; Jumpponen, Ari

2014-09-17

Soils process and store large amounts of C; however, considerable uncertainty still exists about the details of that influence microbial partitioning of C into soil C pools, and what are the main influential forces that control the fraction of the C input that is stabilized. The soil microbial community is genotypically and phenotypically diverse. Despite our ability to predict the kinds of regional environmental changes that will accompany global climate change, it is not clear how the microbial community will respond to climate-induced modification of precipitation and inter-precipitation intervals, and if this response will affect the fate of C depositedmore » into soil by the local plant community. Part of this uncertainty lies with our ignorance of how the microbial community adapts genotypically and physiologically to changes in soil moisture brought about by shifts in precipitation. Our overarching goal is to harness the power of multiple meta-omics tools to gain greater understanding of the functioning of whole-soil microbial communities and their role in C cycling. We will do this by meeting the following three objectives: 1. Further develop and optimize a combination of meta-omics approaches to study how environmental factors affect microbially-mediated C cycling processes. 2. Determine the impacts of long-term changes in precipitation timing on microbial C cycling using an existing long-term field manipulation of a tallgrass prairie soil. 3. Conduct laboratory experiments that vary moisture and C inputs to confirm field observations of the linkages between microbial communities and C cycling processes. We took advantage of our state-of-the-art expertise in community “omics” to better understand the functioning soil C cycling within the Great Prairie ecosystem, including our ongoing Konza Prairie soil metagenome flagship project at JGI and the unique rainfall manipulation plots (RaMPs) established at this site more than a decade ago. We employed a systems biology approach, considering the complex soil microbial community as a functioning system and using state-of-the-art metatranscriptomic, metaproteomic, and metabolomic approaches. These omics tools were refined, applied to field experiments, and confirmed with controlled laboratory studies. Our experiments were designed to specifically identify microbial community members and processes that are instrumental players in processing of C in the prairie soils and how these processes are impacted by wetting and drying events. This project addresses a key ecosystem in the United States that current climate models predict will be subjected to dramatic changes in rainfall patterns as a result of global warming. Currently Mollisols, such as those of the tallgrass prairie, are thought to sequester more C than is released into the atmosphere, but it is not known what changes in rainfall patterns will have on future C fluxes. Through an analysis of the molecular response of the soil microbial community to shifts in precipitation cycles that are accompanied by phenologically driven changes in quality of plant C rhizodeposits, we gained deeper insight into how the metabolism of microbes has adapted to different precipitation regimes and the impact of this adaption on the fate of C deposited into soil. In doing so, we addressed key questions about the microbial cycling of C in soils that have been identified by the DOE.« less

[Influence of PCR cycle number on microbial diversity analysis through next generation sequencing].

PubMed

An, Yunhe; Gao, Lijuan; Li, Junbo; Tian, Yanjie; Wang, Jinlong; Zheng, Xuejuan; Wu, Huijuan

2016-08-25

Using of high throughput sequencing technology to study the microbial diversity in complex samples has become one of the hottest issues in the field of microbial diversity research. In this study, the soil and sheep rumen chyme samples were used to extract DNA, respectively. Then the 25 ng total DNA was used to amplify the 16S rRNA V3 region with 20, 25, 30 PCR cycles, and the final sequencing library was constructed by mixing equal amounts of purified PCR products. Finally, the operational taxonomic unit (OUT) amount, rarefaction curve, microbial number and species were compared through data analysis. It was found that at the same amount of DNA template, the proportion of the community composition was not the best with more numbers of PCR cycle, although the species number was much more. In all, when the PCR cycle number is 25, the number of species and proportion of the community composition were the most optimal both in soil or chyme samples.

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

PubMed

Long, Philip E; Williams, Kenneth H; Hubbard, Susan S; Banfield, Jillian F

2016-08-01

Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O. Copyright © 2016 Elsevier Ltd. All rights reserved.

Soil mineralogy and microbes determine forest life history strategy and carbon cycling in humid tropical forests

NASA Astrophysics Data System (ADS)

Soong, J.; Verbruggen, E.; Peñuelas, J.; Janssens, I. A.; Grau, O.

2017-12-01

Tropical forests account for over one third of global terrestrial gross primary productivity and cycle more C than any other ecosystem on Earth. However, we still lack a mechanistic understanding of how such high productivity is maintained on the old, highly weathered and phosphorus depleted soils in the tropics. We hypothesized that heterogeneity in soil texture, mineralogy and microbial community composition may be the major drivers of differences in soil C storage and P limitation across tropical forests. We sampled 12 forest sites across a 200 km transect in the humid neo-tropics of French Guiana that varied in soil texture, precipitation and mineralogy. We found that soil texture was a major driver of soil carbon stocks and forest life history strategy, where sandy forests have lower soil C stocks, slower turnover and decomposition and a more closed nutrient cycle while clayey forests have higher soil C stocks, faster turnover and a more leaky nutrient cycle (using natural abundance stable isotope evidence). We found that although the presence of Al and Fe oxides in the clayey soils occludes soil organic matter and P, a greater abundance of arbuscular mycorrhizal fungi help forests to access occluded P in clayey soils fueling higher turnover and faster decomposition rates. Evidence from a laboratory incubation of tropical soils with nutrient additions further demonstrates the de-coupling of microbial P demands from C:N limitations providing further evidence for the need to examine microbial stoichiometry to explain C cycling in the P-limited tropics. We argue that microbial community composition and physiological demands, constrained within the limitations of soil mineralogical reactivity, largely controls nutrient and C cycling in tropical forest soils. Together our observational field study and laboratory incubation provide a unique dataset to shed light on the mineralogical and microbial controls on C and nutrient cycling in tropical soils. By integrating microbial, soil, litter and forest metrics we describe how microbes, minerals and soil organic matter act as an ecosystem property driving forest dynamics via microbial and plant stoichiometric constraints.

Geobiological Comparisons of Preservation Potential within Hypersaline Mineral-Microbe Systems

NASA Astrophysics Data System (ADS)

Perl, S. M.; Celestian, A. J.; Vaishampayan, P.; Seuylemezian, A.; Mahseredjian, T.; Baxter, B.; Corsetti, F. A.

2017-12-01

The purpose of these investigations is to show comparative measurements between known biological sources of biomarkers and biosignatures and how they can be independently verified, within instrumentation limits, by laboratory investigations analogous to future surface missions to Mars and Europa. Precipitated hypersaline mineralogy can provide a biotic record of microbial activity and habitation within evaporating lake systems. The extent of microbial preservation is a direct relationship between the magnitudes of aqueous activity post-precipitation, original or in-situ biological habitats, dissolution events due to chemical weathering, and organic matter degradation due to UV exposure and desiccation. Chemical biomarkers and physical biosignatures to be quantified and correlated based from preserved DNA as the most sensitive biomarker to more recalcitrant biomarkers such as lipids and Total Organic Carbon (TOC). Moreover the timing of cell movement during nutrient cycling within specific evaporite minerals can be associated to the formation of physical biosignatures as a function of already active and abundant biomarkers allowing for relative timelines of biogenic actions (e.g., nutrient cycling, cell division) to be correlated together. Our investigation has compared hypersaline biotic activity within different photosynthetic and chemosynthetic settings to quantify preservation and detection profiles given measured DNA as the source validation standard and micron-scale Raman measurements for specific paleoenvironmental mineral sampling.

Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin

PubMed Central

Ren, Min; Zhang, Zhufeng; Wang, Xuelian; Zhou, Zhiwei; Chen, Dong; Zeng, Hui; Zhao, Shumiao; Chen, Lingling; Hu, Yuanliang; Zhang, Changyi; Liang, Yunxiang; She, Qunxin; Zhang, Yi; Peng, Nan

2018-01-01

Arid and semi-arid regions comprise nearly one-fifth of the earth's terrestrial surface. However, the diversities and functions of their soil microbial communities are not well understood, despite microbial ecological importance in driving biogeochemical cycling. Here, we analyzed the geochemistry and microbial communities of the desert soils from Tarim Basin, northwestern China. Our geochemical data indicated half of these soils are saline. Metagenomic analysis showed that bacterial phylotypes (89.72% on average) dominated the community, with relatively small proportions of Archaea (7.36%) and Eukaryota (2.21%). Proteobacteria, Firmicutes, Actinobacteria, and Euryarchaeota were most abundant based on metagenomic data, whereas genes attributed to Proteobacteria, Actinobacteria, Euryarchaeota, and Thaumarchaeota most actively transcribed. The most abundant phylotypes (Halobacterium, Halomonas, Burkholderia, Lactococcus, Clavibacter, Cellulomonas, Actinomycetospora, Beutenbergia, Pseudomonas, and Marinobacter) in each soil sample, based on metagenomic data, contributed marginally to the population of all microbial communities, whereas the putative halophiles, which contributed the most abundant transcripts, were in the majority of the active microbial population and is consistent with the soil salinity. Sample correlation analyses according to the detected and active genotypes showed significant differences, indicating high diversity of microbial communities among the Tarim soil samples. Regarding ecological functions based on the metatranscriptomic data, transcription of genes involved in various steps of nitrogen cycling, as well as carbon fixation, were observed in the tested soil samples. Metatranscriptomic data also indicated that Thaumarchaeota are crucial for ammonia oxidation and Proteobacteria play the most important role in other steps of nitrogen cycle. The reductive TCA pathway and dicarboxylate-hydroxybutyrate cycle attributed to Proteobacteria and Crenarchaeota, respectively, were highly represented in carbon fixation. Our study reveals that the microbial communities could provide carbon and nitrogen nutrients for higher plants in the sandy saline soils of Tarim Basin. PMID:29593680

Dynamic processes of the microbiota - from metagenomics to biofilms

NASA Astrophysics Data System (ADS)

Wingreen, Ned

The extent, origin, and impact of microbial diversity is a central question in biology. We expect that physical processes contribute to this diversity, but we are only beginning to explore the nature of these interactions. I will briefly discuss two approaches to this question, one based on metagenomics the other on observation of bacterial biofilms. First, I will address the challenge of identifying the constituents of microbial systems by presenting a new approach to analyzing community sequencing data that identifies microbial subpopulations while avoiding problematic clustering-based methods. Using data from a time-series study of human tongue microbiota, we were able to resolve within the standard definition of a ``species'' up to 20 ecologically distinct subpopulations with tag sequences differing by as little as one nucleotide (99.2% similarity). This fine resolution allowed us decouple sequence similarity from dynamical similarity, and to resolve dynamics on multiple time scales, including the slow appearance and disappearance of strains over months. Second, I will present recent results on the growth and competition of bacteria within biofilms. We imaged the growth ofliving biofilms of Vibrio choleraefrom single founder cells to ten thousand cells at single cell spatial resolution and with temporal resolution of one cell cycle. We discovered a transition from a branched 2D colony to a dense 3D cluster, in which cells at the biofilm center exhibit collective vertical alignment and local nematic packing. Our results suggest that biofilm cells exploit mechanics to simultaneously achieve strong surface adhesion, access to 3D space, resistance to invasion, and dominance over surface territory.

KF-finder: identification of key factors from host-microbial networks in cervical cancer.

PubMed

Hu, Jialu; Gao, Yiqun; Zheng, Yan; Shang, Xuequn

2018-04-24

The human body is colonized by a vast number of microbes. Microbiota can benefit many normal life processes, but can also cause many diseases by interfering the regular metabolism and immune system. Recent studies have demonstrated that the microbial community is closely associated with various types of cell carcinoma. The search for key factors, which also refer to cancer causing agents, can provide an important clue in understanding the regulatory mechanism of microbiota in uterine cervix cancer. In this paper, we investigated microbiota composition and gene expression data for 58 squamous and adenosquamous cell carcinoma. A host-microbial covariance network was constructed based on the 16s rRNA and gene expression data of the samples, which consists of 259 abundant microbes and 738 differentially expressed genes (DEGs). To search for risk factors from host-microbial networks, the method of bi-partite betweenness centrality (BpBC) was used to measure the risk of a given node to a certain biological process in hosts. A web-based tool KF-finder was developed, which can efficiently query and visualize the knowledge of microbiota and differentially expressed genes (DEGs) in the network. Our results suggest that prevotellaceade, tissierellaceae and fusobacteriaceae are the most abundant microbes in cervical carcinoma, and the microbial community in cervical cancer is less diverse than that of any other boy sites in health. A set of key risk factors anaerococcus, hydrogenophilaceae, eubacterium, PSMB10, KCNIP1 and KRT13 have been identified, which are thought to be involved in the regulation of viral response, cell cycle and epithelial cell differentiation in cervical cancer. It can be concluded that permanent changes of microbiota composition could be a major force for chromosomal instability, which subsequently enables the effect of key risk factors in cancer. All our results described in this paper can be freely accessed from our website at http://www.nwpu-bioinformatics.com/KF-finder/ .

Bacterial abundance and composition in marine sediments beneath the Ross Ice Shelf, Antarctica.

PubMed

Carr, S A; Vogel, S W; Dunbar, R B; Brandes, J; Spear, J R; Levy, R; Naish, T R; Powell, R D; Wakeham, S G; Mandernack, K W

2013-07-01

Marine sediments of the Ross Sea, Antarctica, harbor microbial communities that play a significant role in the decomposition, mineralization, and recycling of organic carbon (OC). In this study, the cell densities within a 153-cm sediment core from the Ross Sea were estimated based on microbial phospholipid fatty acid (PLFA) concentrations and acridine orange direct cell counts. The resulting densities were as high as 1.7 × 10⁷ cells mL⁻¹ in the top ten centimeters of sediments. These densities are lower than those calculated for most near-shore sites but consistent with deep-sea locations with comparable sedimentation rates. The δ¹³C measurements of PLFAs and sedimentary and dissolved carbon sources, in combination with ribosomal RNA (SSU rRNA) gene pyrosequencing, were used to infer microbial metabolic pathways. The δ¹³C values of dissolved inorganic carbon (DIC) in porewaters ranged downcore from -2.5‰ to -3.7‰, while δ¹³C values for the corresponding sedimentary particulate OC (POC) varied from -26.2‰ to -23.1‰. The δ¹³C values of PLFAs ranged between -29‰ and -35‰ throughout the sediment core, consistent with a microbial community dominated by heterotrophs. The SSU rRNA gene pyrosequencing revealed that members of this microbial community were dominated by β-, δ-, and γ-Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Among the sequenced organisms, many appear to be related to known heterotrophs that utilize OC sources such as amino acids, oligosaccharides, and lactose, consistent with our interpretation from δ¹³CPLFA analysis. Integrating phospholipids analyses with porewater chemistry, δ¹³CDIC and δ¹³CPOC values and SSU rRNA gene sequences provides a more comprehensive understanding of microbial communities and carbon cycling in marine sediments, including those of this unique ice shelf environment. © 2013 John Wiley & Sons Ltd.

Anoxic conditions drive phosphorus limitation in humid tropical forest soil microorganisms

NASA Astrophysics Data System (ADS)

Gross, A.; Pett-Ridge, J.; Weber, P. K.; Blazewicz, S.; Silver, W. L.

2017-12-01

The elemental stoichiometry of carbon (C), nitrogen (N) and phosphorus (P) of soil microorganisms (C:N:P ratios) regulates transfers of energy and nutrients to higher trophic levels. In humid tropical forests that grow on P-depleted soils, the ability of microbes to concentrate P from their surroundings likely plays a critical role in P-retention and ultimately in forest productivity. Models predict that climate change will cause dramatic changes in rainfall patterns in the humid tropics and field studies have shown these changes can affect the redox state of tropical forest soils, influencing soil respiration and biogeochemical cycling. However, the responses of soil microorganisms to changing environmental conditions are not well known. Here, we incubated humid tropical soils under oxic or anoxic conditions with substrates differing in both C:P stoichiometry and lability, to assess how soil microorganisms respond to different redox regimes. We found that under oxic conditions, microbial C:P ratios were similar to the global optimal ratio (55:1), indicating most microbial cells can adapt to persistent aerated conditions in these soils. However, under anoxic conditions, the ability of soil microbes to acquire soil P declined and their C:P ratios shifted away from the optimal ratio. NanoSIMS elemental imaging of single cells extracted from soil revealed that under anoxic conditions, C:P ratios were above the microbial optimal value in 83% of the cells, in comparison to 41% under oxic conditions. These data suggest microbial growth efficiency switched from being energy limited under oxic conditions to P-limited under anoxic conditions, indicating that, microbial growth in low P humid tropical forests soils may be most constrained by P-limitation when conditions are oxygen-limited. We suggest that differential microbial responses to soil redox states could have important implications for productivity of humid tropical forests under future climate scenarios.

From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality

PubMed Central

Kreft, Jan-Ulrich; Plugge, Caroline M.; Prats, Clara; Leveau, Johan H. J.; Zhang, Weiwen; Hellweger, Ferdi L.

2017-01-01

Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level. We review published models that explicitly consider genes and make predictions at the population or ecosystem level. The models can be grouped into three general approaches, i.e., metabolic flux, gene-centric and agent-based. We describe and contrast these approaches by applying them to a hypothetical ecosystem and discuss their strengths and weaknesses. An important distinguishing feature is how variation between individual cells (individuality) is handled. In microbial ecosystems, individual heterogeneity is generated by a number of mechanisms including stochastic interactions of molecules (e.g., gene expression), stochastic and deterministic cell division asymmetry, small-scale environmental heterogeneity, and differential transport in a heterogeneous environment. This heterogeneity can then be amplified and transferred to other cell properties by several mechanisms, including nutrient uptake, metabolism and growth, cell cycle asynchronicity and the effects of age and damage. For example, stochastic gene expression may lead to heterogeneity in nutrient uptake enzyme levels, which in turn results in heterogeneity in intracellular nutrient levels. Individuality can have important ecological consequences, including division of labor, bet hedging, aging and sub-optimality. Understanding the importance of individuality and the mechanism(s) underlying it for the specific microbial system and question investigated is essential for selecting the optimal modeling strategy. PMID:29230200

Studying the rapid bioconversion of lignocellulosic sugars into ethanol using high cell density fermentations with cell recycle

PubMed Central

2014-01-01

Background The Rapid Bioconversion with Integrated recycle Technology (RaBIT) process reduces capital costs, processing times, and biocatalyst cost for biochemical conversion of cellulosic biomass to biofuels by reducing total bioprocessing time (enzymatic hydrolysis plus fermentation) to 48 h, increasing biofuel productivity (g/L/h) twofold, and recycling biocatalysts (enzymes and microbes) to the next cycle. To achieve these results, RaBIT utilizes 24-h high cell density fermentations along with cell recycling to solve the slow/incomplete xylose fermentation issue, which is critical for lignocellulosic biofuel fermentations. Previous studies utilizing similar fermentation conditions showed a decrease in xylose consumption when recycling cells into the next fermentation cycle. Eliminating this decrease is critical for RaBIT process effectiveness for high cycle counts. Results Nine different engineered microbial strains (including Saccharomyces cerevisiae strains, Scheffersomyces (Pichia) stipitis strains, Zymomonas mobilis 8b, and Escherichia coli KO11) were tested under RaBIT platform fermentations to determine their suitability for this platform. Fermentation conditions were then optimized for S. cerevisiae GLBRCY128. Three different nutrient sources (corn steep liquor, yeast extract, and wheat germ) were evaluated to improve xylose consumption by recycled cells. Capacitance readings were used to accurately measure viable cell mass profiles over five cycles. Conclusion The results showed that not all strains are capable of effectively performing the RaBIT process. Acceptable performance is largely correlated to the specific xylose consumption rate. Corn steep liquor was found to reduce the deleterious impacts of cell recycle and improve specific xylose consumption rates. The viable cell mass profiles indicated that reduction in specific xylose consumption rate, not a drop in viable cell mass, was the main cause for decreasing xylose consumption. PMID:24847379

[Advances in microbial solar cells--A review].

PubMed

Guo, Xiaoyun; Yu, Changping; Zheng, Tianling

2015-08-04

The energy crisis has become one of the major problems hindering the development of the world. The emergence of microbial fuel cells provides a new solution to the energy crisis. Microbial solar cells, integrating photosynthetic organisms such as plants and microalgae into microbial fuel cells, can convert solar energy into electrical energy. Microbial solar cell has steady electric energy, and broad application prospects in wastewater treatment, biodiesel processing and intermediate metabolites production. Here we reviewed recent progress of microbial solar cells from the perspective of the role of photosynthetic organisms in microbial fuel cells, based on a vast amount of literature, and discussed their advantages and deficiency. At last, brief analysis of the facing problems and research needs of microbial fuel cells are undertaken. This work was expected to be beneficial for the application of the microbial solar cells technology.

Evidence for microbial carbon and sulfur cycling in deeply buried ridge flank basalt

USGS Publications Warehouse

Lever, Mark A.; Rouxel, Olivier; Alt, Jeffrey C.; Shimizu, Nobumichi; Ono, Shuhei; Coggon, Rosalind M.; Shanks, Wayne C.; Lapham, Laura; Elvert, Marcus; Prieto-Mollar, Xavier; Hinrichs, Kai-Uwe; Inagaki, Fumio; Teske, Andreas

2013-01-01

Sediment-covered basalt on the flanks of mid-ocean ridges constitutes most of Earth's oceanic crust, but the composition and metabolic function of its microbial ecosystem are largely unknown. By drilling into 3.5-million-year-old subseafloor basalt, we demonstrated the presence of methane- and sulfur-cycling microbes on the eastern flank of the Juan de Fuca Ridge. Depth horizons with functional genes indicative of methane-cycling and sulfate-reducing microorganisms are enriched in solid-phase sulfur and total organic carbon, host δ13C- and δ34S-isotopic values with a biological imprint, and show clear signs of microbial activity when incubated in the laboratory. Downcore changes in carbon and sulfur cycling show discrete geochemical intervals with chemoautotrophic δ13C signatures locally attenuated by heterotrophic metabolism.

Applications of Microbial Cell Sensors

NASA Astrophysics Data System (ADS)

Shimomura-Shimizu, Mifumi; Karube, Isao

Since the first microbial cell sensor was studied by Karube et al. in 1977, many types of microbial cell sensors have been developed as analytical tools. The microbial cell sensor utilizes microbes as a sensing element and a transducer. The characteristics of microbial cell sensors as sensing devices are a complete contrast to those of enzyme sensors or immunosensors, which are highly specific for the substrates of interest, although the specificity of the microbial cell sensor has been improved by genetic modification of the microbe used as the sensing element. Microbial cell sensors have the advantages of tolerance to measuring conditions, a long lifetime, and good cost performance, and have the disadvantage of a long response time. In this review, applications of microbial cell sensors are summarized.

Global biogeography of microbial nitrogen-cycling traits in soil

NASA Astrophysics Data System (ADS)

Nelson, M.; Martiny, A.; Martiny, J. B. H.

2016-12-01

Microorganisms drive much of the Earth's nitrogen (N) cycle. However, despite their importance, many ecosystem models do not explicitly consider microbial communities and their functions. One obstacle in doing this is that we lack a complete understanding of the role that microbes play in biogeochemical processes. To address this challenge we used metagenomics to assess various N cycling traits of soil microorganisms in samples from around the globe. As measurable characteristics of an organism, traits can be used to quantify the role of microbes in ecosystem processes. Using 365 publically available soil metagenomes, we characterized the biogeography of microbial N cycling traits, defined as the abundance and composition of eight N pathways. We found strong biogeographic patterns in the frequency of N pathway traits; however, our models explained much less variation in taxonomic composition across sites. Focusing on individual N pathways, we identified the prominent taxa harboring these pathways. In addition, we found an unexpectedly high frequency of Bacteria encoding the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a little studied N cycle process in soils. Finally, across all N pathways, phylogenetic analysis revealed that some phyla seem to be N cycle generalists (i.e delta-Proteobacteria), with the potential to carry out many N transformations, whereas others seem to be specialists (i.e. Cyanobacteria). As the most comprehensive map to date of the global distribution of microbial N traits, this study provides a springboard for further investigation of the prominent players in N cycling in soils. Overall, biogeographic patterns of traits can provide a foundation for understanding how microbial diversity impacts ecosystem processes and ultimately predicting how this diversity may shift in the face of global change.

Lipids as paleomarkers to constrain the marine nitrogen cycle.

PubMed

Rush, Darci; Sinninghe Damsté, Jaap S

2017-06-01

Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction-oxidation transformations of bio-available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio-available nitrogen species. As most microorganisms are soft-bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically-important cycle, and provides examples of biomarker applications in the geological past. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Electricity and biomass production in a bacteria-Chlorella based microbial fuel cell treating wastewater

NASA Astrophysics Data System (ADS)

Commault, Audrey S.; Laczka, Olivier; Siboni, Nachshon; Tamburic, Bojan; Crosswell, Joseph R.; Seymour, Justin R.; Ralph, Peter J.

2017-07-01

The chlorophyte microalga Chlorella vulgaris has been exploited within bioindustrial settings to treat wastewater and produce oxygen at the cathode of microbial fuel cells (MFCs), thereby accumulating algal biomass and producing electricity. We aimed to couple these capacities by growing C. vulgaris at the cathode of MFCs in wastewater previously treated by anodic bacteria. The bioelectrochemical performance of the MFCs was investigated with different catholytes including phosphate buffer and anode effluent, either in the presence or absence of C. vulgaris. The power output fluctuated diurnally in the presence of the alga. The maximum power when C. vulgaris was present reached 34.2 ± 10.0 mW m-2, double that observed without the alga (15.6 ± 9.7 mW m-2), with a relaxation of 0.19 gL-1 d-1 chemical oxygen demand and 5 mg L-1 d-1 ammonium also removed. The microbial community associated with the algal biofilm included nitrogen-fixing (Rhizobiaceae), denitrifying (Pseudomonas stutzeri and Thauera sp., from Pseudomonadales and Rhodocyclales orders, respectively), and nitrate-reducing bacteria (Rheinheimera sp. from the Alteromonadales), all of which likely contributed to nitrogen cycling processes at the cathode. This paper highlights the importance of coupling microbial community screening to electrochemical and chemical analyses to better understand the processes involved in photo-cathode MFCs.

Streptomyces exploration is triggered by fungal interactions and volatile signals.

PubMed

Jones, Stephanie E; Ho, Louis; Rees, Christiaan A; Hill, Jane E; Nodwell, Justin R; Elliot, Marie A

2017-01-03

It has long been thought that the life cycle of Streptomyces bacteria encompasses three developmental stages: vegetative hyphae, aerial hyphae and spores. Here, we show interactions between Streptomyces and fungi trigger a previously unobserved mode of Streptomyces development. We term these Streptomyces cells 'explorers', for their ability to adopt a non-branching vegetative hyphal conformation and rapidly transverse solid surfaces. Fungi trigger Streptomyces exploratory growth in part by altering the composition of the growth medium, and Streptomyces explorer cells can communicate this exploratory behaviour to other physically separated streptomycetes using an airborne volatile organic compound (VOC). These results reveal that interkingdom interactions can trigger novel developmental behaviours in bacteria, here, causing Streptomyces to deviate from its classically-defined life cycle. Furthermore, this work provides evidence that VOCs can act as long-range communication signals capable of propagating microbial morphological switches.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system.

PubMed

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J D; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-04

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S 0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S 0 and Fe 2+ , which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

NASA Astrophysics Data System (ADS)

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

PubMed Central

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-01-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system. PMID:27698381

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station

USGS Publications Warehouse

Repert, Deborah A.; Underwood, Jennifer C.; Smith, Richard L.; Song, Bongkeun

2014-01-01

Information on the contribution of nitrogen (N)-cycling processes in bed sediments to river nutrient fluxes in large northern latitude river systems is limited. This study examined the relationship between N-cycling processes in bed sediments and N speciation and loading in the Yukon River near its mouth at the Bering Sea. We conducted laboratory bioassays to measure N-cycling processes in sediment samples collected over distinct water cycle seasons. In conjunction, the microbial community composition in the bed sediments using genes involved in N-cycling (narG, napA, nosZ, and amoA) and 16S rRNA gene pyrosequences was examined. Temporal variation was observed in net N mineralization, nitrate uptake, and denitrification rate potentials and correlated strongly with sediment carbon (C) and extractable N content and microbial community composition rather than with river water nutrient concentrations. The C content of the bed sediment was notably impacted by the spring flood, ranging from 1.1% in the midst of an ice-jam to 0.1% immediately after ice-out, suggesting a buildup of organic material (OM) prior to scouring of the bed sediments during ice break up. The dominant members of the microbial community that explained differences in N-processing rates belonged to the genera Crenothrix,Flavobacterium, and the family of Comamonadaceae. Our results suggest that biogeochemical processing rates in the bed sediments appear to be more coupled to hydrology, nutrient availability in the sediments, and microbial community composition rather than river nutrient concentrations at Pilot Station.

Molecular Insights on Dissolved Organic Matter Transformation by Supraglacial Microbial Communities.

PubMed

Antony, Runa; Willoughby, Amanda S; Grannas, Amanda M; Catanzano, Victoria; Sleighter, Rachel L; Thamban, Meloth; Hatcher, Patrick G; Nair, Shanta

2017-04-18

Snow overlays the majority of Antarctica and is an important repository of dissolved organic matter (DOM). DOM transformations by supraglacial microbes are not well understood. We use ultrahigh resolution mass spectrometry to elucidate molecular changes in snowpack DOM by in situ microbial processes (up to 55 days) in a coastal Antarctic site. Both autochthonous and allochthonous DOM is highly bioavailable and is transformed by resident microbial communities through parallel processes of degradation and synthesis. DOM thought to be of a more refractory nature, such as dissolved black carbon and carboxylic-rich alicyclic molecules, was also rapidly and extensively reworked. Microbially reworked DOM exhibits an increase in the number and magnitude of N-, S-, and P-containing formulas, is less oxygenated, and more aromatic when compared to the initial DOM. Shifts in the heteroatom composition suggest that microbial processes may be important in the cycling of not only C, but other elements such as N, S, and P. Microbial reworking also produces photoreactive compounds, with potential implications for DOM photochemistry. Refined measurements of supraglacial DOM and their cycling by microbes is critical for improving our understanding of supraglacial DOM cycling and the biogeochemical and ecological impacts of DOM export to downstream environments.

Microbial communities in carbonate rocks-from soil via groundwater to rocks.

PubMed

Meier, Aileen; Singh, Manu K; Kastner, Anne; Merten, Dirk; Büchel, Georg; Kothe, Erika

2017-09-01

Microbial communities in soil, groundwater, and rock of two sites in limestone were investigated to determine community parameters differentiating habitats in two lithostratigraphic untis. Lower Muschelkalk and Middle Muschelkalk associated soils, groundwater, and rock samples showed different, but overlapping microbial communities linked to carbon fluxes. The microbial diversities in soil were highest, groundwater revealed overlapping taxa but lower diversity, and rock samples were predominantly characterized by endospore forming bacteria and few archaea. Physiological profiles could establish a differentiation between habitats (soil, groundwater, rock). From community analyses and physiological profiles, different element cycles in limestone could be identified for the three habitats. While in soil, nitrogen cycling was identified as specific determinant, in rock methanogenesis linked carbonate rock to atmospheric methane cycles. These patterns specifically allowed for delineation of lithostratigraphic connections to physiological parameters. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.

PubMed

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L; de Bruijn, Ino; Andersson, Anders F; Leupin, Olivier X; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-10-14

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

PubMed Central

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L.; de Bruijn, Ino; Andersson, Anders F.; Leupin, Olivier X.; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-01-01

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present. PMID:27739431

Nano-scale investigation of the association of microbial nitrogen residues with iron (hydr)oxides in a forest soil O-horizon

Treesearch

M. Keiluweit; J.J. Bougoure; L. Zeglin; D.D. Myrold; P.K. Weber; J. Pett-Ridge; M. Kleber; P.S. Nico

2012-01-01

Amino sugars in fungal cell walls (such as chitin) represent an important source of nitrogen (N) in many forest soil ecosystems. Despite the importance of this material in soil nitrogen cycling, comparatively little is known about abiotic and biotic controls on and the timescale of its turnover. Part of the reason for this lack of information is the inaccessibility of...

Investigating microbial cycling of recalcitrant organic matter in marine sediments using natural isotope respirometry in a novel, carbon-free bioreactor

NASA Astrophysics Data System (ADS)

Mahmoudi, N.; Beaupre, S. R.; Pearson, A.

2016-02-01

Marine sediments harbor complex microbial communities that play a key role in the cycling of carbon and nutrients. Reactions initiated by microbial enzymes at the molecular scale drive the rate and extent of organic matter degradation to CO2 and CH4. Organic matter is comprised of multiple carbon pools with different intrinsic turnover times. It is hypothesized that microbes will degrade younger pools with more labile compounds, while older pools with refractory compounds will remain unutilized. However, many studies have shown that microbes are capable of respiring older, refractory pools of organic matter in a number of environments. In order to better understand microbial carbon cycling and the fate of recalcitrant organic matter, we constructed a novel bioreactor system to measure carbon isotopes during microbial degradation of complex organic matter. This system enables us to measure the natural isotopic signature (δ13C and Δ14C ) of microbially-respired CO2, thereby allowing us to determine the age of the organic matter that is being respired. We investigated microbial carbon utilization in sediments from Falmouth, MA and observed a pattern of successive microbial respiration such that several peaks appear over the course of a 7-day incubation. Δ14C signatures of CO2 fractions collected during incubation ranged from -185 to +70‰ with the majority of CO2 appearing to be modern. This indicates that the microbial community is primarily are respiring labile organic matter from fast cycling pools. Interestingly, the observation of multiple peaks with similar Δ14C signatures suggests that organic matter is degraded in a step-wise manner by a succession of microbial taxa. Illumina sequencing of 16S rRNA genes will identify these successions of bacteria (and archaea), while enzymatic analyses may help determine the metabolic pathways that correspond to each peak. Our study will provide a molecular-level framework for organic matter degradation and provide insight into patterns of microbial carbon utilization, linking these observations to genomic and metabolomics information.

Meltwater export of prokaryotic cells from the Greenland ice sheet.

PubMed

Cameron, Karen A; Stibal, Marek; Hawkings, Jon R; Mikkelsen, Andreas B; Telling, Jon; Kohler, Tyler J; Gözdereliler, Erkin; Zarsky, Jakub D; Wadham, Jemma L; Jacobsen, Carsten S

2017-02-01

Microorganisms are flushed from the Greenland Ice Sheet (GrIS) where they may contribute towards the nutrient cycling and community compositions of downstream ecosystems. We investigate meltwater microbial assemblages as they exit the GrIS from a large outlet glacier, and as they enter a downstream river delta during the record melt year of 2012. Prokaryotic abundance, flux and community composition was studied, and factors affecting community structures were statistically considered. The mean concentration of cells exiting the ice sheet was 8.30 × 10 4 cells mL -1 and we estimate that ∼1.02 × 10 21 cells were transported to the downstream fjord in 2012, equivalent to 30.95 Mg of carbon. Prokaryotic microbial assemblages were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Cell concentrations and community compositions were stable throughout the sample period, and were statistically similar at both sample sites. Based on our observations, we argue that the subglacial environment is the primary source of the river-transported microbiota, and that cell export from the GrIS is dependent on discharge. We hypothesise that the release of subglacial microbiota to downstream ecosystems will increase as freshwater flux from the GrIS rises in a warming world. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

DOE PAGES

Labonté, Jessica M.; Swan, Brandon K.; Poulos, Bonnie; ...

2015-04-07

Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus–host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. Furthermore, a combination of comparative genomics, metagenomic fragmentmore » recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus–host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically and geographically diverse single amplified genomes (SAGs) of marine bacteria and archaea. At least four phage–host interactions had the characteristics of late lytic infections, all of which were found in metabolically active cells. One virus had genetic potential for lysogeny. Our findings include first known viruses of Thaumarchaeota, Marinimicrobia, Verrucomicrobia and Gammaproteobacteria clusters SAR86 and SAR92. Viruses were also found in SAGs of Alphaproteobacteria and Bacteroidetes. A high fragment recruitment of viral metagenomic reads confirmed that most of the SAG-associated viruses are abundant in the ocean. This study demonstrates that single-cell genomics, in conjunction with sequence-based computational tools, enable in situ, cultivation-independent insights into host–virus interactions in complex microbial communities.« less

USE OF THE COMPOSITION AND STABLE CARBONIISOTOPE RATIO OF MICROBIAL FATTY ACIDS TO STUDY CARBON CYCLING

EPA Science Inventory

We use measurements of the concentration and stable carbon isotopic ratio (*13C) of individual microbial phospholipid fatty acids (PLFAs) in soils and sediments as indicators of live microbial biomass levels and microbial carbon source. For studies of soil organic matter (SOM) cy...

Production and Consumption of Hydrogen in Hot Spring Microbial Mats Dominated by a Filamentous Anoxygenic Photosynthetic Bacterium

PubMed Central

Otaki, Hiroyo; Everroad, R. Craig; Matsuura, Katsumi; Haruta, Shin

2012-01-01

Microbial mats containing the filamentous anoxygenic photosynthetic bacterium Chloroflexus aggregans develop at Nakabusa hot spring in Japan. Under anaerobic conditions in these mats, interspecies interaction between sulfate-reducing bacteria as sulfide producers and C. aggregans as a sulfide consumer has been proposed to constitute a sulfur cycle; however, the electron donor utilized for microbial sulfide production at Nakabusa remains to be identified. In order to determine this electron donor and its source, ex situ experimental incubation of mats was explored. In the presence of molybdate, which inhibits biological sulfate reduction, hydrogen gas was released from mat samples, indicating that this hydrogen is normally consumed as an electron donor by sulfate-reducing bacteria. Hydrogen production decreased under illumination, indicating that C. aggregans also functions as a hydrogen consumer. Small amounts of hydrogen may have also been consumed for sulfur reduction. Clone library analysis of 16S rRNA genes amplified from the mats indicated the existence of several species of hydrogen-producing fermentative bacteria. Among them, the most dominant fermenter, Fervidobacterium sp., was successfully isolated. This isolate produced hydrogen through the fermentation of organic carbon. Dispersion of microbial cells in the mats resulted in hydrogen production without the addition of molybdate, suggesting that simultaneous production and consumption of hydrogen in the mats requires dense packing of cells. We propose a cyclic electron flow within the microbial mats, i.e., electron flow occurs through three elements: S (elemental sulfur, sulfide, sulfate), C (carbon dioxide, organic carbon) and H (di-hydrogen, protons). PMID:22446313

Life in the Clouds of Venus? An Experimental Synthetic Biology Approach

NASA Technical Reports Server (NTRS)

Rothschild, L. J.; Paulino-Lima, I. G.; Amatya, D.; Bajar, B.; Geilich, B.; Hu, J.; Jackson, C. J.

2015-01-01

The surface of Venus constitutes the most hellish and biologically inhospitable planetary surface in our solar system, boasting a pH of 0, blistering winds that can melt lead, and pressures of 60 atm. However, during the earlier years of the solar system, without the runaway greenhouse effect that has plagued the planet, Venus potentially housed oceans and perhaps even life. There is a possibility that microbes could have retreated into hospitable niches in the atmosphere, as suggested by Carl Sagan as early as 1967 [1]. For example, 50 km above the raging hell of the Venusian surface, exists a relatively temperate environment that might serve as reservoir for life. This astrobiology project seeks to explore life at the extremes and to theorize whether microbial communities could not only survive but also reproduce in the Venusian atmosphere. Specifically, we ask: are aerosols viable microbial environments? But before we can test for life in the clouds, we have to develop a proper reporter to visualize cell growth in situ. For this purpose, we aimed to develop cell-growth dependent reporters to serve as remote biosensors for cell growth. We developed two using the polA promoter, a DNA-replication dependent promoter, and nrd operon promoter, a cell-cycle dependent promoter. Using these cell-growth reporters, the next step is to aerosolize microbes expressing these reporters in a suspension chamber adapted from a Millikan Drop Apparatus to assay reproduction in an aerosolized environment. Better yet is to test the reproduction of microbes in a microgravity regime such as on ISS.Approach: We engineered two cell-cycle dependent genetic reporters. One was the polA promoter which codes for DNA Polymerase I, a gene active in DNA replication [2]. The other was the nrdP. The activation of ribonucleotide reductase reduces ribonucleotides into deoxyribonucleotides and is involved in the bacterial cell cycle [3]. This promoter began activation during the initiation of DNA replication and is cell-cycle dependent [4]. These promoters were fused to a GFP reporter, transformed into E. coli. The constructs were deposited in the iGEM registry as K847210: Escherichia coli DNA-replication dependent polA promoter K847211: Escherichia coli cell-division dependent nrd promoter Results: Our constructs displayed fluorescence when transformed into NEB-5alpha competent cells. While nrdP-E0840 displayed sufficient fluorescence as verified by fluorescent microscopy, the original polAP-E0840 construct (which uses mut3b GFP) exhibited low expression; while fluorescence was visible under the microscope, the signal was too weak for the camera to recognize. The polA promoter was therefore digest-ed with EcoRI and SpeI then ligated into plasmid pNCS containing a RBS, Clover, and a terminator. Clover is a highly engineered green fluorescent protein that exhibits extreme brightness [5] Fluoresence time course data demonsrated that the genes were induced in a cell cycle dependant manner [6]. Our assays via microscopy and the bulk assay shows that our promoters are functional as cell cycle reporters.Conclusions: The application of such tools are widespread and not limited to astrobiology; nrdP could be used to determine doubling times empirically and could possibly extrapolate DNA content from intensity of signals expressed by polAP. However, we are pri-marily interested in its use in astrobiology.

Interactions between microbial iron reduction and metal geochemistry: effect of redox cycling on transition metal speciation in iron bearing sediments.

PubMed

Cooper, D Craig; Picardal, Flynn F; Coby, Aaron J

2006-03-15

Microbial iron reduction is an important biogeochemical process that can affect metal geochemistry in sediments through direct and indirect mechanisms. With respectto Fe(III) (hydr)oxides bearing sorbed divalent metals, recent reports have indicated that (1) microbial reduction of goethite/ferrihydrite mixtures preferentially removes ferrihydrite, (2) this process can incorporate previously sorbed Zn(II) into an authigenic crystalline phase that is insoluble in 0.5 M HCl, (3) this new phase is probably goethite, and (4) the presence of nonreducible minerals can inhibit this transformation. This study demonstrates that a range of sorbed transition metals can be selectively sequestered into a 0.5 M HCl insoluble phase and that the process can be stimulated through sequential steps of microbial iron reduction and air oxidation. Microbial reduction experiments with divalent Cd, Co, Mn, Ni, Pb, and Zn indicate that all metals save Mn experienced some sequestration, with the degree of metal incorporation into the 0.5 M HCl insoluble phase correlating positively with crystalline ionic radius at coordination number = 6. Redox cycling experiments with Zn adsorbed to synthetic goethite/ferrihydrite or iron-bearing natural sediments indicate that redox cycling from iron reducing to iron oxidizing conditions sequesters more Zn within authigenic minerals than microbial iron reduction alone. In addition, the process is more effective in goethite/ferrihydrite mixtures than in iron-bearing natural sediments. Microbial reduction alone resulted in a -3x increase in 0.5 M HCl insoluble Zn and increased aqueous Zn (Zn-aq) in goethite/ferrihydrite, but did not significantly affect Zn speciation in natural sediments. Redox cycling enhanced the Zn sequestration by approximately 12% in both goethite/ferrihydrite and natural sediments and reduced Zn-aq to levels equal to the uninoculated control in goethite/ferrihydrite and less than the uninoculated control in natural sediments. These data suggest that in situ redox cycling may serve as an effective method for

The microbial perspective of organic matter turnover and nutrient cycling in tropical soils

NASA Astrophysics Data System (ADS)

Rasche, Frank

2017-04-01

A primary goal of low-input small-holder farming systems in the tropics is the appropriate management of organic matter (OM) turnover and nutrient cycling via adapted agricultural practices. These emphasize the promotion of soil organic matter (SOM) turnover and carbon (C) sequestration, nutrient use efficiency and soil microbial activity. Since soil microbial communities are acknowledged as key players in the terrestrial C and nutrient (e.g., nitrogen (N), phosphorus (P)) cycles, they may respond sensitively to agricultural management with shifts in their community structure as well as functional traits (i.e., decomposition, mineralization). This may be in particular evident for tropical, agricultural soils which show an accelerated microbial decomposition activity induced by favourable climatic and unique physico-chemical soil conditions. While modern molecular techniques advanced primarily the understanding about the microbiome and their functional traits interacting closely with SOM dynamics in temperate soils, tropical soils under agricultural use have been still neglected to a great extent. The majority of available studies revealed mainly descriptive data on the structural composition of microbial communities rather than questioning if detected structural alterations of the soil microbiome influenced key processes in N and P cycling which actually maintain ecosystem functioning and soil productivity. This talk highlights latest efforts in deploying molecular techniques to study the compositional status of soil microbial decomposer communities and their functional attributes in response to land use change and OM management in tropical agro-ecosystems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allison, Steven D.

The role of specific micro-organisms in the carbon cycle, and their responses to environmental change, are unknown in most ecosystems. This knowledge gap limits scientists’ ability to predict how important ecosystem processes, like soil carbon storage and loss, will change with climate and other environmental factors. The investigators addressed this knowledge gap by transplanting microbial communities from different environments into new environments and measuring the response of community composition and carbon cycling over time. Using state-of-the-art sequencing techniques, computational tools, and nanotechnology, the investigators showed that microbial communities on decomposing plant material shift dramatically with natural and experimentally-imposed drought. Microbialmore » communities also shifted in response to added nitrogen, but the effects were smaller. These changes had implications for carbon cycling, with lower rates of carbon loss under drought conditions, and changes in the efficiency of decomposition with nitrogen addition. Even when transplanted into the same conditions, microbial communities from different environments remained distinct in composition and functioning for up to one year. Changes in functioning were related to differences in enzyme gene content across different microbial groups. Computational approaches developed for this project allowed the conclusions to be tested more broadly in other ecosystems, and new computer models will facilitate the prediction of microbial traits and functioning across environments. The data and models resulting from this project benefit the public by improving the ability to predict how microbial communities and carbon cycling functions respond to climate change, nutrient enrichment, and other large-scale environmental changes.« less

15N indicates an active N-cycling microbial community in low carbon, freshwater sediments.

NASA Astrophysics Data System (ADS)

Sheik, C.

2017-12-01

Earth's large lakes are unique aquatic ecosystems, but we know little of the microbial life driving sedimentary biogeochemical cycles and ultimately the isotopic record. In several of these large lakes, water column productivity is constrained by element limitation, such as phosphorus and iron, creating oligotrophic water column conditions that drive low organic matter content in sediments. Yet, these sediments are biogeochemically active and have been shown to have oxygen consumption rates akin to pelagic ocean sediments and complex sulfur cycling dynamics. Thus, large oligotrophic lakes provide unique and interesting biogeochemical contrast to highly productive freshwater and coastal marine systems. Using Lake Superior as our study site, we found microbial community structure followed patterns in bulk sediment carbon and nitrogen concentrations. These observed patterns were loosely driven by land proximity, as some stations are more coastal and have higher rates of sedimentation, allochthonous carbon inputs and productivity than pelagic sites. Interestingly, upper sediment carbon and nitrogen stable isotopes were quite different from water column. Sediment carbon and nitrogen isotopes correlated significantly with microbial community structure. However, 15N showed much stronger correlation than 13C, and became heavier with core depth. Coinciding with the increase in 15N values, we see evidence of both denitrification and anammox processes in 16S rRNA gene libraries and metagenome assembled genomes. Given that microorganisms prefer light isotopes and that these N-cycling processes both contribute to N2 production and efflux from the sediment, the increase in 15N with sediment depth suggests microbial turnover. Abundance of these genomes also varies with depth suggesting these novel microorganisms are partitioning into specific sediment geochemical zones. Additionally, several of these genomes contain genes involved in sulphur cycling, suggesting a dual biogeochemical role and potential for a cryptic sulfur cycle. Together, Lake Superior sediments offer a glimpse into microbial metabolism in carbon limited environments. Further the pervasiveness of co-metabolic pathways suggests interpretation of isotopic records may be messier than previously thought.

Proteomic Characterization of Central Pacific Oxygen Minimum Zone Microbial Communities

NASA Astrophysics Data System (ADS)

Saunders, J. K.; McIlvin, M. M.; Moran, D.; Held, N.; Futrelle, J.; Webb, E.; Santoro, A.; Dupont, C.; Saito, M.

2018-05-01

Microbial proteomic profiles are excellent for surveying vast expanses of pelagic ecosystems for links between microbial communities and the biogeochemical cycles they mediate. Data from the ProteOMZ expedition supports the utility of this method.

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage.

PubMed

Porter, Matthew D; Andrus, J Malia; Bartolerio, Nicholas A; Rodriguez, Luis F; Zhang, Yuanhui; Zilles, Julie L; Kent, Angela D

2015-10-01

Denitrifying bioreactors, consisting of water flow control structures and a woodchip-filled trench, are a promising approach for removing nitrate from agricultural subsurface or tile drainage systems. To better understand the seasonal dynamics and the ecological drivers of the microbial communities responsible for denitrification in these bioreactors, we employed microbial community "fingerprinting" techniques in a time-series examination of three denitrifying bioreactors over 2 years, looking at bacteria, fungi, and the denitrifier functional group responsible for the final step of complete denitrification. Our analysis revealed that microbial community composition responds to depth and seasonal variation in moisture content and inundation of the bioreactor media, as well as temperature. Using a geostatistical analysis approach, we observed recurring temporal patterns in bacterial and denitrifying bacterial community composition in these bioreactors, consistent with annual cycling. The fungal communities were more stable, having longer temporal autocorrelations, and did not show significant annual cycling. These results suggest a recurring seasonal cycle in the denitrifying bioreactor microbial community, likely due to seasonal variation in moisture content.

Inactivation of Escherichia coli by citral.

PubMed

Somolinos, M; García, D; Condón, S; Mackey, B; Pagán, R

2010-06-01

The aim was to evaluate (i) the resistance of Escherichia coli BJ4 to citral in a buffer system as a function of citral concentration, treatment medium pH, storage time and initial inoculum size, (ii) the role of the sigma factor RpoS on citral resistance of E. coli, (iii) the role of the cell envelope damage in the mechanism of microbial inactivation by citral and (iiii) possible synergistic effects of mild heat treatment and pulsed electric fields (PEF) treatment combined with citral. The initial inoculum size greatly affected the efficacy of citral against E. coli cells. Exposure to 200 microl l(-1) of citral at pH 4.0 for 24 h at 20 degrees C caused the inactivation of more than 5 log(10) cycles of cells starting at an inoculum size of 10(6) or 10(7) CFU ml(-1), whereas increasing the cell concentration to 10(9) CFU ml(-1) caused <1 log(10) cycle of inactivation. Escherichia coli showed higher resistance to citral at pH 4.0 than pH 7.0. The rpoS null mutant strain E. coli BJ4L1 was less resistant to citral than the wild-type strain. Occurrence of sublethal injury to both the cytoplasmic and outer membranes was demonstrated by adding sodium chloride or bile salts to the recovery media. The majority of sublethally injured cells by citral required energy and lipid synthesis for repair. A strongly synergistic lethal effect was shown by mild heat treatment combined with citral but the presence of citral during the application of a PEF treatment did not show any advantage. This work confirms that cell envelope damage is an important event in citral inactivation of bacteria, and it describes the key factors on the inactivation of E. coli cells by citral. Knowledge about the mechanism of microbial inactivation by citral helps establish successful combined preservation treatments.

A mechanism for bacterial transformation of dimethylsulfide to dimethylsulfoxide: a missing link in the marine organic sulfur cycle.

PubMed

Lidbury, Ian; Kröber, Eileen; Zhang, Zhidong; Zhu, Yijun; Murrell, J Colin; Chen, Yin; Schäfer, Hendrik

2016-09-01

The volatile organosulfur compound, dimethylsulfide (DMS), plays an important role in climate regulation and global sulfur biogeochemical cycles. Microbial oxidation of DMS to dimethylsulfoxide (DMSO) represents a major sink of DMS in surface seawater, yet the underlying molecular mechanisms and key microbial taxa involved are not known. Here, we reveal that Ruegeria pomeroyi, a model marine heterotrophic bacterium, can oxidize DMS to DMSO using trimethylamine monooxygenase (Tmm). Purified Tmm oxidizes DMS to DMSO at a 1:1 ratio. Mutagenesis of the tmm gene in R. pomeroyi completely abolished DMS oxidation and subsequent DMSO formation. Expression of Tmm and DMS oxidation in R. pomeroyi is methylamine-dependent and regulated at the post-transcriptional level. Considering that Tmm is present in approximately 20% of bacterial cells inhabiting marine surface waters, particularly the marine Roseobacter clade and the SAR11 clade, our observations contribute to a mechanistic understanding of biological DMSO production in surface seawater. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial and geochemical investigations of dissolved organic carbon and microbial ecology of native waters from the Biscayne and Upper Floridan Aquifers

USGS Publications Warehouse

Lisle, John T.; Harvey, Ron W.; Aiken, George R.; Metge, David W.

2010-01-01

Groundwater resources in the United States are under ever-increasing demands for potable, irrigation, and recreational uses. Additionally, aquifer systems are being used or targeted for use as storage areas for treated surface waters and (or) groundwaters via injection (for example, aquifer storage and recovery). To date, the influence that the nutrients, including carbon, in the injected water have on native microbial communities and the biogeochemistry in the subsurface zones used for storage of the injectate has not been determined. In this report, we describe a series of experiments that establishes a baseline dataset for the quantity and quality of organic and inorganic carbon and nutrients in the Biscayne Aquifer (BA) and Upper Floridan Aquifer (UFA) in south Florida. The most significant differences between the BA (26 meters below surface) and UFA (366 meters below surface) are the average specific conductance (0.552 and 6.12 microsiemens per centimeter, respectively), dissolved oxygen (1.6 and 0 milligrams per liter, respectively), and oxidation-reduction potential (40.3 and -358 millivolts, respectively). The dissolved organic carbon from the BA is characterized by carbon originating from terrestrial sources and microbial activities, while the UFA has a distinctive microbial signature. Acetate and lactate are the dominant carbon constituents in both aquifers. Additionally, components of the dissolved organic carbon from the UFA have a total trihalomethane-formation potential that is approximately threefold greater than the maximum contaminat level of 80 micrograms per liter established by the U.S. Environmental Protection Agency. The average native bacterial abundances in the aquifers are similar with 4.69x10^4 cells per milliliter in the BA and 1.33x10^4 cells per milliliter in the UFA. The average bacteriophage abundances are also similar with 1.15x10^5 virus-like particles in the BA and 1.92x10^5 virus-like particles in the UFA. Interestingly, ciliated protozoa are present in both aquifers. The average abundance of ciliates in the BA (2.97x10^3 ciliates per milliliter) is approximately twentyfold greater than abundances in the UFA (1.39x10^2 ciliates per milliliter). Collectively, these data indicate that microbial processes are the dominant contributor to the cycling of carbon and inorganic carbon in the BA and may be the only carbon cycling process in the UFA, as this aquifer has not had a terrestrial influx of carbon for more than 15,000 years. The rates of carbon, in the form of acetate, utilization by the native microbial communities are significantly different between the two aquifers. Based on data from 14C-acetate-utilization experiments, the microbial communities in the BA turn over the native acetate in 2.5 years, whereas communities in the UFA turn over native acetate in 6.8 years. These data support the hypothesis derived from the microbial-abundance data, in that the carbon for bacterial maintainence and growth is recycled from bacterial biomass released during cell lysis, especially in the UFA. An in situ diffusion chamber was designed to retain bacterial cells within the chamber while allowing native water constituents to move through the chamber. A series of 1-week deployments of chambers filled with fluorescent beads, inactivated native bacteria and laboratory grown and viable bacteria into the UFA, permitted by the State of Florida Environmental Protection Agency, was successfully completed. This was the first time this type of deployment into an aquifer system that is used for potable water supply has been permitted within the United States. This technology will allow, for the first time, in situ studies on the survival of microbial indicators of fecal pollution and true pathogens in groundwater systems.

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

PubMed Central

Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

2016-01-01

Modern microbial mats are potential analogues of some of Earth's earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats. PMID:26023869

Microbial dormancy improves development and experimental validation of ecosystem model

DOE PAGES

Wang, Gangsheng; Jagadamma, Sindhu; Mayes, Melanie; ...

2014-07-11

Climate feedbacks from soils can result from environmental change followed by response of plant and microbial communities, and/or associated changes in nutrient cycling. Explicit consideration of microbial life history traits and functions may be necessary to predict climate feedbacks due to changes in the physiology and community composition of microbes and their associated effect on carbon cycling. Here, we enhanced the Microbial-Enzyme-mediated Decomposition (MEND) model by incorporating microbial dormancy and the ability to track multiple isotopes of carbon. We tested two versions of MEND, i.e., MEND with dormancy and MEND without dormancy, against long-term (270 d) lab incubations of fourmore » soils with isotopically-labeled substrates. MEND without dormancy adequately fitted multiple observations (total and 14C respiration, and dissolved organic carbon), but at the cost of significantly underestimating the total microbial biomass. The MEND with dormancy improved estimates of microbial biomass by 20 71% over the MEND without dormancy. We observed large differences for two fitted model parameters, the specific maintenance and growth rates for active microbes, depending on whether dormancy was considered. Together our model extrapolations of the incubation study show that long-term soil incubations with observations in multiple carbon pools are necessary to estimate both decomposition and microbial parameters. These efforts should provide essential support to future field- and global-scale simulations and enable more confident predictions of feedbacks between environmental change and carbon cycling.« less

Dynamics of Marine Microbial Metabolism and Physiology at Station ALOHA

NASA Astrophysics Data System (ADS)

Casey, John R.

Marine microbial communities influence global biogeochemical cycles by coupling the transduction of free energy to the transformation of Earth's essential bio-elements: H, C, N, O, P, and S. The web of interactions between these processes is extraordinarily complex, though fundamental physical and thermodynamic principles should describe its dynamics. In this collection of 5 studies, aspects of the complexity of marine microbial metabolism and physiology were investigated as they interact with biogeochemical cycles and direct the flow of energy within the Station ALOHA surface layer microbial community. In Chapter 1, and at the broadest level of complexity discussed, a method to relate cell size to metabolic activity was developed to evaluate allometric power laws at fine scales within picoplankton populations. Although size was predictive of metabolic rates, within-population power laws deviated from the broader size spectrum, suggesting metabolic diversity as a key determinant of microbial activity. In Chapter 2, a set of guidelines was proposed by which organic substrates are selected and utilized by the heterotrophic community based on their nitrogen content, carbon content, and energy content. A hierarchical experimental design suggested that the heterotrophic microbial community prefers high nitrogen content but low energy density substrates, while carbon content was not important. In Chapter 3, a closer look at the light-dependent dynamics of growth on a single organic substrate, glycolate, suggested that growth yields were improved by photoheterotrophy. The remaining chapters were based on the development of a genome-scale metabolic network reconstruction of the cyanobacterium Prochlorococcus to probe its metabolic capabilities and quantify metabolic fluxes. Findings described in Chapter 4 pointed to evolution of the Prochlorococcus metabolic network to optimize growth at low phosphate concentrations. Finally, in Chapter 5 and at the finest scale of complexity, a method was developed to predict hourly changes in both physiology and metabolic fluxes in Prochlorococcus by incorporating gene expression time-series data within the metabolic network model. Growth rates predicted by this method more closely matched experimental data, and diel changes in elemental composition and the energy content of biomass were predicted. Collectively, these studies identify and quantify the potential impact of variations in metabolic and physiological traits on the melee of microbial community interactions.

Short-term Dynamics of Photopriming Increase Carbon Loss During Litter Decomposition

NASA Astrophysics Data System (ADS)

Lin, Y.; King, J. Y.; Karlen, S. D.; Ralph, J.

2017-12-01

Solar radiation plays a key role in carbon (C) cycling by increasing the decomposition rates of plant litter through photodegradation. This process is particularly important in drylands where solar radiation is high and microbial activity may be limited by water availability. One mechanism of photodegradation may be the facilitation of microbial decomposition of litter by altering litter chemistry and consequently degradability, termed photopriming. However, it remains unclear to what extent photopriming contributes to litter decomposition. We evaluated photopriming by ultraviolet (UV) radiation through two laboratory experiments. In one experiment, we found that four months of UV exposure increased mass loss by 3-4% compared to dark treatment in two of three litter species commonly found in California oak savanna; however, UV exposure did not alter litter degradability as measured by microbial respiration in an incubation study. UV exposure had limited effects on lignin and other cell wall structures, but one month of microbial decomposition in the dark significantly reduced lignin β-aryl ether inter-unit linkages and acetylated xylans, which interestingly was the same pattern seen in litter exposed to UV radiation under field conditions and may account for the significant effects of UV exposure on litter mass loss observed in situ. These results indicate that microbial decomposition, not abiotic photodegradation, was ultimately responsible for changes in litter chemistry observed in the field. In a separate experiment, litter of a common grass was incubated for 128 days under either alternating UV radiation and dark conditions at two-day intervals or continuous darkness. During the second half of the experiment, alternating UV exposure increased CO2 production by 35% compared to continuous darkness, suggesting that UV exposure induces subtle but important changes in litter chemistry that facilitate microbial decomposition on a temporal scale of days. Together the results point to microbial facilitation as the primary mechanism of photodegradation and suggest that photopriming is governed by short-term dynamics at the litter-microbe interface. The C cycling associated with these short-term dynamics may be especially sensitive to anticipated increases in drought conditions in drylands.

Groundwater-fed Iron-rich Microbial Mats in a Freshwater Creek: Growth Cycles and Fossilization Potential of Microbial Features

NASA Astrophysics Data System (ADS)

Schieber, J.

2004-03-01

Study of modern microbial mats produced by iron precipitating microbes. Aging and compaction experiments to evaluate fossilization potential and likelihood to recognize these deposits in the rock record.

Microbial fuel cells: From fundamentals to applications. A review.

PubMed

Santoro, Carlo; Arbizzani, Catia; Erable, Benjamin; Ieropoulos, Ioannis

2017-07-15

In the past 10-15 years, the microbial fuel cell (MFC) technology has captured the attention of the scientific community for the possibility of transforming organic waste directly into electricity through microbially catalyzed anodic, and microbial/enzymatic/abiotic cathodic electrochemical reactions. In this review, several aspects of the technology are considered. Firstly, a brief history of abiotic to biological fuel cells and subsequently, microbial fuel cells is presented. Secondly, the development of the concept of microbial fuel cell into a wider range of derivative technologies, called bioelectrochemical systems, is described introducing briefly microbial electrolysis cells, microbial desalination cells and microbial electrosynthesis cells. The focus is then shifted to electroactive biofilms and electron transfer mechanisms involved with solid electrodes. Carbonaceous and metallic anode materials are then introduced, followed by an explanation of the electro catalysis of the oxygen reduction reaction and its behavior in neutral media, from recent studies. Cathode catalysts based on carbonaceous, platinum-group metal and platinum-group-metal-free materials are presented, along with membrane materials with a view to future directions. Finally, microbial fuel cell practical implementation, through the utilization of energy output for practical applications, is described.

Microbial fuel cells: From fundamentals to applications. A review

NASA Astrophysics Data System (ADS)

Santoro, Carlo; Arbizzani, Catia; Erable, Benjamin; Ieropoulos, Ioannis

2017-07-01

In the past 10-15 years, the microbial fuel cell (MFC) technology has captured the attention of the scientific community for the possibility of transforming organic waste directly into electricity through microbially catalyzed anodic, and microbial/enzymatic/abiotic cathodic electrochemical reactions. In this review, several aspects of the technology are considered. Firstly, a brief history of abiotic to biological fuel cells and subsequently, microbial fuel cells is presented. Secondly, the development of the concept of microbial fuel cell into a wider range of derivative technologies, called bioelectrochemical systems, is described introducing briefly microbial electrolysis cells, microbial desalination cells and microbial electrosynthesis cells. The focus is then shifted to electroactive biofilms and electron transfer mechanisms involved with solid electrodes. Carbonaceous and metallic anode materials are then introduced, followed by an explanation of the electro catalysis of the oxygen reduction reaction and its behavior in neutral media, from recent studies. Cathode catalysts based on carbonaceous, platinum-group metal and platinum-group-metal-free materials are presented, along with membrane materials with a view to future directions. Finally, microbial fuel cell practical implementation, through the utilization of energy output for practical applications, is described.

Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments.

PubMed

Currie, Ashleigh R; Tait, Karen; Parry, Helen; de Francisco-Mora, Beatriz; Hicks, Natalie; Osborn, A Mark; Widdicombe, Steve; Stahl, Henrik

2017-01-01

Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO 2 ) and elevated temperature (ambient +4°C) on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase ( amoA ) and bacterial nitrite reductase ( nirS ) were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO 2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes ( amoA and nirS ) were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

The impact of post-fire salvage logging on microbial nitrogen cyclers in Mediterranean forest soil.

PubMed

Pereg, Lily; Mataix-Solera, Jorge; McMillan, Mary; García-Orenes, Fuensanta

2018-04-01

Forest fires are a regular occurrence in the Mediterranean basin. High severity fires and post-fire management can affect biological, chemical and physical properties of soil, including the composition and abundance of soil microbial communities. Salvage logging is a post-fire management strategy, which involves the removal of burnt wood from land after a fire. The main objective of this work was to evaluate the impact of post-fire salvage logging and microaggregation on soil microbial communities, specifically on the abundance of nitrogen cyclers and, thus, the potential of the soil for microbial nitrogen cycling. The abundance of nitrogen cyclers was assessed by quantification of microbial nitrogen cycling genes in soil DNA, including nifH (involved in nitrogen fixation), nirS/K and nosZ (involved in denitrification), amoA-B and amoA-Arch (involved in bacterial and archaeal nitrification, respectively). It was demonstrated that salvage logging reduced bacterial load post-fire when compared to tree retention control and resulted in significant changes to the abundance of functional bacteria involved in nitrogen cycling. Microbial gene pools involved in various stages of the nitrogen cycle were larger in control soil than in soil subjected to post-fire salvage logging and were significantly correlated with organic matter, available phosphorous, nitrogen and aggregate stability. The microaggregate fraction of the soil, which has been associated with greater organic carbon, was shown to be a hotspot for nitrogen cyclers particularly under salvage logging. The impact of post-fire management strategies on soil microbial communities needs to be considered in relation to maintaining ecosystem productivity, resilience and potential impact on climate change. Copyright © 2017 Elsevier B.V. All rights reserved.

The Impact of Climate Change on Microbial Communities and Carbon Cycling in High Arctic Permafrost Soil from Spitsbergen, Northern Norway

NASA Astrophysics Data System (ADS)

de Leon, K. C.; Schwery, D.; Yoshikawa, K.; Christiansen, H. H.; Pearce, D.

2014-12-01

Permafrost-affected soils are among the most fragile ecosystems in which current microbial controls on organic matter decomposition are changing as a result of climate change. Warmer conditions in the high Arctic will lead to a deepening of the seasonal active layer of permafrost, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. The viable and non-viable fractions of the microbial community in a permafrost soil from Adventdalen, Spitsbergen, Norway were subjected to a comprehensive investigation using culture-dependent and culture-independent methods. Molecular analyses using FISH (with CTC-DAPI) and amplified rDNA restriction analysis (ARDRA) on a 257cm deep core, revealed the presence of all major microbial soil groups, with the active layer having more viable cells, and a higher microbial community diversity. Carbon dioxide (CO2) and methane (CH4) flux measurements were performed to show the amount of C stored in the sample. We demonstrated that the microbial community composition from the soil in the center of the core was most likely influenced by small scale variations in environmental conditions. Community structure showed distinct shift of presence of bacterial groups along the vertical temperature gradient profile and microbial counts and diversity was found to be highest in the surface layers, decreasing with depth. It was observed that soil properties driving microbial diversity and functional potential varied across the permafrost table. Data on the variability of CO2 and CH4 distribution described in peat structure heterogeneity are important for modeling emissions on a larger scale. Furthermore, linking microbial biomass to gas distribution may elucidate the cause of peak CO2 and CH4 and their changes in relation to environmental change and peat composition.

USE OF THE COMPOSITION AND STABLE CARBON ISOTOPE RATIO OF MICROBIAL FATTY ACIDS TO STUDY CARBON CYCLING

EPA Science Inventory

We use measurements of the concentration and stable carbon isotopic ratio (Gamma 13C) of individual microbial phospholipid fatty acids (PLFAS) in soils and sediments as indicators of live microbial biomass levels and microbial carbon source. For studies of soil organic matter (SO...

Electricity generation and removal performance of a microbial fuel cell using sulfonated poly (ether ether ketone) as proton exchange membrane to treat phenol/acetone wastewater.

PubMed

Wu, Hao; Fu, Yu; Guo, Chunyu; Li, Yanbo; Jiang, Nanzhe; Yin, Chengri

2018-07-01

The microbial fuel cell (MFC) has emerged as a promising technology for wastewater treatment and energy recovery, but the expensive cost of proton exchange membranes (PEMs) is a problem that need to be solved. In this study, a two-chamber MFC based on our self-made PEM sulfonated poly (ether ether ketone) membrane was set up to treat phenol/acetone wastewater and synchronously generate power. The maximum output voltage was 240-250 mV. Using phenol and acetone as substrates, the power generation time in an operation cycle was 289 h. The MFC exhibited good removal performance, with no phenol or acetone detected, respectively, when the phenol concentration was lower than 50 mg/L and the acetone concentration was lower than 100 mg/L. This study provides a cheap and eco-friendly way to treat phenol/acetone wastewater and generate useful energy by MFC technology. Copyright © 2018 Elsevier Ltd. All rights reserved.

Impact of volatile fatty acids on microbial electrolysis cell performance.

PubMed

Yang, Nan; Hafez, Hisham; Nakhla, George

2015-10-01

This study investigated the performance of microbial electrolysis cells (MECs) fed with three common fermentation products: acetate, butyrate, and propionate. Each substrate was fed to the reactor for three consecutive-batch cycles. The results showed high current densities for acetate, but low current densities for butyrate and propionate (maximum values were 6.0 ± 0.28, 2.5 ± 0.06, 1.6 ± 0.14 A/m(2), respectively). Acetate also showed a higher coulombic efficiency of 87 ± 5.7% compared to 72 ± 2.0 and 51 ± 6.4% for butyrate and propionate, respectively. This paper also revealed that acetate could be easily oxidized by anode respiring bacteria in MEC, while butyrate and propionate could not be oxidized to the same degree. The utilization rate of the substrates in MEC followed the order: acetate > butyrate > propionate. The ratio of suspended biomass to attached biomass was approximately 1:4 for all the three substrates. Copyright © 2015 Elsevier Ltd. All rights reserved.

Energy-neutral sustainable nutrient recovery incorporated with the wastewater purification process in an enlarged microbial nutrient recovery cell

NASA Astrophysics Data System (ADS)

Sun, Dongya; Gao, Yifan; Hou, Dianxun; Zuo, Kuichang; Chen, Xi; Liang, Peng; Zhang, Xiaoyuan; Ren, Zhiyong Jason; Huang, Xia

2018-04-01

Recovery of nutrient resources from the wastewater is now an inevitable strategy to maintain the supply of both nutrient and water for our huge population. While the intensive energy consumption in conventional nutrient recovery technologies still remained as the bottleneck towards the sustainable nutrient recycle. This study proposed an enlarged microbial nutrient recovery cell (EMNRC) which was powered by the energy contained in wastewater and achieved multi-cycle nutrient recovery incorporated with in situ wastewater treatment. With the optimal recovery solution of 3 g/L NaCl and the optimal volume ratio of wastewater to recovery solution of 10:1, >89% of phosphorus and >62% of ammonium nitrogen were recovered into struvite. An extremely low water input ratio of <1% was required to obtain the recovered fertilizer and the purified water. It was proved the EMNRC system was a promising technology which could utilize the chemical energy contained in wastewater itself and energy-neutrally recover nutrient during the continuous wastewater purification process.

Enhanced bioelectricity generation of air-cathode buffer-free microbial fuel cells through short-term anolyte pH adjustment.

PubMed

Ren, Yueping; Chen, Jinli; Li, Xiufen; Yang, Na; Wang, Xinhua

2018-04-01

Short-term initial anolyte pH adjustment can relieve the performance deterioration of the single-chamber air-cathode buffer-free microbial fuel cell (BFMFC) caused by anolyte acidification. Adjusting the initial anolyte pH to 9 in 5 running cycles is the optimum strategy. The relative abundance of the electrochemically active Geobacter in the KCl-pH9-MFC anode biofilm increased from 59.01% to 75.13% after the short-term adjustment. The maximum power density (P max ) of the KCl-pH9-MFC was elevated from 316.4mW·m -2 to 511.6mW·m -2 , which was comparable with that of the PBS-MFC. And, after the short-term adjusting, new equilibrium between the anolyte pH and the anode biofilm electrochemical activity has been established in the BFMFC, which ensured the sustainability of the improved bioelectricity generation performance. Copyright © 2017 Elsevier B.V. All rights reserved.

A Carbon-Neutral Photosynthetic Microbial Fuel Cell Powered by Microcystis aeruginosa.

PubMed

Ma, Meirong; Cao, Limin; Chen, Li; Ying, Xiaofang; Deng, Zongwu

2015-07-01

A photosynthetic microbial fuel cell (m-PMFC) is developed for generating electricity by harnessing solar energy using Microcystis aeruginosa. In this m-PMFC, commensal bacteria can consume the nutrients that Microcystis aeruginosa produces to generate electricity so that no net CO₂production occurs. A b-MFC is constructed to confirm the role of commensal bacteria in electric generation. An s-PMFC is constructed to confirm the contribution of Microcystis aeruginosa as substrates. The power outputs of m-PMFCs exhibit no significant difference in terms of different inoculation amount of Microcystis aeruginosa or light/dark cycles. The power density of m-PMFC exhibits similar response to bubbling of N₂and O₂as that of b-MFC, as confirmed by cyclic voltammetry analysis of m-PMFC and b-MFC. Scanning electron microscope images demonstrate that the biofilm of m-PMFC consists mainly of commensal bacteria. These results suggest that commensal bacteria act as the main biocatalysts and Microcystis aeruginosa as the anode substrates in the m-PMFC.

Streptomyces exploration is triggered by fungal interactions and volatile signals

PubMed Central

Jones, Stephanie E; Ho, Louis; Rees, Christiaan A; Hill, Jane E; Nodwell, Justin R; Elliot, Marie A

2017-01-01

It has long been thought that the life cycle of Streptomyces bacteria encompasses three developmental stages: vegetative hyphae, aerial hyphae and spores. Here, we show interactions between Streptomyces and fungi trigger a previously unobserved mode of Streptomyces development. We term these Streptomyces cells ‘explorers’, for their ability to adopt a non-branching vegetative hyphal conformation and rapidly transverse solid surfaces. Fungi trigger Streptomyces exploratory growth in part by altering the composition of the growth medium, and Streptomyces explorer cells can communicate this exploratory behaviour to other physically separated streptomycetes using an airborne volatile organic compound (VOC). These results reveal that interkingdom interactions can trigger novel developmental behaviours in bacteria, here, causing Streptomyces to deviate from its classically-defined life cycle. Furthermore, this work provides evidence that VOCs can act as long-range communication signals capable of propagating microbial morphological switches. DOI: http://dx.doi.org/10.7554/eLife.21738.001 PMID:28044982

Fully reversible current driven by a dual marine photosynthetic microbial community.

PubMed

Darus, Libertus; Lu, Yang; Ledezma, Pablo; Keller, Jürg; Freguia, Stefano

2015-11-01

The electrochemical activity of two seawater microbial consortia were investigated in three-electrode bioelectrochemical cells. Two seawater inocula - from the Sunshine Coast (SC) and Gold Coast (GC) shores of Australia - were enriched at +0.6 V vs. SHE using 12/12 h day/night cycles. After re-inoculation, the SC consortium developed a fully-reversible cathodic/anodic current, with a max. of -62 mA m(-2) during the day and +110 mA m(-2) at night, while the GC exhibited negligible daytime output but +98 mA m(-2) at night. Community analysis revealed that both enrichments were dominated by cyanobacteria, indicating their potential as biocatalysts for indirect light conversion to electricity. Moreover, the presence of γ-proteobacterium Congregibacter in SC biofilm was likely related to the cathodic reductive current, indicating its effectiveness at catalysing cathodic oxygen reduction at a surprisingly high potential. For the first time a correlation between a dual microbial community and fully reversible current is reported. Copyright © 2015 Elsevier Ltd. All rights reserved.

In Situ Search for Extraterrestrial Life: A Microbial Fuel Cell-Based Sensor for the Detection of Photosynthetic Metabolism.

PubMed

Figueredo, Federico; Cortón, Eduardo; Abrevaya, Ximena C

2015-09-01

Microbial fuel cells (MFCs) are bioelectrochemical systems (BES) capable of harvesting electrons from redox reactions involved in metabolism. In a previous work, we used chemoorganoheterotrophic microorganisms from the three domains of life-Bacteria, Archaea, and Eukarya-to demonstrate that these BES could be applied to the in situ detection of extraterrestrial life. Since metabolism can be considered a common signature of life "as we know it," we extended in this study the ability to use MFCs as sensors for photolithoautotrophic metabolisms. To achieve this goal, two different photosynthetic microorganisms were used: the microalgae Parachlorella kessleri and the cyanobacterium Nostoc sp. MFCs were loaded with nonsterilized samples, sterilized samples, or sterilized culture medium of both microorganisms. Electric potential measurements were recorded for each group in single experiments or in continuum during light-dark cycles, and power and current densities were calculated. Our results indicate that the highest power and current density values were achieved when metabolically active microorganisms were present in the anode of the MFC. Moreover, when continuous measurements were performed during light-dark cycles, it was possible to see a positive response to light. Therefore, these BES could be used not only to detect chemoorganoheterotrophic metabolisms but also photolithoautotrophic metabolisms, in particular those involving oxygenic photosynthesis. Additionally, the positive response to light when using these BES could be employed to distinguish photosynthetic from nonphotosynthetic microorganisms in a sample.

Photodegradation alleviates the lignin bottleneck for carbon turnover in terrestrial ecosystems

PubMed Central

Austin, Amy T.; Méndez, M. Soledad; Ballaré, Carlos L.

2016-01-01

A mechanistic understanding of the controls on carbon storage and losses is essential for our capacity to predict and mitigate human impacts on the global carbon cycle. Plant litter decomposition is an important first step for carbon and nutrient turnover, and litter inputs and losses are essential in determining soil organic matter pools and the carbon balance in terrestrial ecosystems. Photodegradation, the photochemical mineralization of organic matter, has been recently identified as a mechanism for previously unexplained high rates of litter mass loss in arid lands; however, the global significance of this process as a control on carbon cycling in terrestrial ecosystems is not known. Here we show that, across a wide range of plant species, photodegradation enhanced subsequent biotic degradation of leaf litter. Moreover, we demonstrate that the mechanism for this enhancement involves increased accessibility to plant litter carbohydrates for microbial enzymes. Photodegradation of plant litter, driven by UV radiation, and especially visible (blue–green) light, reduced the structural and chemical bottleneck imposed by lignin in secondary cell walls. In leaf litter from woody species, specific interactions with UV radiation obscured facilitative effects of solar radiation on biotic decomposition. The generalized effect of sunlight exposure on subsequent microbial activity, mediated by increased accessibility to cell wall polysaccharides, suggests that photodegradation is quantitatively important in determining rates of mass loss, nutrient release, and the carbon balance in a broad range of terrestrial ecosystems. PMID:27044070

A synthetic microbial consortium of Shewanella and Bacillus for enhanced generation of bioelectricity.

PubMed

Liu, Ting; Yu, Yang-Yang; Chen, Tao; Chen, Wei Ning

2017-03-01

In this study, a synthetic microbial consortium containing exoelectrogen Shewanella oneidensis MR-1 and riboflavin-producing strain, Bacillus subtilis RH33, was rationally designed and successfully constructed, enabling a stable, multiple cycles of microbial fuel cells (MFCs) operation for more than 500 h. The maximum power density of MFCs with this synthetic microbial consortium was 277.4 mW/m 2 , which was 4.9 times of that with MR-1 (56.9 mW/m 2 ) and 40.2 times of RH33 (6.9 mW/m 2 ), separately. At the same time, the Coulombic efficiency of the synthetic microbial consortium (5.6%) was higher than MR-1 (4.1%) and RH33 (2.3%). Regardless the high concentration of riboflavin produced by RH33, the power density of RH33 was rather low. The low bioelectricity generation can be ascribed to the low efficiency of RH33 in utilizing riboflavin for extracellular electron transfer (EET). In the synthetic microbial consortium of MR-1 and RH33, it was found that both mediated and direct electron transfer efficiencies were enhanced. By exchanging the anolyte of MR-1 and RH33, it was confirmed that the improved MFC performance with the synthetic microbial consortium was because MR-1 could efficiently utilize the high concentration of riboflavin produced by RH33. Biotechnol. Bioeng. 2017;114: 526-532. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont.

PubMed

Cai, Lin; Zhou, Guowei; Tian, Ren-Mao; Tong, Haoya; Zhang, Weipeng; Sun, Jin; Ding, Wei; Wong, Yue Him; Xie, James Y; Qiu, Jian-Wen; Liu, Sheng; Huang, Hui; Qian, Pei-Yuan

2017-08-24

Coral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of "Candidatus Prosthecochloris korallensis" was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows "Ca. P. korallensis" belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals "Ca. P. korallensis" has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests "Ca. P. korallensis" is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: "Ca. P. korallensis" might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide "Ca. P. korallensis" with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.

Microbial proliferation on gill structures of juvenile European lobster ( Homarus gammarus) during a moult cycle

NASA Astrophysics Data System (ADS)

Middlemiss, Karen L.; Urbina, Mauricio A.; Wilson, Rod W.

2015-12-01

The morphology of gill-cleaning structures is not well described in European lobster ( Homarus gammarus). Furthermore, the magnitude and time scale of microbial proliferation on gill structures is unknown to date. Scanning electron microscopy was used to investigate development of setae in zoea, megalopa and juvenile stages (I-V). Microbes were classified and quantified on gill structures throughout a moult cycle from megalopa (stage IV) to juvenile (stage V). Epipodial serrulate setae, consisting of a naked proximal setal shaft with the distal portion possessing scale-like outgrowths (setules), occur only after zoea stage III. After moulting to megalopa (stage IV), gill structures were completely clean and no microbes were visible on days 1 or 5 postmoult. Microbial proliferation was first evident on day 10 postmoult, with a significant 16-fold increase from day 10 to 15. Rod-shaped bacteria were initially predominant (by day 10); however, by day 15 the microbial community was dominated by cocci-shaped bacteria. This research provides new insights into the morphology of gill-grooming structures, the timing of their development, and the magnitude, timescale and characteristics of gill microbial proliferation during a moult cycle. To some degree, the exponential growth of epibionts on gills found during a moult cycle will likely impair respiratory (gas exchange) and ion regulatory function, yet further research is needed to evaluate the physiological effects of the exponential bacterial proliferation documented here.

An investigation of anaerobic methane oxidation by consortia of methanotrophic archaea and bacterial partners using nanoSIMS and process-based modeling

NASA Astrophysics Data System (ADS)

Shi, Y.; Kempes, C.; Chadwick, G.; McGlynn, S.; He, X.; Orphan, V. J.; Meile, C. D.

2016-02-01

The anaerobic oxidation of methane in marine sediments plays an important role in the global methane cycle. Mediated by a microbial consortium consisting of archaea and bacteria, it is estimated that almost 80% of all the methane that arises from marine sediments is oxidized anaerobically by this process (Reeburgh 2007, Chemical Reviews 107, 486-513). We used reactive transport modeling to compare and contrast potential mechanisms of methane oxidation. This included acetate, hydrogen, formate, and disulfide acting as intermediates that are exchanged between archaea and bacteria. Moreover, we investigated electron transport through nanowires, facilitating the electron exchange between the microbial partners. It was shown that reaction kinetics, transport intensities, and energetic considerations all could decisively impact the overall rate of methane consumption. Informed by observed microbial cell distribution, we applied the model to a range of spatial distribution patterns of archaea and bacteria. We found that a consortium with evenly distributed archaeal and bacterial cells has the potential to more efficiently oxidize methane, because the vicinity of bacteria and archaea counteracts the build up of products and therefore prevents the thermodynamic shutdown of microbial metabolism. Single cell stable isotope enrichment in archaeal-bacterial consortia observed by nanoSIMS revealed rather uniform levels of anabolic activity within consortia with different spatial distribution patterns. Comparison to model simulation illustrates that efficient exchange is necessary to reproduce such observations and prevent conditions that are energetically unfavorable for methane oxidation to take place. Model simulations indicate that a recently described mechanism of direct interspecies electron transport between the methanotrophic archaea and its bacterial partner through a conductive matrix (McGlynn et al. 2015, Nature, 10.1038/nature15512) is consistent with observations.

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

DOE PAGES

Kim, Young-Mo; Nowack, Shane; Olsen, Millie; ...

2015-04-17

Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptative and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number ofmore » predominant taxa inhabiting this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate) and fermentation (e.g. acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2) Synechococcus spp. produce CH4 via metabolism of phosphonates, and photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4) fluctuations in many metabolite pools (e.g. wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.« less

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Young-Mo; Nowack, Shane; Olsen, Millie

Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptative and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number ofmore » predominant taxa inhabiting this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate) and fermentation (e.g. acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2) Synechococcus spp. produce CH4 via metabolism of phosphonates, and photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4) fluctuations in many metabolite pools (e.g. wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.« less

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

PubMed Central

Kim, Young-Mo; Nowack, Shane; Olsen, Millie T.; Becraft, Eric D.; Wood, Jason M.; Thiel, Vera; Klapper, Isaac; Kühl, Michael; Fredrickson, James K.; Bryant, Donald A.; Ward, David M.; Metz, Thomas O.

2015-01-01

Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g., glycolate) and fermentation (e.g., acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gasses (e.g., H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and (4) fluctuations in many metabolite pools (e.g., wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches. PMID:25941514

Hydrodynamics of microbial filter feeding

PubMed Central

Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H.; Andersen, Anders

2017-01-01

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis, and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling. PMID:28808016

Hydrodynamics of microbial filter feeding.

PubMed

Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H; Kiørboe, Thomas; Andersen, Anders

2017-08-29

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis , and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling.

A microbial biogeochemistry network for soil carbon and nitrogen cycling and methane flux: model structure and application to Asia

NASA Astrophysics Data System (ADS)

Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.

2017-12-01

A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.

Effects of a simulated hurricane disturbance on forest floor microbial communities

Treesearch

Sharon A. Cantrell; Marirosa Molina; D. Jean Lodge; Francisco J. Rivera-Figueroa; Maria Ortiz; Albany A. Marchetti; Mike J. Cyterski; José R. Pérez-Jiménez

2014-01-01

Forest floor microbial communities play a critical role in the processes of decomposition and nutrient cycling. The impact of cultivation, contamination, fire, and land management on soil microbial communities have been studied but there are few studies of microbial responses to the effects of tropical storms. The Canopy Trimming Experiment was executed in the Luquillo...

Changes in Microbial Nitrogen Across a 100-Year Chronosequence of Upland Hardwood Forests

Treesearch

Travis W. Idol; Phillip E. Pope; Felix, Jr. Ponder

2002-01-01

Soil microorganisms mediate many of the major processes involved in soil N cycling. Also, they are strong competitors with plants for available soil N. Thus, changes in microbial N because of forest harvesting may have significant impacts on N availability and overall forest N cycling. A chronosequence of upland hardwood forest stands in southern Indiana, USA, ranging...

MICROBIAL ENZYME ACTIVITY FOR CHARACTERIZING NUTRIENT LOADING TO GREAT LAKES COASTAL WETLANDS

EPA Science Inventory

Energy and material flows in aquatic ecosystems are mediated by microbial carbon and nutrient cycling. Extracellular enzymes produced by the microbial community aid in the degradation of organic matter and the resultant acquisition of limiting nutrients. Organic carbon sequestrat...

Integrating Environmental Genomics and Biogeochemical Models: a Gene-centric Approach

NASA Astrophysics Data System (ADS)

Reed, D. C.; Algar, C. K.; Huber, J. A.; Dick, G.

2013-12-01

Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models that uses genomics data and provides predictions that are readily testable using cutting-edge molecular tools. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modelled to examine key questions about cryptic sulphur cycling and dinitrogen production pathways in OMZs. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

Influence of coral and algal exudates on microbially mediated reef metabolism.

PubMed

Haas, Andreas F; Nelson, Craig E; Rohwer, Forest; Wegley-Kelly, Linda; Quistad, Steven D; Carlson, Craig A; Leichter, James J; Hatay, Mark; Smith, Jennifer E

2013-01-01

Benthic primary producers in tropical reef ecosystems can alter biogeochemical cycling and microbial processes in the surrounding seawater. In order to quantify these influences, we measured rates of photosynthesis, respiration, and dissolved organic carbon (DOC) exudate release by the dominant benthic primary producers (calcifying and non-calcifying macroalgae, turf-algae and corals) on reefs of Mo'orea French Polynesia. Subsequently, we examined planktonic and benthic microbial community response to these dissolved exudates by measuring bacterial growth rates and oxygen and DOC fluxes in dark and daylight incubation experiments. All benthic primary producers exuded significant quantities of DOC (roughly 10% of their daily fixed carbon) into the surrounding water over a diurnal cycle. The microbial community responses were dependent upon the source of the exudates and whether the inoculum of microbes included planktonic or planktonic plus benthic communities. The planktonic and benthic microbial communities in the unamended control treatments exhibited opposing influences on DO concentration where respiration dominated in treatments comprised solely of plankton and autotrophy dominated in treatments with benthic plus plankon microbial communities. Coral exudates (and associated inorganic nutrients) caused a shift towards a net autotrophic microbial metabolism by increasing the net production of oxygen by the benthic and decreasing the net consumption of oxygen by the planktonic microbial community. In contrast, the addition of algal exudates decreased the net primary production by the benthic communities and increased the net consumption of oxygen by the planktonic microbial community thereby resulting in a shift towards net heterotrophic community metabolism. When scaled up to the reef habitat, exudate-induced effects on microbial respiration did not outweigh the high oxygen production rates of benthic algae, such that reef areas dominated with benthic primary producers were always estimated to be net autotrophic. However, estimates of microbial consumption of DOC at the reef scale surpassed the DOC exudation rates suggesting net consumption of DOC at the reef-scale. In situ mesocosm experiments using custom-made benthic chambers placed over different types of benthic communities exhibited identical trends to those found in incubation experiments. Here we provide the first comprehensive dataset examining direct primary producer-induced, and indirect microbially mediated alterations of elemental cycling in both benthic and planktonic reef environments over diurnal cycles. Our results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs.

Maximizing efficiency of rumen microbial protein production

PubMed Central

Hackmann, Timothy J.; Firkins, Jeffrey L.

2015-01-01

Rumen microbes produce cellular protein inefficiently partly because they do not direct all ATP toward growth. They direct some ATP toward maintenance functions, as long-recognized, but they also direct ATP toward reserve carbohydrate synthesis and energy spilling (futile cycles that dissipate heat). Rumen microbes expend ATP by vacillating between (1) accumulation of reserve carbohydrate after feeding (during carbohydrate excess) and (2) mobilization of that carbohydrate thereafter (during carbohydrate limitation). Protozoa account for most accumulation of reserve carbohydrate, and in competition experiments, protozoa accumulated nearly 35-fold more reserve carbohydrate than bacteria. Some pure cultures of bacteria spill energy, but only recently have mixed rumen communities been recognized as capable of the same. When these communities were dosed glucose in vitro, energy spilling could account for nearly 40% of heat production. We suspect that cycling of glycogen (a major reserve carbohydrate) is a major mechanism of spilling; such cycling has already been observed in single-species cultures of protozoa and bacteria. Interconversions of short-chain fatty acids (SCFA) may also expend ATP and depress efficiency of microbial protein production. These interconversions may involve extensive cycling of intermediates, such as cycling of acetate during butyrate production in certain butyrivibrios. We speculate this cycling may expend ATP directly or indirectly. By further quantifying the impact of reserve carbohydrate accumulation, energy spilling, and SCFA interconversions on growth efficiency, we can improve prediction of microbial protein production and guide efforts to improve efficiency of microbial protein production in the rumen. PMID:26029197

Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats.

PubMed

Klatt, Christian G; Bryant, Donald A; Ward, David M

2007-08-01

Stable carbon isotope signatures of diagnostic lipid biomarkers have suggested that Roseiflexus spp., the dominant filamentous anoxygenic phototrophic bacteria inhabiting microbial mats of alkaline siliceous hot springs, may be capable of fixing bicarbonate via the 3-hydroxypropionate pathway, which has been characterized in their distant relative, Chloroflexus aurantiacus. The genomes of three filamentous anoxygenic phototrophic Chloroflexi isolates (Roseiflexus sp. RS-1, Roseiflexus castenholzii and Chloroflexus aggregans), but not that of a non-photosynthetic Chloroflexi isolate (Herpetosiphon aurantiacus), were found to contain open reading frames that show a high degree of sequence similarity to genes encoding enzymes in the C. aurantiacus pathway. Metagenomic DNA sequences from the microbial mats of alkaline siliceous hot springs also contain homologues of these genes that are highly similar to genes in both Roseiflexus spp. and Chloroflexus spp. Thus, Roseiflexus spp. appear to have the genetic capacity for carbon dioxide reduction via the 3-hydroxypropionate pathway. This may contribute to heavier carbon isotopic signatures of the cell components of native Roseiflexus populations in mats compared with the signatures of cyanobacterial cell components, as a similar isotopic signature would be expected if Roseiflexus spp. were participating in photoheterotrophic uptake of cyanobacterial photosynthate produced by the reductive pentose phosphate cycle.

Microbial models with data-driven parameters predict stronger soil carbon responses to climate change.

PubMed

Hararuk, Oleksandra; Smith, Matthew J; Luo, Yiqi

2015-06-01

Long-term carbon (C) cycle feedbacks to climate depend on the future dynamics of soil organic carbon (SOC). Current models show low predictive accuracy at simulating contemporary SOC pools, which can be improved through parameter estimation. However, major uncertainty remains in global soil responses to climate change, particularly uncertainty in how the activity of soil microbial communities will respond. To date, the role of microbes in SOC dynamics has been implicitly described by decay rate constants in most conventional global carbon cycle models. Explicitly including microbial biomass dynamics into C cycle model formulations has shown potential to improve model predictive performance when assessed against global SOC databases. This study aimed to data-constrained parameters of two soil microbial models, evaluate the improvements in performance of those calibrated models in predicting contemporary carbon stocks, and compare the SOC responses to climate change and their uncertainties between microbial and conventional models. Microbial models with calibrated parameters explained 51% of variability in the observed total SOC, whereas a calibrated conventional model explained 41%. The microbial models, when forced with climate and soil carbon input predictions from the 5th Coupled Model Intercomparison Project (CMIP5), produced stronger soil C responses to 95 years of climate change than any of the 11 CMIP5 models. The calibrated microbial models predicted between 8% (2-pool model) and 11% (4-pool model) soil C losses compared with CMIP5 model projections which ranged from a 7% loss to a 22.6% gain. Lastly, we observed unrealistic oscillatory SOC dynamics in the 2-pool microbial model. The 4-pool model also produced oscillations, but they were less prominent and could be avoided, depending on the parameter values. © 2014 John Wiley & Sons Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Labonté, Jessica M.; Swan, Brandon K.; Poulos, Bonnie

Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus–host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. Furthermore, a combination of comparative genomics, metagenomic fragmentmore » recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus–host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically and geographically diverse single amplified genomes (SAGs) of marine bacteria and archaea. At least four phage–host interactions had the characteristics of late lytic infections, all of which were found in metabolically active cells. One virus had genetic potential for lysogeny. Our findings include first known viruses of Thaumarchaeota, Marinimicrobia, Verrucomicrobia and Gammaproteobacteria clusters SAR86 and SAR92. Viruses were also found in SAGs of Alphaproteobacteria and Bacteroidetes. A high fragment recruitment of viral metagenomic reads confirmed that most of the SAG-associated viruses are abundant in the ocean. This study demonstrates that single-cell genomics, in conjunction with sequence-based computational tools, enable in situ, cultivation-independent insights into host–virus interactions in complex microbial communities.« less

Modeling the survival responses of a multi-component biofilm to environmental stress

NASA Astrophysics Data System (ADS)

Carles Brangarí, Albert; Manzoni, Stefano; Sanchez-Vila, Xavier; Fernàndez-Garcia, Daniel

2017-04-01

Biofilms are consortia of microorganisms embedded in self-produced matrices of biopolymers. The survival of such communities depends on their capacity to improve the environmental conditions of their habitat by mitigating, or even benefitting from some adverse external factors. The mechanisms by which the microbial habitat is regulated remain mostly unknown. However, many studies have reported physiological responses to environmental stresses that include the release of extracellular polymeric substances (EPS) and the induction of a dormancy state. A sound understanding of these capacities is required to enhance the knowledge of the microbial dynamics in soils and its potential role in the carbon cycle, with significant implications for the degradation of contaminants and the emission of greenhouse gases, among others. We present a numerical analysis of the dynamics of soil microbes and their responses to environmental stresses. The conceptual model considers a multi-component heterotrophic biofilm made up of active cells, dormant cells, EPS, and extracellular enzymes. Biofilm distribution and properties are defined at the pore-scale and used to determine nutrient availability and water saturation via feedbacks of biofilm on soil hydraulic properties. The pore space micro-habitat is modeled as a simplified pore-network of cylindrical tubes in which biofilms proliferate. Microbial compartments and most of the carbon fluxes are defined at the bulk level. Microbial processes include the synthesis, decay and detachment of biomass, the activation/deactivation of cells, and the release and reutilization of EPS. Results suggest that the release of EPS and the capacity to enter a dormant state offer clear evolutionary advantages in scenarios characterized by environmental stress. On the contrary, when the conditions are favorable, the diversion of carbon into the production of the aforementioned survival mechanisms does not confer any additional benefit and the population of active cells decline. The proposed model (including complex relations between active biomass and biofilm) has been proved useful to capture the most relevant processes involved in biofilm proliferation and its adaptation to environmental conditions. These aspects are largely neglected in biogeochemical models, but could be relevant in soils where strong feedbacks of microbial activity on hydraulic properties emerge.

Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient

USGS Publications Warehouse

Chapman, Eric; Cadillo-Quiroz, Hinsby; Childers, Daniel L.; Turetsky, Merritt R.; Waldrop, Mark P.

2017-01-01

Climate change is modifying global biogeochemical cycles. Microbial communities play an integral role in soil biogeochemical cycles; knowledge about microbial composition helps provide a mechanistic understanding of these ecosystem-level phenomena. Next generation sequencing approaches were used to investigate changes in microbial functional groups during ecosystem development, in response to climate change, in northern boreal wetlands. A gradient of wetlands that developed following permafrost degradation was used to characterize changes in the soil microbial communities that mediate C cycling: a bog representing an “undisturbed” system with intact permafrost, and a younger bog and an older bog that formed following the disturbance of permafrost thaw. Reference 16S rRNA databases and several diversity indices were used to assess structural differences among these communities, to assess relationships between soil microbial community composition and various environmental variables including redox potential and pH. Rates of potential CO2 and CH4 gas production were quantified to correlate sequence data with gas flux. The abundance of organic C degraders was highest in the youngest bog, suggesting higher rates of microbial processes, including potential CH4 production. In addition, alpha diversity was also highest in the youngest bog, which seemed to be related to a more neutral pH and a lower redox potential. These results could potentially be driven by increased niche differentiation in anaerobic soils. These results suggest that ecosystem structure, which was largely driven by changes in edaphic and plant community characteristics between the “undisturbed” permafrost bog and the two bogs formed following permafrost thaw, strongly influenced microbial function.

Sub-soil microbial activity under rotational cotton crops in Australia

NASA Astrophysics Data System (ADS)

Polain, Katherine; Knox, Oliver; Wilson, Brian; Pereg, Lily

2016-04-01

Soil microbial communities contribute significantly to soil organic matter formation, stabilisation and destabilisation, through nutrient cycling and biodegradation. The majority of soil microbial research examines the processes occurring in the top 0 cm to 30 cm of the soil, where organic nutrients are easily accessible. In soils such as Vertosols, the high clay content causes swelling and cracking. When soil cracking is coupled with rain or an irrigation event, a flush of organic nutrients can move down the soil profile, becoming available for subsoil microbial community use and potentially making a significant contribution to nutrient cycling and biodegradation in soils. At present, the mechanisms and rates of soil nutrient turnover (such as carbon and nitrogen) at depth under cotton rotations are mostly speculative and the process-response relationships remain unclear, although they are undoubtedly underpinned by microbial activity. Our research aims to determine the contribution and role of soil microbiota to the accumulation, cycling and mineralisation of carbon and nitrogen through the whole root profile under continuous cotton (Gossypium hirsutum) and cotton-maize rotations in regional New South Wales, Australia. Through seasonal work, we have established both baseline and potential microbial activity rates from 0 cm to 100 cm down the Vertosol profile, using respiration and colourimetric methods. Further whole soil profile analyses will include determination of microbial biomass and isotopic carbon signatures using phospholipid fatty acid (PLFA) methodology, identification of microbial communities (sequencing) and novel experiments to investigate potential rates of nitrogen mineralisation and quantification of associated genes. Our preliminary observations and the hypotheses tested in this three-year study will be presented.

Mixed cellulose ester filter as a separator for air-diffusion cathode microbial fuel cells.

PubMed

Wang, Zejie; Lim, Bongsu

2017-04-01

Separator is important to prevent bio-contamination of the catalyst layer of air-diffusion cathode microbial fuel cells (MFCs). Mixed cellulose ester filter (MCEF) was examined as a separator for an air-cathode MFC in the present study. The MCEF-MFC produced a maximum power density of 780.7 ± 18.7 mW/m 2 , which was comparable to 770.9 ± 35.9 mW/m 2 of MFC with Nafion membrane (NFM) as a separator. Long-term examination demonstrated a more stable performance of the MCEF-MFC than NFM-MFC. After 25 cycles, the maximum voltage of the MCEF-MFC decreased by only 1.3% from 425.1 ± 4.3 mV (initial 5 cycles) to 419.5 ± 2.3 mV (last 5 cycles). However, it was decreased by 9.1% from 424.8 ± 5.7 to 386 ± 2.5 mV for the NFM-MFC. The coulombic efficiency (CE) of the MCEF-MFC did not change (from 3.11 ± 0.09% to 3.13 ± 0.02%), while it decreased by 9.12% from 3.18 ± 0.04% to 2.89 ± 0.02% for the NFM-MFC. The MCEF separator was with less biofouling than the NFM separator over 60 days' operation, which might be the reason for the more table long-term performance of the MCEF-MFC. The results demonstrated that MCEF was feasible as a separator to set up good-performing and cost-effective air-diffusion cathode MFC.

Electricity generation of single-chamber microbial fuel cells at low temperatures.

PubMed

Cheng, Shaoan; Xing, Defeng; Logan, Bruce E

2011-01-15

Practical applications of microbial fuel cells (MFCs) for wastewater treatment will require operation of these systems over a wide range of wastewater temperatures. MFCs at room or higher temperatures (20-35°C) are relatively well studied compared those at lower temperatures. MFC performance was examined here over a temperature range of 4-30°C in terms of startup time needed for reproducible power cycles, and performance. MFCs initially operated at 15°C or higher all attained a reproducible cycles of power generation, but the startup time to reach stable operation increased from 50 h at 30°C to 210 h at 15°C. At temperatures below 15°C, MFCs did not produce appreciable power even after one month of operation. If an MFC was first started up at temperature of 30°C, however, reproducible cycles of power generation could then be achieved at even the two lowest temperatures of 4°C and 10°C. Power production increased linearly with temperature at a rate of 33±4 mW °C(-1), from 425±2 mW m(-2) at 4°C to 1260±10 mW m(-2) at 30°C. Coulombic efficiency decreased by 45% over this same temperature range, or from CE=31% at 4°C to CE=17% at 30°C. These results demonstrate that MFCs can effectively be operated over a wide range of temperatures, but our findings have important implications for the startup of larger scale reactors where low wastewater temperatures could delay or prevent adequate startup of the system. Copyright © 2010 Elsevier B.V. All rights reserved.

Where's the P in Plankton? Phosphorus Allocation to DNA across Diverse Marine Picoplankton

NASA Astrophysics Data System (ADS)

Raney, S. E.; Popendorf, K.; Duhamel, S.

2016-02-01

Phosphorus (P) is a critical nutrient for survival, particularly in oligotrophic environments such as the Sargasso Sea. Microbes require phosphorus to build and maintain cellular components, including DNA, RNA, and lipids. We expect variation across microbes in the fraction of cellular P allocated to each of these components. We hypothesized that a high but variable percentage of cellular P will be allocated towards DNA. Studying cellular P allocation can offer insight into the role of different microbes in phosphorus cycling in low-P regions like the Sargasso Sea. To assess allocation of P to DNA, we first tested the efficiency of different DNA extraction methods and then analyzed the amount of extracted DNA from different microbial groups. We performed DNA extractions using four different extraction kits and determined Promega Reliaprep Blood gDNA Miniprep System to be the most efficient. We extracted DNA from cultured picoplankton which are representative of the most abundant species in the Sargasso Sea: Synechococcus (WH8102), Prochlorococcus (MED4 and MIT9301), and heterotrophic bacteria (HTCC2516 and HTCC2601). We found that the percentage of P allocated towards DNA varies across microbial species and across strains within the same genera. Additionally, we estimated the relative number of copies of the genome per cell, and found that more copies of the genome per cell, not necessarily a larger genome size, may correlate with allocating a larger percentage of cellular P towards DNA. By understanding how phosphorus cycling works on the molecular level in different species of picoplankton, we can develop a greater understanding of the role of these picoplankton in phosphorus cycling as a whole in the Sargasso Sea.

Embedded biofilm, a new biofilm model based on the embedded growth of bacteria.

PubMed

Jung, Yong-Gyun; Choi, Jungil; Kim, Soo-Kyoung; Lee, Joon-Hee; Kwon, Sunghoon

2015-01-01

A variety of systems have been developed to study biofilm formation. However, most systems are based on the surface-attached growth of microbes under shear stress. In this study, we designed a microfluidic channel device, called a microfluidic agarose channel (MAC), and found that microbial cells in the MAC system formed an embedded cell aggregative structure (ECAS). ECASs were generated from the embedded growth of bacterial cells in an agarose matrix and better mimicked the clinical environment of biofilms formed within mucus or host tissue under shear-free conditions. ECASs were developed with the production of extracellular polymeric substances (EPS), the most important feature of biofilms, and eventually burst to release planktonic cells, which resembles the full developmental cycle of biofilms. Chemical and genetic effects have also confirmed that ECASs are a type of biofilm. Unlike the conventional biofilms formed in the flow cell model system, this embedded-type biofilm completes the developmental cycle in only 9 to 12 h and can easily be observed with ordinary microscopes. We suggest that ECASs are a type of biofilm and that the MAC is a system for observing biofilm formation. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Dietary requirements of seaweed flies ( Coelopa frigida)

NASA Astrophysics Data System (ADS)

Cullen, Sally J.; Young, Alison M.; Day, Thomas H.

1987-05-01

The seaweed fly, Coelopa frigida (Fabricius), is mostly found in piles of decomposing seaweed deposited on the seashore which form its only breeding sites. It is shown that C. frigida can complete its life cycle in a wide variety of marine algae, and that the larvae are unable to survive without some, as yet unidentified, consituent of seaweed. The larvae also have a requirement for a microbial gut flora which probably derives from the bacterial flora naturally associated with algae growing in the sea. After deposition of the seaweed on the shore, the bacterial population increases enormously, and is ingested by the feeding Coelopa larvae. The dietary requirement for bacteria can be satisfied by a variety of pure bacterial cultures of marine origin, and also by pure cultures of Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae. It is suggested that the microbial cells are being used by the larvae as their principal source of energy. The bacterial populations naturally found on stranded seaweed are grazed by the feeding larvae. It is the combined activities of microbial and insect populations that result in rapid decomposition of the seaweed. The ecological relationships between marine algae, the microbial flora, and dipteran larvae are discussed.

Analysis of Particulate and Dissolved Metabolite Pools at Station ALOHA

NASA Astrophysics Data System (ADS)

Boysen, A.; Carlson, L.; Hmelo, L.; Ingalls, A. E.

2016-02-01

Metabolomic studies focus on identifying and quantifying the small organic molecules that are the currency by which an organism lives and dies. Metabolite profiles of microorganisms have the potential to elucidate mechanisms of chemically mediated interactions that influence the success of microbial groups living in a complex environment. However, the chemical diversity of metabolites makes resolving a wide range of compounds analytically challenging. As such, metabolomics has lagged behind other genomic analyses. Here we conduct targeted analysis of over 200 primary and secondary metabolites present in the intracellular and extracellular metabolite pools at Station ALOHA using both reverse phase and hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry. We selected the metabolites in our method due to their known importance in primary metabolism, secondary metabolism, and interactions between marine microorganisms such as nutrient exchange, growth promotion, and cell signaling. Through these analyses we obtain a snapshot of microbial community status that, blended with other forms of genomic data, can further our understanding of microbial dynamics. We hypothesize that monitoring a large suite of important metabolites across environmental gradients and diurnal cycles can elucidate factors controlling the distribution and activity of important microbial groups.

In Situ Analysis of a Silver Nanoparticle-Precipitating Shewanella Biofilm by Surface Enhanced Confocal Raman Microscopy

PubMed Central

Schkolnik, Gal; Schmidt, Matthias; Mazza, Marco G.; Harnisch, Falk; Musat, Niculina

2015-01-01

Shewanella oneidensis MR-1 is an electroactive bacterium, capable of reducing extracellular insoluble electron acceptors, making it important for both nutrient cycling in nature and microbial electrochemical technologies, such as microbial fuel cells and microbial electrosynthesis. When allowed to anaerobically colonize an Ag/AgCl solid interface, S. oneidensis has precipitated silver nanoparticles (AgNp), thus providing the means for a surface enhanced confocal Raman microscopy (SECRaM) investigation of its biofilm. The result is the in-situ chemical mapping of the biofilm as it developed over time, where the distribution of cytochromes, reduced and oxidized flavins, polysaccharides and phosphate in the undisturbed biofilm is monitored. Utilizing AgNp bio-produced by the bacteria colonizing the Ag/AgCl interface, we could perform SECRaM while avoiding the use of a patterned or roughened support or the introduction of noble metal salts and reducing agents. This new method will allow a spatially and temporally resolved chemical investigation not only of Shewanella biofilms at an insoluble electron acceptor, but also of other noble metal nanoparticle-precipitating bacteria in laboratory cultures or in complex microbial communities in their natural habitats. PMID:26709923

Dynamic monitoring of horizontal gene transfer in soil

NASA Astrophysics Data System (ADS)

Cheng, H. Y.; Masiello, C. A.; Silberg, J. J.; Bennett, G. N.

2015-12-01

Soil microbial gene expression underlies microbial behaviors (phenotypes) central to many aspects of C, N, and H2O cycling. However, continuous monitoring of microbial gene expression in soils is challenging because genetically-encoded reporter proteins widely used in the lab are difficult to deploy in soil matrices: for example, green fluorescent protein cannot be easily visualized in soils, even in the lab. To address this problem we have developed a reporter protein that releases small volatile gases. Here, we applied this gas reporter in a proof-of-concept soil experiment, monitoring horizontal gene transfer, a microbial activity that alters microbial genotypes and phenotypes. Horizontal gene transfer is central to bacterial evolution and adaptation and is relevant to problems such as the spread of antibiotic resistance, increasing metal tolerance in superfund sites, and bioremediation capability of bacterial consortia. This process is likely to be impacted by a number of matrix properties not well-represented in the petri dish, such as microscale variations in water, nutrients, and O2, making petri-dish experiments a poor proxy for environmental processes. We built a conjugation system using synthetic biology to demonstrate the use of gas-reporting biosensors in safe, lab-based biogeochemistry experiments, and here we report the use of these sensors to monitor horizontal gene transfer in soils. Our system is based on the F-plasmid conjugation in Escherichia coli. We have found that the gas signal reports on the number of cells that acquire F-plasmids (transconjugants) in a loamy Alfisol collected from Kellogg Biological Station. We will report how a gas signal generated by transconjugants varies with the number of F-plasmid donor and acceptor cells seeded in a soil, soil moisture, and soil O2 levels.

Flow-through SIP - A novel stable isotope probing approach limiting cross-feeding

NASA Astrophysics Data System (ADS)

Mooshammer, Maria; Kitzinger, Katharina; Schintlmeister, Arno; Kjedal, Henrik; Nielsen, Jeppe Lund; Nielsen, Per; Wagner, Michael

2017-04-01

Stable isotope probing (SIP) is a widely applied tool to link specific microbial populations to metabolic processes in the environment without the prerequisite of cultivation, which has greatly advanced our understanding of the role of microorganisms in biogeochemical cycling. SIP relies on tracing specific isotopically labeled substrates (e.g., 13C, 15N, 18O) into cellular biomarkers, such as DNA, RNA or phospholipid fatty acids, and is considered to be a robust technique to identify microbial populations that assimilate the labeled substrate. However, cross-feeding can occur when labeled metabolites are released from a primary consumer and then used by other microorganisms. This leads to erroneous identification of organisms that are not directly responsible for the process of interest, but are rather connected to primary consumers via a microbial food web. Here, we introduce a new approach that has the potential to eliminate the effect of cross-feeding in SIP studies and can thus also be used to distinguish primary consumers from other members of microbial food webs. In this approach, a monolayer of microbial cells are placed on a filter membrane, and labeled substrates are supplied by a continuous flow. By means of flow-through, labeled metabolites and degradation products are constantly removed, preventing secondary consumption of the substrate. We present results from a proof-of-concept experiment using nitrifiers from activated sludge as model system, in which we used fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes for identification of nitrifiers in combination with nanoscale secondary ion mass spectrometry (NanoSIMS) for visualization of isotope incorporation at the single-cell level. Our results show that flow-through SIP is a promising approach to significantly reduce cross-feeding and secondary substrate consumption in SIP experiments.

Soil mineral assemblage influences on microbial communities and carbon cycling under fresh organic matter input

NASA Astrophysics Data System (ADS)

Finley, B. K.; Schwartz, E.; Koch, B.; Dijkstra, P.; Hungate, B. A.

2017-12-01

The interactions between soil mineral assemblages and microbial communities are important drivers of soil organic carbon (SOC) cycling and storage, although the mechanisms driving these interactions remain unclear. There is increasing evidence supporting the importance of associations with poorly crystalline, short-range order (SRO) minerals in protection of SOC from microbial utilization. However, how the microbial processing of SRO-associated SOC may be influenced by fresh organic matter inputs (priming) remains poorly understood. The influence on SRO minerals on soil microbial community dynamics is uncertain as well. Therefore, we conducted a priming incubation by adding either a simulated root exudate mixture or conifer needle litter to three soils from a mixed-conifer ecosystem. The parent material of the soils were andesite, basalt, and granite and decreased in SRO mineral content, respectively. We also conducted a parallel quantitative stable isotope probing incubation by adding 18O-labelled water to the soils to isotopically label microbial DNA in situ. This allowed us to characterize and identify the active bacterial and archaeal community and taxon-specific growth under fresh organic matter input. While the granite soil (lowest SRO content), had the largest total mineralization, the least priming occurred. The andesite and basalt soils (greater SRO content) had lower total respiration, but greater priming. Across all treatments, the granite soil, while having the lowest species richness of the entire community (249 taxa, both active and inactive), had a larger active community (90%) in response to new SOC input. The andesite and basalt soils, while having greater total species richness of the entire community at 333 and 325 taxa, respectively, had fewer active taxa in response to new C compared to the granite soil (30% and 49% taxa, respectively). These findings suggest that the soil mineral assemblage is an important driver on SOC cycling under fresh organic matter inputs, as well as on the activity and diversity of the microbial community. Often, microbial diversity is associated with function. Our results suggest that the soil environment, in this case SRO mineral content, may be more important on SOC cycling and storage than microbial diversity alone.

The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Methe, Barbara; Lipton, Mary; Mahadevan, Krishna

Microbes exist in communities in the environment where they are fundamental drivers of global carbon, nutrient and metal cycles. In subsurface environments, they possess significant metabolic potential to affect these global cycles including the transformation of radionuclides. This study examined the influence of microbial communities in sediment zones undergoing biogeochemical cycling of carbon, nutrients and metals including natural attenuation of uranium. This study examined the relationship of both the microbiota (taxonomy) and their metabolic capacity (function) in driving carbon, nutrient and metal cycles including uranium reduction at the Department of Energy (DOE) Rifle Integrated Field Research Challenge (RIFRC). Objectives ofmore » this project were: 1) to apply systems-level biology through application of ‘metaomics’ approaches (collective analyses of whole microbial community DNA, RNA and protein) to the study of microbial environmental processes and their relationship to C, N and metals including the influence of microbial communities on uranium contaminant mobility in subsurface settings undergoing natural attenuation, 2) improve methodologies for data generation using metaomics (collectively metagenomics, metatranscriptomics and proteomics) technologies and analysis and interpretation of that data and 3) use the data generated from these studies towards microbial community-scale metabolic modeling. The strategy for examining these subsurface microbial communities was to generate sequence reads from microbial community DNA (metagenomics or whole genome shotgun sequencing (WGS)) and RNA (metatranscriptomcs or RNAseq) and protein information using proteomics. Results were analyzed independently and through computational modeling. Overall, the community model generated information on the microbial community structure that was observed using metaomic approaches at RIFRC sites and thus provides an important framework for continued community modeling development. The model as created is capable of predicting the response of the community structure in changing environments such as anoxic/oxic conditions or limitations by carbon or nutrients. The ability to more accurately model these responses is critical to understanding carbon and energy flows in an ecosystem is critical towards improving our ability to make predictions that can be used to design more efficient remediation and management strategies, and better understand the implications of environmental perturbations on these ecosystems.« less

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe.

PubMed

Delgado-Baquerizo, Manuel; Eldridge, David J; Ochoa, Victoria; Gozalo, Beatriz; Singh, Brajesh K; Maestre, Fernando T

2017-10-01

The relationship between soil microbial communities and the resistance of multiple ecosystem functions linked to C, N and P cycling (multifunctionality resistance) to global change has never been assessed globally in natural ecosystems. We collected soils from 59 dryland ecosystems worldwide to investigate the importance of microbial communities as predictor of multifunctionality resistance to climate change and nitrogen fertilisation. Multifunctionality had a lower resistance to wetting-drying cycles than to warming or N deposition. Multifunctionality resistance was regulated by changes in microbial composition (relative abundance of phylotypes) but not by richness, total abundance of fungi and bacteria or the fungal: bacterial ratio. Our results suggest that positive effects of particular microbial taxa on multifunctionality resistance could potentially be controlled by altering soil pH. Together, our work demonstrates strong links between microbial community composition and multifunctionality resistance in dryland soils from six continents, and provides insights into the importance of microbial community composition for buffering effects of global change in drylands worldwide. © 2017 John Wiley & Sons Ltd/CNRS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony

Modern microbial mats are potential analogues of some of Earth’s earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic nextgeneration sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marinemore » mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.« less

Microbial Community Structure in Lake and Wetland Sediments from a High Arctic Polar Desert Revealed by Targeted Transcriptomics

PubMed Central

Stoeva, Magdalena K.; Aris-Brosou, Stéphane; Chételat, John; Hintelmann, Holger; Pelletier, Philip; Poulain, Alexandre J.

2014-01-01

While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake. PMID:24594936

Engineering biological systems using automated biofoundries

PubMed Central

Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, Huimin

2017-01-01

Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges. PMID:28602523

Analysis of organic compounds' degradation and electricity generation in anaerobic fluidized bed microbial fuel cell for coking wastewater treatment.

PubMed

Liu, Xinmin; Wu, Jianjun; Guo, Qingjie

2017-12-01

A single-chambered packing-type anaerobic fluidized microbial fuel cell (AFBMFC) with coking wastewater (CWW) as fuel was built to treat CWW, which not only has high treating efficiency, but also can convert organic matter in wastewater into electricity. AFBMFC was constructed by using anaerobic sludge that was domesticated as inoculation sludge, which was used to biochemically treat CWW. The organic compounds in CWW were extracted by liquid-liquid extraction step by step every day. The extraction phase was concentrated by a rotary evaporator and a nitrogen sweeping device and was analyzed by GC-MS. And the electricity-generation performances of AFBMFC were investigated. The results show that the composition of CWW was complicated, which mainly contains hydrocarbons, phenols, nitrogenous organic compounds, alcohols and aldehydes, esters and acids and so on. After a cycle of anaerobic biochemical treatment, the content of organic compounds in the effluent decreased significantly. After the treatment of AFBMFC, 99.9% phenols, 98.4% alcohol and aldehydes and 95.3% nitrogenous compounds were biodegraded. In the effluent, some new compounds (such as tricosane and dibutyl phthalate) were produced. The chemical oxygen demand (COD) of CWW decreased from 3372 to 559 mg/L in the closed-circuit microbial fuel cell, and the COD removal was 83.4 ± 1.0%. The maximum power density of AFBMFC was 2.13 ± 0.01 mW m -2 .

Strong Effects of a Shelfbreak Jet on Microbial Enzyme Activities

NASA Astrophysics Data System (ADS)

Hoarfrost, A.; Balmonte, J. P.; Ziervogel, K.; Ghobrial, S.; Gawarkiewicz, G.; Arnosti, C.

2016-02-01

The activities of extracellular enzymes are critical in initiating microbial cycling of organic carbon, yet the dynamics of heterotrophic enzyme activities in marine environments are still poorly understood. Variations at a given site in rates of activity and the spectrum of organic substrates hydrolyzed may depend upon environmental context. We measured the extracellular enzymatic hydrolysis of 13 high- and low-molecular-weight organic substrates in surface and bottom waters along a closely spaced 4-station transect at 71 W on the North Atlantic continental shelf, in the vicinity of the shelfbreak front. This transect intersects a robust upwelling cell that typically shows high biologic productivity, and is locatable by changes in T/S profiles and chl a concentrations along sharp spatial gradients. At the time of sampling, cold pool waters over the continental shelf were relatively cold, 3.5 Deg. C, compared to 12 Deg. C over the upper continental slope. Satellite thermal imagery indicated that shelf water extended offshore and interacted with a large crest of the Gulf Stream. The surface and bottom waters associated with the upwelling jet were characterized by enzyme activities a factor of 20 more rapid than closer inshore waters, and surface water chl a concentrations that were two to three times higher than the inshore waters. The spectrum of enzyme activities also differed markedly between surface and bottom waters both within the jet and at near-shore stations. Microbial extracellular enzymatic activities were strongly influenced by differences in their environmental context along the continental slope and shelfbreak front. Constraining the factors controlling heterotrophic activity across the diverse marine environment is an important step in understanding microbial controls on carbon cycling.

Towards Biogeochemical Modeling of Anaerobic Oxidation of Methane: Characterization of Microbial Communities in Methane-bearing North American Continental Margin Sediments

NASA Astrophysics Data System (ADS)

Graw, M. F.; Solomon, E. A.; Chrisler, W.; Krause, S.; Treude, T.; Ruppel, C. D.; Pohlman, J.; Colwell, F. S.

2015-12-01

Methane advecting through continental margin sediments may enter the water column and potentially contribute to ocean acidification and increase atmospheric methane concentrations. Anaerobic oxidation of methane (AOM), mediated by syntrophic consortia of anaerobic methanotrophic archaea and sulfate-reducing bacteria (ANME-SRB), consumes nearly all dissolved methane in methane-bearing sediments before it reaches the sediment-water interface. Despite the significant role ANME-SRB play in carbon cycling, our knowledge of these organisms and their surrounding microbial communities is limited. Our objective is to develop a metabolic model of ANME-SRB within methane-bearing sediments and to couple this to a geochemical reaction-transport model for these margins. As a first step towards this goal, we undertook fluorescent microscopic imaging, 16S rRNA gene deep-sequencing, and shotgun metagenomic sequencing of sediments from the US Pacific (Washington) and northern Atlantic margins where ANME-SRB are present. A successful Illumina MiSeq sequencing run yielded 106,257 bacterial and 857,834 archaeal 16S rRNA gene sequences from 12 communities from the Washington Margin using both universal prokaryotic and archaeal-specific primer sets. Fluorescent microscopy confirmed the presence of cells of the ANME-2c lineage in the sequenced communities. Microbial community characterization was coupled with measurements of sediment physical and geochemical properties and, for samples from the US Atlantic margin, 14C-based measurements of AOM rates and 35S-based measurements of sulfate reduction rates. These findings have the potential to increase understanding of ANME-SRB, their surrounding microbial communities, and their role in carbon cycling within continental margins. In addition, they pave the way for future efforts at developing a metabolic model of ANME-SRB and coupling it to geochemical models of the US Washington and Atlantic margins.

Targeting Unknowns Just Underfoot: Microbial Ecology and Community Genomics of C Cycling in Soil Informed and Enabled with DNA-SIP

NASA Astrophysics Data System (ADS)

Pepe-Ranney, C. P.; Campbell, A.; Buckley, D. H.

2015-12-01

Microorganisms drive biogeochemical cycles and because soil is a large global carbon (C) reservoir (soil contains more C than plants and the atmosphere combined), soil microorganisms are important players in the global C-cycle. Frustratingly, however, many soil microorganisms resist cultivation and soil communities are astoundingly complex. This makes soil microbiology difficult to study and without a solid understanding of soil microbial ecology, models of soil C feedbacks to climate change are under-informed. Stable isotope probing (SIP) is a useful approach for establishing identity-function connections in microbial communities but has been challenging to employ in soil due to the inadequate resolution of microbial community fingerprinting techniques. High throughput DNA sequencing improves SIP resolving power transforming it into a powerful tool for studying the soil C cycle. We conducted a DNA-SIP experiment to track flow of xylose-C, a labile component of plant biomass, and cellulose-C, the most abundant global biopolymer, through a soil microbial community. We could track 13C into microbial DNA even when added 13C amounted to less than 5% of native C and found Spartobacteria, Chloroflexi, and Planctomycetes taxa were among those that assimilated 13C cellulose. These lineages are cosmopolitan in soil but little is known of their ecophysiology. By profiling SSU rRNA genes across entire DNA-SIP density gradients, we assessed relative DNA atom % 13C per taxon in 13C treatments and found cellulose degraders exhibited signal consistent with a specialist lifestyle with respect to C preference. Further, DNA-SIP enriches DNA of targeted microorganisms (Verrucomicrobia cellulose degraders were enriched by nearly two orders of magnitude) and this enriched DNA can serve as template for community genomics. We produced draft genomes from soil cellulose degraders including microorganisms belonging to Verrucomicrobia, Chloroflexi, and Planctomycetes from SIP enriched DNA. This study demonstrates how DNA-SIP can be used to study microbial ecology and target guilds of microorganisms for community genomics. Improving our fundamental understanding of ecophysiology relevant to terrestrial C cycling is essential for tuning global C models.

Nutrient cycling Microbial Ecosystems: Assembly, Function and Targeted Design

DTIC Science & Technology

2017-05-05

different chemical transformations, converting potentially harmful chemicals via a series of intermediates, to harmless waste products. This shuttling of...Report: Nutrient-cycling Microbial Ecosystems: Assembly, Function and Targeted Design The views, opinions and/or findings contained in this report...are those of the author(s) and should not contrued as an official Department of the Army position, policy or decision, unless so designated by other

Novel Barite Chimneys at the Loki's Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems.

PubMed

Steen, Ida H; Dahle, Håkon; Stokke, Runar; Roalkvam, Irene; Daae, Frida-Lise; Rapp, Hans Tore; Pedersen, Rolf B; Thorseth, Ingunn H

2015-01-01

In order to fully understand the cycling of elements in hydrothermal systems it is critical to understand intra-field variations in geochemical and microbiological processes in both focused, high-temperature and diffuse, low-temperature areas. To reveal important causes and effects of this variation, we performed an extensive chemical and microbiological characterization of a low-temperature venting area in the Loki's Castle Vent Field (LCVF). This area, located at the flank of the large sulfide mound, is characterized by numerous chimney-like barite (BaSO4) structures (≤ 1 m high) covered with white cotton-like microbial mats. Results from geochemical analyses, microscopy (FISH, SEM), 16S rRNA gene amplicon-sequencing and metatranscriptomics were compared to results from previous analyses of biofilms growing on black smoker chimneys at LCVF. Based on our results, we constructed a conceptual model involving the geochemistry and microbiology in the LCVF. The model suggests that CH4 and H2S are important electron donors for microorganisms in both high-temperature and low-temperature areas, whereas the utilization of H2 seems restricted to high-temperature areas. This further implies that sub-seafloor processes can affect energy-landscapes, elemental cycling, and the metabolic activity of primary producers on the seafloor. In the cotton-like microbial mats on top of the active barite chimneys, a unique network of single cells of Epsilonproteobacteria interconnected by threads of extracellular polymeric substances (EPS) was seen, differing significantly from the long filamentous Sulfurovum filaments observed in biofilms on the black smokers. This network also induced nucleation of barite crystals and is suggested to play an essential role in the formation of the microbial mats and the chimneys. Furthermore, it illustrates variations in how different genera of Epsilonproteobacteria colonize and position cells in different vent fluid mixing zones within a vent field. This may be related to niche-specific physical characteristics. Altogether, the model provides a reference for future studies and illustrates the importance of systematic comparative studies of spatially closely connected niches in order to fully understand the geomicrobiology of hydrothermal systems.

Bacteria and fluorescent organic matter: processing and production.

NASA Astrophysics Data System (ADS)

Fox, B. G.; Thorn, R. M. S.; Reynolds, D. M.

2017-12-01

There is a need for a greater understanding of the importance of aquatic organic matter (OM) within global biogeochemical cycling. This need has prompted characterisation of OM using fluorescence spectroscopy. The origin, transformation and fate of fluorescent organic matter (FOM) is not fully understood within freshwater systems. This work demonstrates the importance of microbial processing in the creation and transformation of FOM, highlighting the dynamics of microbial-FOM interactions, using a model system. The FOM signature of different bacterial species common to surface freshwaters were analysed using a non-fluorescent media; Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa. By undertaking bacterial growth curves, alongside fluorescence spectroscopy, we have been able to determine FOM development in relation to population growth. Within this, we have identified that FOM peaks are associated with different species and driven by bacterial processes, such as cell multiplication or as metabolic by-products. The intracellular and extracellular fluorescence signature of each species has also been analysed to better understand how the microbial community structure may impact the FOM signal in aquatic systems. For example, Peak T develops within the growth curves of all the cultured species and has been identified as both intracellular and extracellular FOM. Whilst Peak T has been termed `microbially-derived' previously, other fluorescence peaks associated with terrestrial high molecular weight compounds, e.g. Peak C, have also been shown to be produced by bacteria throughout growth stages. Additionally, the notion that cell lysis is responsible for the presence of larger FOM compounds was also explored. Our work highlights the capacity of bacteria to not only utilise and process OM but to actively be a source of both labile and recalcitrant OM in situ. The bacteria fluorescence signatures seen are complex with comparable fluorescence peaks to those seen in real-world freshwaters. Interestingly, this includes a range of FOM currently considered high molecular weight compounds attributed to terrestrial origin. The role of bacterial processing in aquatic systems may prove to have a wider impact on DOM transformation along the hydrological continuum and global biogeochemical cycling.

Exploring frontiers of the deep biosphere through scientific ocean drilling

NASA Astrophysics Data System (ADS)

Inagaki, F.; D'Hondt, S.; Hinrichs, K. U.

2015-12-01

Since the first deep biosphere-dedicated Ocean Drilling Program (ODP) Leg 201 using the US drill ship JOIDES Resolution in 2002, scientific ocean drilling has offered unique opportunities to expand our knowledge of the nature and extent of the deep biosphere. The latest estimate of the global subseafloor microbial biomass is ~1029cells, accounting for 4 Gt of carbon and ~1% of the Earth's total living biomass. The subseafloor microbial communities are evolutionarily diverse and their metabolic rates are extraordinarily slow. Nevertheless, accumulating activity most likely plays a significant role in elemental cycles over geological time. In 2010, during Integrated Ocean Drilling Program (IODP) Expedition 329, the JOIDES Resolutionexplored the deep biosphere in the open-ocean South Pacific Gyre—the largest oligotrophic province on our planet. During Expedition 329, relatively high concentrations of dissolved oxygen and significantly low biomass of microbial populations were observed in the entire sediment column, indicating that (i) there is no limit to life in open-ocean sediment and (ii) a significant amount of oxygen reaches through the sediment to the upper oceanic crust. This "deep aerobic biosphere" inhabits the sediment throughout up to ~37 percent of the world's oceans. The remaining ~63 percent of the oceans is comprised of higher productivity areas that contain the "deep anaerobic biosphere". In 2012, during IODP Expedition 337, the Japanese drill ship Chikyu explored coal-bearing sediments down to 2,466 meters below the seafloor off the Shimokita Peninsula, Japan. Geochemical and microbiological analyses consistently showed the occurrence of methane-producing communities associated with the coal beds. Cell concentrations in deep sediments were notably lower than those expected from the global regression line, implying that the bottom of the deep biosphere is approached in these beds. Taxonomic composition of the deep coal-bearing communities profoundly differs from those in shallower marine sediments and instead resembles organotrophic communities in forest soils. These findings suggest that the terrigenous microbial ecosystem has been partly retained from the original depositional setting over 20 million years and contributed to deep carbon cycling ever since.

Exploring Microbial Life in Oxic Sediments Underlying Oligotrophic Ocean Gyres

NASA Astrophysics Data System (ADS)

Ziebis, W.; Orcutt, B.; Wankel, S. D.; D'Hondt, S.; Szubin, R.; Kim, J. N.; Zengler, K.

2015-12-01

Oxygen, carbon and nutrient availability are defining parameters for microbial life. In contrast to organic-rich sediments of the continental margins, where high respiration rates lead to a depletion of O2 within a thin layer at the sediment surface, it was discovered that O2 penetrates several tens of meters into organic-poor sediments underlying oligotrophic ocean gyres. In addition, nitrate, another important oxidant, which usually disappears rapidly with depth in anoxic sediments, tends to accumulate above seawater concentrations in the oxic subsurface, reflecting the importance of nitrogen cycling processes, including both nitrification and denitrification. Two IODP drilling expeditions were vital for exploring the nature of the deep subsurface beneath oligotrophic ocean gyres, expedition 329 to the South Pacific Gyre (SPG) and expedition 336 to North Pond, located on the western flank of the Mid-Atlantic ridge beneath the North Atlantic Gyre. Within the ultra-oligotrophic SPG O2 penetrates the entire sediment column from the sediment-water interface to the underlying basement to depths of > 75 m. At North Pond, a topographic depression filled with sediment and surrounded by steep basaltic outcrops, O2 penetrates deeply into the sediment (~ 30 m) until it eventually becomes depleted. O2 also diffuses upward into the sediment from seawater circulating within the young crust underlying the sediment, resulting in a deep oxic layer several meters above the basalt. Despite low organic carbon contents microbial cells persist throughout the entire sediment column within the SPG (> 75 m) and at North Pond, albeit at low abundances. We explored the nature of the subsurface microbial communities by extracting intact cells from large volumes of sediment obtained from drill cores of the two expeditions. By using CARD-FiSH, amplicon (16s rRNA) and metagenome sequencing we shed light on the phylogenetic and functional diversity of the elusive communities residing in the deep oxic sediments of these two different areas. Given the global extent of this oxic subsurface studies of the diversity and metabolic potential of its biome, together with the analyses of porewater geochemical and isotopic composition, are beginning to reveal its role in global biogeochemical cycles.

Cell-free synthetic biology for in vitro prototype engineering.

PubMed

Moore, Simon J; MacDonald, James T; Freemont, Paul S

2017-06-15

Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. © 2017 The Author(s).

Cell-free synthetic biology for in vitro prototype engineering

PubMed Central

Moore, Simon J.; MacDonald, James T.

2017-01-01

Cell-free transcription–translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. PMID:28620040

Microorganisms meet solid minerals: interactions and biotechnological applications.

PubMed

Ng, Daphne H P; Kumar, Amit; Cao, Bin

2016-08-01

In natural and engineered environments, microorganisms often co-exist and interact with various minerals or mineral-containing solids. Microorganism-mineral interactions contribute significantly to environmental processes, including biogeochemical cycles in natural ecosystems and biodeterioration of materials in engineered environments. In this mini-review, we provide a summary of several key mechanisms involved in microorganism-mineral interactions, including the following: (i) solid minerals serve as substrata for biofilm development; (ii) solid minerals serve as an electron source or sink for microbial respiration; (iii) solid minerals provide microorganisms with macro or micronutrients for cell growth; and (iv) (semi)conductive solid minerals serve as extracellular electron conduits facilitating cell-to-cell interactions. We also highlight recent developments in harnessing microbe-mineral interactions for biotechnological applications.

Microbial anaerobic methane cycling in the subseafloor at the Von Damm hydrothermal vent field, Mid-Cayman Rise

NASA Astrophysics Data System (ADS)

Huber, J. A.; Reveillaud, J. C.; Stepanauskas, R.; McDermott, J. M.; Sylva, S. P.; Seewald, J.

2013-12-01

The Mid-Cayman Rise (MCR) is Earth's deepest and slowest spreading mid-ocean ridge located in the western Caribbean. With an axial rift valley floor at a depth of ~4200-6500 m, it represents one of the deepest sections of ridge crest worldwide. In 2009, the world's deepest hydrothermal vents (Piccard at 4960 m) and an ultramafic-influenced system only 20 km away on top of an oceanic core complex (Von Damm at 2350 m) were discovered along the MCR. Each site is hosted in a distinct geologic setting with different thermal and chemical regimes. The Von Damm site is a particularly interesting location to examine chemolithoautotrophic subseafloor microbial communities due to the abundant hydrogen, methane, and organic compounds in the venting fluids. Here, we used a combination of stable isotope tracing, next-generation sequencing, and single cell techniques to determine the identity, activity, and genomic repertoire of subseafloor anaerobic archaea involved in methane cycling in hydrothermal fluids venting at the Von Damm site. Molecular sequencing of phylogenetic marker genes revealed the presence of diverse archaea that both generate and consume methane across a geochemical and thermal spectrum of vents. Stable isotope tracing experiments were used to detect biological utilization of formate and dissolved inorganic carbon, and methane generation at 70 °C under anaerobic conditions. Results indicate that methanogenesis with formate as a substrate is occurring at 70 °C at two Von Damm sites, Ginger Castle and the Main Orifice. The results are consistent with thermodynamic predictions for carbon speciation at the temperatures encountered at the ultramafic-hosted Von Damm, where formate is predicted to be thermodynamically stable, and may thus serve as a an important source of carbon. Diverse thermophilic methanogenic archaea belonging to the genera Methanothermococcus were detected at all vent sites with both 16S rRNA tag sequencing and single cell sorting. Other methanogenic archaea are also present, including the hyperthermophile Methanopyrus, as well as methanogens that can use acetate, methanol, and other simple carbon compounds for methane generation, such as the genera Methanosaeta and Methermicoccus. In addition, uncultivated lineages related to putative anaerobic methane cycling archaea were detected in the fluids. These include the GOM Arc I clade within the Methanosarcinales, a group previously described from Gulf of Mexico methane seeps and thought to be methanogenic, as well as the ANME-1 and ANME-2 lineages, which are likely anaerobically oxidizing methane. On-going metagenomic sequencing of both mixed microbial communities and single cells from venting fluids will reveal the genomic repertoire, evolutionary relationships, and adaptations of these unique methane-cycling anaerobic archaea in the subseafloor at the Von Damm hydrothermal vent field.

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition.

PubMed

Ma, Xingyu; Zhao, Cancan; Gao, Ying; Liu, Bin; Wang, Tengxu; Yuan, Tong; Hale, Lauren; Nostrand, Joy D Van; Wan, Shiqiang; Zhou, Jizhong; Yang, Yunfeng

2017-08-01

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling. © 2017 John Wiley & Sons Ltd.

Deoxygenation alters bacterial diversity and community composition in the ocean's largest oxygen minimum zone.

PubMed

Beman, J Michael; Carolan, Molly T

2013-01-01

Oceanic oxygen minimum zones (OMZs) have a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that control these cycles is unclear. Here we sample across dissolved oxygen gradients in the oceans' largest OMZ and show that bacterial richness displays a unimodal pattern with decreasing dissolved oxygen, reaching maximum values on the edge of the OMZ and decreasing within it. Rare groups on the OMZ margin are abundant at lower dissolved oxygen concentrations, including sulphur-cycling Chromatiales, for which 16S rRNA was amplified from extracted RNA. Microbial species distribution models accurately replicate community patterns based on multivariate environmental data, demonstrate likely changes in distributions and diversity in the eastern tropical North Pacific Ocean, and highlight the sensitivity of key bacterial groups to deoxygenation. Through these mechanisms, OMZ expansion may alter microbial composition, competition, diversity and function, all of which have implications for biogeochemical cycling in OMZs.

Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone

NASA Astrophysics Data System (ADS)

Beman, J. Michael; Carolan, Molly T.

2013-10-01

Oceanic oxygen minimum zones (OMZs) have a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that control these cycles is unclear. Here we sample across dissolved oxygen gradients in the oceans’ largest OMZ and show that bacterial richness displays a unimodal pattern with decreasing dissolved oxygen, reaching maximum values on the edge of the OMZ and decreasing within it. Rare groups on the OMZ margin are abundant at lower dissolved oxygen concentrations, including sulphur-cycling Chromatiales, for which 16S rRNA was amplified from extracted RNA. Microbial species distribution models accurately replicate community patterns based on multivariate environmental data, demonstrate likely changes in distributions and diversity in the eastern tropical North Pacific Ocean, and highlight the sensitivity of key bacterial groups to deoxygenation. Through these mechanisms, OMZ expansion may alter microbial composition, competition, diversity and function, all of which have implications for biogeochemical cycling in OMZs.

Chemometrical assessment of the electrical parameters obtained by long-term operating freshwater sediment microbial fuel cells.

PubMed

Mitov, Mario; Bardarov, Ivo; Mandjukov, Petko; Hubenova, Yolina

2015-12-01

The electrical parameters of nine freshwater sediment microbial fuel cells (SMFCs) were monitored for a period of over 20 months. The developed SMFCs, divided into three groups, were started up and continuously operated under different constant loads (100, 510 and 1100 Ω) for 2.5 months. At this stage of the experiment, the highest power density values, reaching 1.2 ± 0.2 mW/m(2), were achieved by the SMFCs loaded with 510 Ω. The maximum power obtained at periodical polarization during the rest period, however, ranged between 26.2 ± 2.8 and 35.3 ± 2.8 mW/m(2), strongly depending on the internal cell resistance. The statistical evaluation of data derived from the polarization curves shows that after 300 days of operation all examined SMFCs reached a steady-state and the system might be assumed as homoscedastic. The estimated values of standard and expanded uncertainties of the electric parameters indicate a high repeatability and reproducibility of the SMFCs' performance. Results obtained in subsequent discharge-recovery cycles reveal the opportunity for practical application of studied SMFCs as autonomous power sources.

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE PAGES

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; ...

2016-02-24

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed Central

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Roey; Salminen, Janne; Newton, Ryan J.; Bürgmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S.; Basiliko, Nathan; Nemergut, Diana R.

2016-01-01

Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology. PMID:26941732

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed

Graham, Emily B; Knelman, Joseph E; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J M; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C; Glanville, Helen C; Jones, Davey L; Angel, Roey; Salminen, Janne; Newton, Ryan J; Bürgmann, Helmut; Ingram, Lachlan J; Hamer, Ute; Siljanen, Henri M P; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C; Lopes, Ana R; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S; Basiliko, Nathan; Nemergut, Diana R

2016-01-01

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Seasonal switchgrass ecotype contributions to soil organic carbon, deep soil microbial community composition and rhizodeposit uptake during an extreme drought

USDA-ARS?s Scientific Manuscript database

The importance of rhizodeposit C and associated microbial communities in deep soil C stabilization is relatively unknown. Phenotypic variability in plant root biomass could impact C cycling through belowground plant allocation, rooting architecture, and microbial community abundance and composition...

STABLE CARBON ISOTOPE RATIO AND COMPOSITION OF MICROBIAL FATTY ACIDS IN TROPICAL SOILS

EPA Science Inventory

The soil microbial community plays a critical part in tropical ecosystem functioning through its role in the soil organic matter (SOM) cycle. This study evaluates the relative effects of soil type and land use on: (1) soil microbial community structure and (2) the contribution o...

A holistic view of polyhydroxyalkanoate metabolism in Pseudomonas putida.

PubMed

Prieto, Auxiliadora; Escapa, Isabel F; Martínez, Virginia; Dinjaski, Nina; Herencias, Cristina; de la Peña, Fernando; Tarazona, Natalia; Revelles, Olga

2016-02-01

Polyhydroxyalkanoate (PHA) metabolism has been traditionally considered as a futile cycle involved in carbon and energy storage. The use of cutting-edge technologies linked to systems biology has improved our understanding of the interaction between bacterial physiology, PHA metabolism and other cell functions in model bacteria such as Pseudomonas putida KT2440. PHA granules or carbonosomes are supramolecular complexes of biopolyester and proteins that are essential for granule segregation during cell division, and for the functioning of the PHA metabolic route as a continuous cycle. The simultaneous activities of PHA synthase and depolymerase ensure the carbon flow to the transient demand for metabolic intermediates to balance the storage and use of carbon and energy. PHA cycle also determines the number and size of bacterial cells. The importance of PHAs as nutrients for members of the microbial community different to those that produce them is illustrated here via examples of bacterial predators such as Bdellovibrio bacteriovorus that prey on PHA producers and produces specific extra-cellular depolymerases. PHA hydrolysis confers Bdellovibrio ecological advantages in terms of motility and predation efficiency, demonstrating the importance of PHA producers predation in population dynamics. Metabolic modulation strategies for broadening the portfolio of PHAs are summarized and their properties are compiled. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

NASA Astrophysics Data System (ADS)

Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

2015-08-01

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework which is developed as part of an interdisciplinary, iterative, model-data based approach fully integrating fieldwork and laboratory experiments with model development, testing, and application. SHIMMER is designed to simulate the establishment of microbial biomass and associated biogeochemical cycling during the initial stages of ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The model mechanistically describes and predicts transformations in carbon, nitrogen and phosphorus through aggregated components of the microbial community as a set of coupled ordinary differential equations. The rationale for development of the model arises from decades of empirical observation on the initial stages of soil development in glacier forefields. SHIMMER enables a quantitative and process focussed approach to synthesising the existing empirical data and advancing understanding of microbial and biogeochemical dynamics. Here, we provide a detailed description of SHIMMER. The performance of SHIMMER is then tested in two case studies using published data from the Damma Glacier forefield in Switzerland and the Athabasca Glacier in Canada. In addition, a sensitivity analysis helps identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass, and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Simulation results indicate that primary production is responsible for the initial build-up of substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter are identified as important in sustaining this productivity. Microbial production in young soils is supported by labile organic matter, whereas carbon stocks in older soils are more refractory. Nitrogen fixing bacteria are responsible for the initial accumulation of available nitrates in the soil. Biogeochemical rates are highly seasonal, as observed in experimental data. The development and application of SHIMMER not only provides important new insights into forefield dynamics, but also highlights aspects of these systems that require further field and laboratory research. The most pressing advances need to come in quantifying nutrient budgets and biogeochemical rates, in exploring seasonality, the fate of allochthonous deposition in relation to autochthonous production, and empirical studies of microbial growth and cell death, to increase understanding of how glacier forefield development contributes to the global biogeochemical cycling and climate in the future.

Microbial community assembly and metabolic function during mammalian corpse decomposition

USGS Publications Warehouse

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-01

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Microbial community assembly and metabolic function during mammalian corpse decomposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metcalf, J. L.; Xu, Z. Z.; Weiss, S.

2015-12-10

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in lowmore » abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.« less

"Panta rhei": Perpetual cycling of the keratin cytoskeleton.

PubMed

Leube, Rudolf E; Moch, Marcin; Kölsch, Anne; Windoffer, Reinhard

2011-01-01

The filamentous cytoskeletal systems fulfil seemingly incompatible functions by maintaining a stable scaffolding to ensure tissue integrity and simultaneously facilitating rapid adaptation to intracellular processes and environmental stimuli. This paradox is particularly obvious for the abundant keratin intermediate filaments in epithelial tissues. The epidermal keratin cytoskeleton, for example, supports the protective and selective barrier function of the skin while enabling rapid growth and remodelling in response to physical, chemical and microbial challenges. We propose that these dynamic properties are linked to the perpetual re-cycling of keratin intermediate filaments that we observe in cultured cells. This cycle of assembly and disassembly is independent of protein biosynthesis and consists of distinct, temporally and spatially defined steps. In this way, the keratin cytoskeleton remains in constant motion but stays intact and is also able to restructure rapidly in response to specific regulatory cues as is needed, e.g., during division, differentiation and wound healing.

In situ detection of microbial c-type cytochrome based on intrinsic peroxidase-like activity using screen-printed carbon electrode.

PubMed

Wen, Junlin; He, Daigui; Yu, Zhen; Zhou, Shungui

2018-08-15

C-type cytochromes (c-cyts) facilitate microbial extracellular electron transfer and play critical roles in biogeochemical cycling, bioelectricity generation and bioremediation. In this study, a simple and effective method has been developed to detect microbial c-cyts by means of peroxidase mimetic reaction on screen-printed carbon electrode (SPCE). To this end, bacteria cells were immobilized onto the working electrode surface of SPCE by a simple drop casting. After introducing 3,3',5,5'-tetramethylbenzidine (TMB) solution, microbial c-cyts with peroxidase-like activity catalyze the oxidation of TMB in the presence of hydrogen peroxide. The oxidized TMB was electrochemically determined and the current signal was employed to calculate the c-cyts content. This electrochemical method is highly sensitive for microbial c-cyts with a low detection limit of 40.78 fmol and a wide detection range between 51.70 fmol and 6.64 pmol. Moreover, the proposed technique can be universally expanded to detect c-cyts in other bacteria species such as Fontibacter ferrireducens, Pseudomonas aeruginosa, Comamonas guangdongensis and Escherichia coli. Furthermore, the proposed method confers an in situ facile and quantitative c-cyts detection without any destructive sample preparations, complex electrode modifications and expensive enzyme- or metal particle- based signal amplification. The suggested method advances an intelligent strategy for in situ quantification of microbial c-cyts and consequently holds promising application potential in microbiology and environmental science. Copyright © 2018 Elsevier B.V. All rights reserved.

Recovery of microbial communities and carbon cycling processes following drought manipulation in southern California

NASA Astrophysics Data System (ADS)

Allison, S. D.; Martiny, J. B. H.; Martiny, A.; Berlemont, R.; Treseder, K. K.; Goulden, M.; Brodie, E.

2016-12-01

Predicting the functioning of microbial communities under changing environmental conditions remains a key challenge in Earth system science. Metagenomics and other high-throughput molecular approaches can help address this challenge by revealing the functional potential of microbial communities. We coupled metagenomics with models and experimental manipulations to address microbial responses to drought in a California grassland ecosystem along with the consequences for carbon cycling. We developed an approach for extracting trait information from metagenomic data and asked: 1) What is the phylogenetic structure of drought response traits? 2) What is the relationship between these traits and those involved in carbohydrate degradation? 3) How do both classes of traits vary seasonally and with precipitation manipulation? 4) How resilient are these traits in the face of perturbation? We found that drought response traits are phylogenetically conserved at an equivalent of 5-8% ribosomal RNA gene sequence dissimilarity. Experimental drought treatment selected for the genetic potential to degrade starch, xylan, and mixed polysaccharides, suggesting a link between drought response and carbon cycling traits. In addition, microbial communities exposed to experimental drought showed a reduced potential to degrade plant biomass. Particularly among bacteria, seasonal drought had a larger impact on microbial composition, abundance, and carbohydrate-degrading genes compared to experimental drought. Bacterial communities were also more resilient to drought perturbation than fungal communities, which showed legacies of drought perturbation for up to three years. Altogether, these findings imply that microbial communities exhibit trait diversity that facilitates resilience but with substantial time lags and consequences for carbon turnover. This information is being used to inform new trait-based models that address the challenge of predicting microbial functioning under precipitation change.

A genomic perspective on stoichiometric regulation of soil carbon cycling.

PubMed

Hartman, Wyatt H; Ye, Rongzhong; Horwath, William R; Tringe, Susannah G

2017-12-01

Similar to plant growth, soil carbon (C) cycling is constrained by the availability of nitrogen (N) and phosphorus (P). We hypothesized that stoichiometric control over soil microbial C cycling may be shaped by functional guilds with distinct nutrient substrate preferences. Across a series of rice fields spanning 5-25% soil C (N:P from 1:12 to 1:70), C turnover was best correlated with P availability and increased with experimental N addition only in lower C (mineral) soils with N:P⩽16. Microbial community membership also varied with soil stoichiometry but not with N addition. Shotgun metagenome data revealed changes in community functions with increasing C turnover, including a shift from aromatic C to carbohydrate utilization accompanied by lower N uptake and P scavenging. Similar patterns of C, N and P acquisition, along with higher ribosomal RNA operon copy numbers, distinguished that microbial taxa positively correlated with C turnover. Considering such tradeoffs in genomic resource allocation patterns among taxa strengthened correlations between microbial community composition and C cycling, suggesting simplified guilds amenable to ecosystem modeling. Our results suggest that patterns of soil C turnover may reflect community-dependent metabolic shifts driven by resource allocation strategies, analogous to growth rate-stoichiometry coupling in animal and plant communities.

A trait-based approach for examining microbial community assembly

NASA Astrophysics Data System (ADS)

Prest, T. L.; Nemergut, D.

2015-12-01

Microorganisms regulate all of Earth's major biogeochemical cycles and an understanding of how microbial communities assemble is a key part in evaluating controls over many types of ecosystem processes. Rapid advances in technology and bioinformatics have led to a better appreciation for the variation in microbial community structure in time and space. Yet, advances in theory are necessary to make sense of these data and allow us to generate unifying hypotheses about the causes and consequences of patterns in microbial biodiversity and what they mean for ecosystem function. Here, I will present a metaanalysis of microbial community assembly from a variety of successional and post-disturbance systems. Our analysis shows various distinct patterns in community assembly, and the potential importance of nutrients and dispersal in shaping microbial community beta diversity in these systems. We also used a trait-based approach to generate hypotheses about the mechanisms driving patterns of microbial community assembly and the implications for function. Our work reveals the importance of rRNA operon copy number as a community aggregated trait in helping to reconcile differences in community dynamics between distinct types of successional and disturbed systems. Specifically, our results demonstrate that decreases in average copy number can be a common feature of communities across various drivers of ecological succession, supporting a transition from an r-selected to a K-selected community. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, from cells to populations and communities, and has implications for both ecology and evolution. Trait-based approaches are an important next step to generate and test hypotheses about the forces structuring microbial communities and the subsequent consequences for ecosystem function.

Licoricidin inhibits the growth of SW480 human colorectal adenocarcinoma cells in vitro and in vivo by inducing cycle arrest, apoptosis and autophagy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ji, Shuai

Licorice (Glycyrrhiza uralensis Fisch.) possesses significant anti-cancer activities, but the active ingredients and underlying mechanisms have not been revealed. By screening the cytotoxic activities of 122 licorice compounds against SW480 human colorectal adenocarcinoma cells, we found that licoricidin (LCD) inhibited SW480 cell viability with an IC{sub 50} value of 7.2 μM. Further studies indicated that LCD significantly induced G1/S cell cycle arrest and apoptosis in SW480 cells, accompanied by inhibition of cyclins/CDK1 expression and activation of caspase-dependent pro-apoptotic signaling. Meanwhile, LCD promoted autophagy in SW480 cells, and activated AMPK signaling and inhibited Akt/mTOR pathway. Overexpression of a dominant-negative AMPKα2 abolishedmore » LCD-induced inhibition of Akt/mTOR, autophagic and pro-apoptotic signaling pathways, and significantly reversed loss of cell viability, suggesting activation of AMPK is essential for the anti-cancer activity of LCD. In vivo anti-tumor experiments indicated that LCD (20 mg/kg, i.p.) significantly inhibited the growth of SW480 xenografts in nude mice with an inhibitory rate of 43.5%. In addition, we obtained the glycosylated product LCDG by microbial transformation, and found that glycosylation slightly enhanced the in vivo anti-cancer activities of LCD. This study indicates that LCD could inhibit SW480 cells by inducing cycle arrest, apoptosis and autophagy, and is a potential chemopreventive or chemotherapeutic agent against colorectal cancer. - Highlights: • Molecular mechanisms for cytotoxic activity of licoricidin (LCD) were investigated. • LCD promoted autophagy of SW480 cells through AMPK and Akt/mTOR signaling pathways. • Both LCD and its glucoside showed in vivo anti-colorectal cancer activities.« less

Resistance may be an important mechanism by which marine microbes respond to environmental toxicants*1

NASA Astrophysics Data System (ADS)

Capriulo, Gerard M.; Flanzenbaum, Jeffrey; Wurster, Charles F.; Rowland, R. George

1983-11-01

The hypothesis, that at least certain marine microbial organisms respond to toxic stress by the development of resistance, was tested using the hypotric marine ciliate Euplotes vannus Muller as the test organism. Resistance to polychlorinated biphenyls (PCB, Aroclor 1254) was developed in E. vannus by exposing the animals to progressively higher PCB concentrations during a period of several months. The resistance to PCB persisted for at least 80 days (greater than 40 generations) after final exposure. This suggests either that genetic selection or persistent (lasting over many cell division cycles) phenotypic trait modification, possibly in the form of Dauermodification, had occurred. If resistance were widespread among marine microbial organisms in polluted environments it would be an important consideration in evaluating the long-term biological impact of both natural and man-induced chemical stress.

Biofouling of reverse osmosis membranes: effects of cleaning on biofilm microbial communities, membrane performance, and adherence of extracellular polymeric substances.

PubMed

Al Ashhab, Ashraf; Sweity, Amer; Bayramoglu, Bihter; Herzberg, Moshe; Gillor, Osnat

2017-05-01

Laboratory-scale reverse osmosis (RO) flat-sheet systems were used with two parallel flow cells, one treated with cleaning agents and a control (ie undisturbed). The cleaning efforts increased the affinity of extracellular polymeric substances (EPS) to the RO membrane and altered the biofilm surface structure. Analysis of the membrane biofilm community composition revealed the dominance of Proteobacteria. However, within the phylum Proteobacteria, γ-Proteobacteria dominated the cleaned membrane biofilm, while β-Proteobacteria dominated the control biofilm. The composition of the fungal phyla was also altered by cleaning, with enhancement of Ascomycota and suppression of Basidiomycota. The results suggest that repeated cleaning cycles select for microbial groups that strongly attach to the RO membrane surface by producing rigid and adhesive EPS that hampers membrane performance.

Microbial ecology of soda lakes: investigating sulfur and nitrogen cycling at Mono Lake, CA, USA

NASA Astrophysics Data System (ADS)

Fairbanks, D.; Phillips, A. A.; Wells, M.; Bao, R.; Fullerton, K. M.; Stamps, B. W.; Speth, D. R.; Johnson, H.; Sessions, A. L.

2017-12-01

Soda lakes represent unique ecosystems characterized by extremes of pH, salinity and distinct geochemical cycling. Despite these extreme conditions, soda lakes are important repositories of biological adaptation and have a highly functional microbial system. We investigated the biogeochemical cycling of sulfur and nitrogen compounds in Mono Lake, California, located east of the Sierra Nevada mountains. Mono lake is characterized by hyperalkaline, hypersaline and high sulfate concentrations and can enter prolonged periods of meromixis due to freshwater inflow. Typically, the microbial sulfur cycle is highly active in soda lakes with both oxidation and reduction of sulfur compounds. However, the biological sulfur cycle is connected to many other main elemental cycles such as carbon, nitrogen and metals. Here we investigated the interaction between sulfur and nitrogen cycling in Mono lake using a combination of molecular, isotopic, and geochemical observations to explore the links between microbial phylogenetic composition and functionality. Metagenomic and 16S rRNA gene amplicon sequencing were determined at two locations and five depths in May 2017. 16S rRNA gene amplicon sequencing analysis revealed organisms capable of both sulfur and nitrogen cycling. The relative abundance and distribution of functional genes (dsrA, soxAB, nifH, etc) were also determined. These genetic markers indicate the potential in situ relevance of specific carbon, nitrogen, and sulfur pathways in the water column prior to the transition to meromictic stratification. However, genes for sulfide oxidation, denitrification, and ammonification were present. Genome binning guided by the most abundant dsrA sequences, GC content, and abundance with depth identified a Thioalkalivibrio paradoxus bin containing genes capable of sulfur oxidation, denitrification, and nitrate reduction. The presence of a large number of sulfur and nitrogen cycling genes associated with Thioalkalivibrio paradoxus suggests thiosulfate oxidation may be coupled to nitrate reduction despite the extremely low level of nitrate in Mono Lake. Our results illustrate the centrality of living organisms in both shaping and responding to geochemical cycles, as well as future directions for exploring coupled biogeochemical cycles in Mono Lake.

Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California.

PubMed

Baker, Nameer R; Khalili, Banafshe; Martiny, Jennifer B H; Allison, Steven D

2018-06-01

Microbial decomposers mediate the return of CO 2 to the atmosphere by producing extracellular enzymes to degrade complex plant polymers, making plant carbon available for metabolism. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. We analyzed mass loss, litter chemistry, microbial biomass, extracellular enzyme activities, and enzyme temperature sensitivities in grassland litter transplanted along a Mediterranean climate gradient in southern California. Microbial community composition was manipulated by caging litter within bags made of nylon membrane that prevent microbial immigration. To test whether grassland microbes were constrained by climate history, half of the bags were inoculated with local microbial communities native to each gradient site. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbial communities were not restricted in their ability to decompose litter under different climate conditions across the gradient, although microbial communities across our gradient may be restricted in their ability to degrade different types of litter. We did find some evidence that local microbial communities were optimized based on climate, but local microbial taxa that proliferated after inoculation into litterbags did not enhance litter decomposition. Our results suggest that microbial community composition does not constrain C-cycling rates under climate change in our system, but optimization to particular resource environments may act as more general constraints on microbial communities. © 2018 by the Ecological Society of America.

Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

Ecology and exploration of the rare biosphere.

PubMed

Lynch, Michael D J; Neufeld, Josh D

2015-04-01

The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance microbial populations—the 'rare biosphere'—have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.

Analysis of metabolomic profile of fermented Orostachys japonicus A. Berger by capillary electrophoresis time of flight mass spectrometry

PubMed Central

Das, Gitishree; Patra, Jayanta Kumar; Lee, Sun-Young; Kim, Changgeon; Park, Jae Gyu

2017-01-01

Microbial cell performance in food biotechnological processes has become an important concern for improving human health worldwide. Lactobacillus plantarum, which is widely distributed in nature, is a lactic acid bacterium with many industrial applications for fermented foods or functional foods (e.g., probiotics). In the present study, using capillary electrophoresis time of flight mass spectrometry, the metabolomic profile of dried Orostachys japonicus A. Berger, a perennial medicinal herb with L. plantarum was compared with that of O. japonicus fermented with L. plantarum to elucidate the metabolomic changes induced by the fermentation process. The levels of several metabolites were changed by the fermentation process, indicating their involvement in microbial performance. For example, glycolysis, the pentose phosphate pathway, the TCA cycle, the urea cycle-related metabolism, nucleotide metabolism, and lipid and amino acid metabolism were altered significantly by the fermentation process. Although the fermented metabolites were not tested using in vivo studies to increase human health benefits, our findings provide an insight into the alteration of metabolites induced by fermentation, and indicated that the metabolomic analysis for the process should be accompanied by fermenting strains and conditions. PMID:28704842

Analysis of metabolomic profile of fermented Orostachys japonicus A. Berger by capillary electrophoresis time of flight mass spectrometry.

PubMed

Das, Gitishree; Patra, Jayanta Kumar; Lee, Sun-Young; Kim, Changgeon; Park, Jae Gyu; Baek, Kwang-Hyun

2017-01-01

Microbial cell performance in food biotechnological processes has become an important concern for improving human health worldwide. Lactobacillus plantarum, which is widely distributed in nature, is a lactic acid bacterium with many industrial applications for fermented foods or functional foods (e.g., probiotics). In the present study, using capillary electrophoresis time of flight mass spectrometry, the metabolomic profile of dried Orostachys japonicus A. Berger, a perennial medicinal herb with L. plantarum was compared with that of O. japonicus fermented with L. plantarum to elucidate the metabolomic changes induced by the fermentation process. The levels of several metabolites were changed by the fermentation process, indicating their involvement in microbial performance. For example, glycolysis, the pentose phosphate pathway, the TCA cycle, the urea cycle-related metabolism, nucleotide metabolism, and lipid and amino acid metabolism were altered significantly by the fermentation process. Although the fermented metabolites were not tested using in vivo studies to increase human health benefits, our findings provide an insight into the alteration of metabolites induced by fermentation, and indicated that the metabolomic analysis for the process should be accompanied by fermenting strains and conditions.

Re-examination of the relationship between marine virus and microbial cell abundances.

PubMed

Wigington, Charles H; Sonderegger, Derek; Brussaard, Corina P D; Buchan, Alison; Finke, Jan F; Fuhrman, Jed A; Lennon, Jay T; Middelboe, Mathias; Suttle, Curtis A; Stock, Charles; Wilson, William H; Wommack, K Eric; Wilhelm, Steven W; Weitz, Joshua S

2016-01-25

Marine viruses are critical drivers of ocean biogeochemistry, and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 10(8) per ml. Over many years, a consensus has emerged that virus abundances are typically tenfold higher than microbial cell abundances. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5,671 microbial cell and virus abundance estimates from 25 distinct marine surveys and find substantial variation in the virus-to-microbial cell ratio, in which a 10:1 model has either limited or no explanatory power. Instead, virus abundances are better described as nonlinear, power-law functions of microbial cell abundances. The fitted scaling exponents are typically less than 1, implying that the virus-to-microbial cell ratio decreases with microbial cell density, rather than remaining fixed. The observed scaling also implies that viral effect sizes derived from 'representative' abundances require substantial refinement to be extrapolated to regional or global scales.

Awakening of a Dormant Cyanobacterium from Nitrogen Chlorosis Reveals a Genetically Determined Program.

PubMed

Klotz, Alexander; Georg, Jens; Bučinská, Lenka; Watanabe, Satoru; Reimann, Viktoria; Januszewski, Witold; Sobotka, Roman; Jendrossek, Dieter; Hess, Wolfgang R; Forchhammer, Karl

2016-11-07

The molecular and physiological mechanisms involved in the transition of microbial cells from a resting state to the active vegetative state are critically relevant for solving problems in fields ranging from microbial ecology to infection microbiology. Cyanobacteria that cannot fix nitrogen are able to survive prolonged periods of nitrogen starvation as chlorotic cells in a dormant state. When provided with a usable nitrogen source, these cells re-green within 48 hr and return to vegetative growth. Here we investigated the resuscitation of chlorotic Synechocystis sp. PCC 6803 cells at the physiological and molecular levels with the aim of understanding the awakening process of a dormant bacterium. Almost immediately upon nitrate addition, the cells initiated a highly organized resuscitation program. In the first phase, they suppressed any residual photosynthetic activity and activated respiration to gain energy from glycogen catabolism. Concomitantly, they restored the entire translational apparatus, ATP synthesis, and nitrate assimilation. After only 12-16 hr, the cells re-activated the synthesis of the photosynthetic apparatus and prepared for metabolic re-wiring toward photosynthesis. When the cells reached full photosynthetic capacity after ∼48 hr, they resumed cell division and entered the vegetative cell cycle. An analysis of the transcriptional dynamics during the resuscitation process revealed a perfect match to the observed physiological processes, and it suggested that non-coding RNAs play a major regulatory role during the lifestyle switch in awakening cells. This genetically encoded program ensures rapid colonization of habitats in which nitrogen starvation imposes a recurring growth limitation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial diversity and carbon cycling in San Francisco Bay wetlands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theroux, Susanna; Hartman, Wyatt; He, Shaomei

Wetland restoration efforts in San Francisco Bay aim to rebuild habitat for endangered species and provide an effective carbon storage solution, reversing land subsidence caused by a century of industrial and agricultural development. However, the benefits of carbon sequestration may be negated by increased methane production in newly constructed wetlands, making these wetlands net greenhouse gas (GHG) sources to the atmosphere. We investigated the effects of wetland restoration on below-ground microbial communities responsible for GHG cycling in a suite of historic and restored wetlands in SF Bay. Using DNA and RNA sequencing, coupled with real-time GHG monitoring, we profiled themore » diversity and metabolic potential of wetland soil microbial communities. The wetland soils harbor diverse communities of bacteria and archaea whose membership varies with sampling location, proximity to plant roots and sampling depth. Our results also highlight the dramatic differences in GHG production between historic and restored wetlands and allow us to link microbial community composition and GHG cycling with key environmental variables including salinity, soil carbon and plant species.« less

Fungal-Induced Cell Cycle Impairment, Chromosome Instability and Apoptosis via Differential Activation of NF-κB

PubMed Central

Ben-Abdallah, Mariem; Sturny-Leclère, Aude; Avé, Patrick; Louise, Anne; Moyrand, Frédérique; Weih, Falk; Janbon, Guilhem; Mémet, Sylvie

2012-01-01

Microbial pathogens have developed efficient strategies to compromise host immune responses. Cryptococcus neoformans is a facultative intracellular pathogen, recognised as the most common cause of systemic fungal infections leading to severe meningoencephalitis, mainly in immunocompromised patients. This yeast is characterized by a polysaccharide capsule, which inhibits its phagocytosis. Whereas phagocytosis escape and macrophage intracellular survival have been intensively studied, extracellular survival of this yeast and restraint of host innate immune response are still poorly understood. In this study, we have investigated whether C. neoformans affected macrophage cell viability and whether NF-κB (nuclear factor-κB), a key regulator of cell growth, apoptosis and inflammation, was involved. Using wild-type (WT) as well as mutant strains of C. neoformans for the pathogen side, and WT and mutant cell lines with altered NF-κB activity or signalling as well as primary macrophages for the host side, we show that C. neoformans manipulated NF-κB-mediated signalling in a unique way to regulate macrophage cell fate and viability. On the one hand, serotype A strains reduced macrophage proliferation in a capsule-independent fashion. This growth decrease, which required a critical dosage of NF-κB activity, was caused by cell cycle disruption and aneuploidy, relying on fungal-induced modification of expression of several cell cycle checkpoint regulators in S and G2/M phases. On the other hand, C. neoformans infection induced macrophage apoptosis in a capsule-dependent manner with a differential requirement of the classical and alternative NF-κB signalling pathways, the latter one being essential. Together, these findings shed new light on fungal strategies to subvert host response through uncoupling of NF-κB activity in pathogen-controlled apoptosis and impairment of cell cycle progression. They also provide the first demonstration of induction of aneuploidy by a fungal pathogen, which may have wider implications for human health as aneuploidy is proposed to promote tumourigenesis. PMID:22396644

Fungal-induced cell cycle impairment, chromosome instability and apoptosis via differential activation of NF-κB.

PubMed

Ben-Abdallah, Mariem; Sturny-Leclère, Aude; Avé, Patrick; Louise, Anne; Moyrand, Frédérique; Weih, Falk; Janbon, Guilhem; Mémet, Sylvie

2012-01-01

Microbial pathogens have developed efficient strategies to compromise host immune responses. Cryptococcus neoformans is a facultative intracellular pathogen, recognised as the most common cause of systemic fungal infections leading to severe meningoencephalitis, mainly in immunocompromised patients. This yeast is characterized by a polysaccharide capsule, which inhibits its phagocytosis. Whereas phagocytosis escape and macrophage intracellular survival have been intensively studied, extracellular survival of this yeast and restraint of host innate immune response are still poorly understood. In this study, we have investigated whether C. neoformans affected macrophage cell viability and whether NF-κB (nuclear factor-κB), a key regulator of cell growth, apoptosis and inflammation, was involved. Using wild-type (WT) as well as mutant strains of C. neoformans for the pathogen side, and WT and mutant cell lines with altered NF-κB activity or signalling as well as primary macrophages for the host side, we show that C. neoformans manipulated NF-κB-mediated signalling in a unique way to regulate macrophage cell fate and viability. On the one hand, serotype A strains reduced macrophage proliferation in a capsule-independent fashion. This growth decrease, which required a critical dosage of NF-κB activity, was caused by cell cycle disruption and aneuploidy, relying on fungal-induced modification of expression of several cell cycle checkpoint regulators in S and G2/M phases. On the other hand, C. neoformans infection induced macrophage apoptosis in a capsule-dependent manner with a differential requirement of the classical and alternative NF-κB signalling pathways, the latter one being essential. Together, these findings shed new light on fungal strategies to subvert host response through uncoupling of NF-κB activity in pathogen-controlled apoptosis and impairment of cell cycle progression. They also provide the first demonstration of induction of aneuploidy by a fungal pathogen, which may have wider implications for human health as aneuploidy is proposed to promote tumourigenesis.

Chlorine stress mediates microbial surface attachment in drinking water systems.

PubMed

Liu, Li; Le, Yang; Jin, Juliang; Zhou, Yuliang; Chen, Guowei

2015-03-01

Microbial attachment to drinking water pipe surfaces facilitates pathogen survival and deteriorates disinfection performance, directly threatening the safety of drinking water. Notwithstanding that the formation of biofilm has been studied for decades, the underlying mechanisms for the origins of microbial surface attachment in biofilm development in drinking water pipelines remain largely elusive. We combined experimental and mathematical methods to investigate the role of environmental stress-mediated cell motility on microbial surface attachment in chlorination-stressed drinking water distribution systems. Results show that at low levels of disinfectant (0.0-1.0 mg/L), the presence of chlorine promotes initiation of microbial surface attachment, while higher amounts of disinfectant (>1.0 mg/L) inhibit microbial attachment. The proposed mathematical model further demonstrates that chlorination stress (0.0-5.0 mg/L)-mediated microbial cell motility regulates the frequency of cell-wall collision and thereby controls initial microbial surface attachment. The results reveal that transport processes and decay patterns of chlorine in drinking water pipelines regulate microbial cell motility and, thus, control initial surface cell attachment. It provides a mechanistic understanding of microbial attachment shaped by environmental disinfection stress and leads to new insights into microbial safety protocols in water distribution systems.

Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat.

PubMed

Steunou, Anne-Soisig; Jensen, Sheila I; Brecht, Eric; Becraft, Eric D; Bateson, Mary M; Kilian, Oliver; Bhaya, Devaki; Ward, David M; Peters, John W; Grossman, Arthur R; Kühl, Michael

2008-04-01

Nitrogen fixation, a prokaryotic, O2-inhibited process that reduces N2 gas to biomass, is of paramount importance in biogeochemical cycling of nitrogen. We analyzed the levels of nif transcripts of Synechococcus ecotypes, NifH subunit and nitrogenase activity over the diel cycle in the microbial mat of an alkaline hot spring in Yellowstone National Park. The results showed a rise in nif transcripts in the evening, with a subsequent decline over the course of the night. In contrast, immunological data demonstrated that the level of the NifH polypeptide remained stable during the night, and only declined when the mat became oxic in the morning. Nitrogenase activity was low throughout the night; however, it exhibited two peaks, a small one in the evening and a large one in the early morning, when light began to stimulate cyanobacterial photosynthetic activity, but O2 consumption by respiration still exceeded the rate of O2 evolution. Once the irradiance increased to the point at which the mat became oxic, the nitrogenase activity was strongly inhibited. Transcripts for proteins associated with energy-producing metabolisms in the cell also followed diel patterns, with fermentation-related transcripts accumulating at night, photosynthesis- and respiration-related transcripts accumulating during the day and late afternoon, respectively. These results are discussed with respect to the energetics and regulation of N2 fixation in hot spring mats and factors that can markedly influence the extent of N2 fixation over the diel cycle.

Metaproteogenomics reveals the soil microbial communities active in nutrient cycling processes under different tree species

NASA Astrophysics Data System (ADS)

Keiblinger, Katharina Maria; Masse, Jacynthe; Zühlke, Daniela; Riedel, Katharina; Zechmeister-Boltenstern, Sophie; Prescott, Cindy E.; Grayston, Sue

2016-04-01

Tree species exert strong effects on microbial communities in litter and soil and may alter rates of soil processes fundamental to nutrient cycling and carbon fluxes (Prescott and Grayston 2013). However, the influence of tree species on decomposition processes are still contradictory and poorly understood. An understanding of the mechanisms underlying plant influences on soil processes is important for our ability to predict ecosystem response to altered global/environmental conditions. In order to link microbial community structure and function to forest-floor nutrient cycling processes, we sampled forest floors under western redcedar (Thuja plicata), Douglas-fir (Pseudotsuga menziesii) and Sitka spruce (Picea sitchensis) grown in nutrient-poor sites in common garden experiments on Vancouver island (Canada). We measured forest-floor total N, total C, initial NH4+ and NO3- concentrations, DOC, Cmic and Nmic. Gross rates of ammonification and NH4+ consumption were measured using the 15N pool-dilution method. Organic carbon quality was assessed through FTIR analyses. Microbial community structure was analysed by a metaproteogenomic approach using 16S and ITS amplification and sequencing with MiSeq platform. Proteins were extracted and peptides characterized via LC-MS/MS on a Velos Orbitrap to assess the active microbial community. Different microbial communities were active under the three tree species and variation in process rates were observed and will be discussed. This research provides new insights on microbial processes during organic matter decomposition. The metaproteogenomic approach enables us to investigate these changes with respect to possible effects on soil C-storage at even finer taxonomic resolution.

Graphite anode surface modification with controlled reduction of specific aryl diazonium salts for improved microbial fuel cells power output.

PubMed

Picot, Matthieu; Lapinsonnière, Laure; Rothballer, Michael; Barrière, Frédéric

2011-10-15

Graphite electrodes were modified with reduction of aryl diazonium salts and implemented as anodes in microbial fuel cells. First, reduction of 4-aminophenyl diazonium is considered using increased coulombic charge density from 16.5 to 200 mC/cm(2). This procedure introduced aryl amine functionalities at the surface which are neutral at neutral pH. These electrodes were implemented as anodes in "H" type microbial fuel cells inoculated with waste water, acetate as the substrate and using ferricyanide reduction at the cathode and a 1000 Ω external resistance. When the microbial anode had developed, the performances of the microbial fuel cells were measured under acetate saturation conditions and compared with those of control microbial fuel cells having an unmodified graphite anode. We found that the maximum power density of microbial fuel cell first increased as a function of the extent of modification, reaching an optimum after which it decreased for higher degree of surface modification, becoming even less performing than the control microbial fuel cell. Then, the effect of the introduction of charged groups at the surface was investigated at a low degree of surface modification. It was found that negatively charged groups at the surface (carboxylate) decreased microbial fuel cell power output while the introduction of positively charged groups doubled the power output. Scanning electron microscopy revealed that the microbial anode modified with positively charged groups was covered by a dense and homogeneous biofilm. Fluorescence in situ hybridization analyses showed that this biofilm consisted to a large extent of bacteria from the known electroactive Geobacter genus. In summary, the extent of modification of the anode was found to be critical for the microbial fuel cell performance. The nature of the chemical group introduced at the electrode surface was also found to significantly affect the performance of the microbial fuel cells. The method used for modification is easy to control and can be optimized and implemented for many carbon materials currently used in microbial fuel cells and other bioelectrochemical systems. Copyright © 2011 Elsevier B.V. All rights reserved.

Effect of short-term alkaline intervention on the performance of buffer-free single-chamber microbial fuel cell.

PubMed

Yang, Na; Ren, Yueping; Li, Xiufen; Wang, Xinhua

2017-06-01

Anolyte acidification is a drawback restricting the electricity generation performance of the buffer-free microbial fuel cells (MFC). In this paper, a small amount of alkali-treated anion exchange resin (AER) was placed in front of the anode in the KCl mediated single-chamber MFC to slowly release hydroxyl ions (OH - ) and neutralize the H + ions that are generated by the anodic reaction in two running cycles. This short-term alkaline intervention to the KCl anolyte has promoted the proliferation of electroactive Geobacter sp. and enhanced the self-buffering capacity of the KCl-AER-MFC. The pH of the KCl anolyte in the KCl-AER-MFC increased and became more stable in each running cycle compared with that of the KCl-MFC after the short-term alkaline intervention. The maximum power density (P max ) of the KCl-AER-MFC increased from 307.5mW·m -2 to 542.8mW·m -2 , slightly lower than that of the PBS-MFC (640.7mW·m -2 ). The coulombic efficiency (CE) of the KCl-AER-MFC increased from 54.1% to 61.2% which is already very close to that of the PBS-MFC (61.9%). The results in this paper indicate that short-term alkaline intervention to the anolyte is an effective strategy to further promote the performance of buffer-free MFCs. Copyright © 2017 Elsevier B.V. All rights reserved.

Dose-dependent regulation of microbial activity on sinking particles by polyunsaturated aldehydes: Implications for the carbon cycle

NASA Astrophysics Data System (ADS)

Edwards, Bethanie R.; Bidle, Kay D.; Van Mooy, Benjamin A. S.

2015-05-01

Diatoms and other phytoplankton play a crucial role in the global carbon cycle, fixing CO2 into organic carbon, which may then be exported to depth via sinking particles. The molecular diversity of this organic carbon is vast and many highly bioactive molecules have been identified. Polyunsaturated aldehydes (PUAs) are bioactive on various levels of the marine food web, and yet the potential for these molecules to affect the fate of organic carbon produced by diatoms remains an open question. In this study, the effects of PUAs on the natural microbial assemblages associated with sinking particles were investigated. Sinking particles were collected from 150 m in the water column and exposed to varying concentrations of PUAs in dark incubations over 24 h. PUA doses ranging from 1 to 10 µM stimulated respiration, organic matter hydrolysis, and cell growth by bacteria associated with sinking particles. PUA dosages near 100 µM appeared to be toxic, resulting in decreased bacterial cell abundance and metabolism, as well as pronounced shifts in bacterial community composition. Sinking particles were hot spots for PUA production that contained concentrations within the stimulatory micromolar range in contrast to previously reported picomolar concentrations of these compounds in bulk seawater. This suggests PUAs produced in situ stimulate the remineralization of phytoplankton-derived sinking organic matter, decreasing carbon export efficiency, and shoaling the average depths of nutrient regeneration. Our results are consistent with a "bioactivity hypothesis" for explaining variations in carbon export efficiency in the oceans.

Dose-dependent regulation of microbial activity on sinking particles by polyunsaturated aldehydes: Implications for the carbon cycle.

PubMed

Edwards, Bethanie R; Bidle, Kay D; Van Mooy, Benjamin A S

2015-05-12

Diatoms and other phytoplankton play a crucial role in the global carbon cycle, fixing CO2 into organic carbon, which may then be exported to depth via sinking particles. The molecular diversity of this organic carbon is vast and many highly bioactive molecules have been identified. Polyunsaturated aldehydes (PUAs) are bioactive on various levels of the marine food web, and yet the potential for these molecules to affect the fate of organic carbon produced by diatoms remains an open question. In this study, the effects of PUAs on the natural microbial assemblages associated with sinking particles were investigated. Sinking particles were collected from 150 m in the water column and exposed to varying concentrations of PUAs in dark incubations over 24 h. PUA doses ranging from 1 to 10 µM stimulated respiration, organic matter hydrolysis, and cell growth by bacteria associated with sinking particles. PUA dosages near 100 µM appeared to be toxic, resulting in decreased bacterial cell abundance and metabolism, as well as pronounced shifts in bacterial community composition. Sinking particles were hot spots for PUA production that contained concentrations within the stimulatory micromolar range in contrast to previously reported picomolar concentrations of these compounds in bulk seawater. This suggests PUAs produced in situ stimulate the remineralization of phytoplankton-derived sinking organic matter, decreasing carbon export efficiency, and shoaling the average depths of nutrient regeneration. Our results are consistent with a "bioactivity hypothesis" for explaining variations in carbon export efficiency in the oceans.

Where microorganisms meet rocks in the Earth's Critical Zone

NASA Astrophysics Data System (ADS)

Akob, D. M.; Küsel, K.

2011-12-01

The Critical Zone (CZ) is the Earth's outer shell where all the fundamental physical, chemical, and biological processes critical for sustaining life occur and interact. As microbes in the CZ drive many of these biogeochemical cycles, understanding their impact on life-sustaining processes starts with an understanding of their biodiversity. In this review, we summarize the factors controlling where terrestrial CZ microbes (prokaryotes and micro-eukaryotes) live and what is known about their diversity and function. Microbes are found throughout the CZ, down to 5 km below the surface, but their functional roles change with depth due to habitat complexity, e.g. variability in pore spaces, water, oxygen, and nutrients. Abundances of prokaryotes and micro-eukaryotes decrease from 1010 or 107 cells g soil-1 or rock-1, or ml water-1 by up to eight orders of magnitude with depth. Although symbiotic mycorrhizal fungi and free-living decomposers have been studied extensively in soil habitats, where they occur up to 103 cells g soil-1, little is known regarding their identity or impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that they are limited in space, nutrients, are unable to cope with oxygen limitations, or some combination thereof. Since deep regions of the CZ have limited access to recent photosynthesis-derived carbon, microbes there depend on deposited organic material or a chemolithoautotrophic metabolism that allows for a complete food chain, independent from the surface, although limited energy flux means cell growth may take tens to thousands of years. Microbes are found in all regions of the CZ and can mediate important biogeochemical processes, but more work is needed to understand how microbial populations influence the links between different regions of the CZ and weathering processes. With the recent development of "omics" technologies, microbial ecologists have new methods that can be used to link the composition and function of in situ microbial communities. In particular, these methods can be used to search for new metabolic pathways that are relevant to biogeochemical nutrient cycling and determine how the activity of microorganisms can affect transport of carbon, particulates, and reactive gases between and within CZ regions.

From position-specific isotope labeling towards soil fluxomics: a novel toolbox to assess the microbial impact on biogeochemical cycles

NASA Astrophysics Data System (ADS)

Apostel, C.; Dippold, M. A.; Kuzyakov, Y.

2015-12-01

Understanding the microbial impact on C and nutrient cycles is one of the most important challenges in terrestrial biogeochemistry. Transformation of low molecular weight organic substances (LMWOS) is a key step in all biogeochemical cycles because 1) all high molecular substances pass the LMWOS pool during their degradation and 2) only LMWOS can be taken up by microorganisms intact. Thus, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the microbial metabolic network and its control mechanism. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools but studies were nearly exclusively based on uniformly labeled substances. However, such tracers do not allow the differentiation of the intact use of the initial substances from its transformation to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of basic metabolites and quantification of isotope incorporation in CO2 and bulk soil enabled following the basic metabolic pathways of microorganisms. However, the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites like phospholipid fatty acids (PLFA) or amino sugars revealed new insights into the soil fluxome: First, it enables tracing specific anabolic pathways in diverse microbial communities in soils e.g. carbon starvation pathways versus pathways reflecting microbial growth. Second, it allows identification of specific pathways of individual functional microbial groups in soils in situ. Tracing metabolic pathways and understanding their regulating factors are crucial for soil C fluxomics i.e. the unravaling of the complex network of C transformations. Quantitative models to assess microbial group specific metabolic pathways can be generated and parameterized by this approach. The knowledge of submolecular C transformation steps and its regulating factors is essential for understanding C cycling and long-term C storage in soils.

Microbial Succession and Nitrogen Cycling in Cultured Biofilms as Affected by the Inorganic Nitrogen Availability.

PubMed

Li, Shuangshuang; Peng, Chengrong; Wang, Chun; Zheng, Jiaoli; Hu, Yao; Li, Dunhai

2017-01-01

Biofilms play important roles in nutrients and energy cycling in aquatic ecosystems. We hypothesized that as eutrophication could change phytoplankton community and decrease phytoplankton diversity, ambient inorganic nitrogen level will affect the microbial community and diversity of biofilms and the roles of biofilms in nutrient cycling. Biofilms were cultured using a flow incubator either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def). The results showed that the biomass and nitrogen and phosphorous accumulation of biofilms were limited by N deficiency; however, as expected, the N-def biofilms had significantly higher microbial diversity than that of N-rep biofilms. The microbial community of biofilms shifted in composition and abundance in response to ambient inorganic nitrogen level. For example, as compared between the N-def and the N-rep biofilms, the former consisted of more diazotrophs, while the latter consisted of more denitrifying bacteria. As a result of the shift of the functional microbial community, the N concentration of N-rep medium kept decreasing, while that of N-def medium showed an increasing trend in the late stage. This indicates that biofilms can serve as the source or the sink of nitrogen in aquatic ecosystems, and it depends on the inorganic nitrogen availability.

Quorum sensing and microbial drug resistance.

PubMed

Chen, Yu-fan; Liu, Shi-yin; Liang, Zhi-bin; Lv, Ming-fa; Zhou, Jia-nuan; Zhang, Lian-hui

2016-10-20

Microbial drug resistance has become a serious problem of global concern, and the evolution and regulatory mechanisms of microbial drug resistance has become a hotspot of research in recent years. Recent studies showed that certain microbial resistance mechanisms are regulated by quorum sensing system. Quorum sensing is a ubiquitous cell-cell communication system in the microbial world, which associates with cell density. High-density microbial cells produce sufficient amount of small signal molecules, activating a range of downstream cellular processes including virulence and drug resistance mechanisms, which increases bacterial drug tolerance and causes infections on host organisms. In this review, the general mechanisms of microbial drug resistance and quorum-sensing systems are summarized with a focus on the association of quorum sensing and chemical signaling systems with microbial drug resistance mechanisms, including biofilm formation and drug efflux pump. The potential use of quorum quenching as a new strategy to control microbial resistance is also discussed.

Methane and nitrous oxide cycling microbial communities in soils above septic leach fields: Abundances with depth and correlations with net surface emissions.

PubMed

Fernández-Baca, Cristina P; Truhlar, Allison M; Omar, Amir-Eldin H; Rahm, Brian G; Walter, M Todd; Richardson, Ruth E

2018-05-31

Onsite septic systems use soil microbial communities to treat wastewater, in the process creating potent greenhouse gases (GHGs): methane (CH 4 ) and nitrous oxide (N 2 O). Subsurface soil dispersal systems of septic tank overflow, known as leach fields, are an important part of wastewater treatment and have the potential to contribute significantly to GHG cycling. This study aimed to characterize soil microbial communities associated with leach field systems and quantify the abundance and distribution of microbial populations involved in CH 4 and N 2 O cycling. Functional genes were used to target populations producing and consuming GHGs, specifically methyl coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) for CH 4 and nitric oxide reductase (cnorB) and nitrous oxide reductase (nosZ) for N 2 O. All biomarker genes were found in all soil samples regardless of treatment (leach field, sand filter, or control) or depth (surface or subsurface). In general, biomarker genes were more abundant in surface soils than subsurface soils suggesting the majority of GHG cycling is occurring in near-surface soils. Ratios of production to consumption gene abundances showed a positive relationship with CH 4 emissions (mcrA:pmoA, p < 0.001) but not with N 2 O emission (cnorB:nosZ, p > 0.05). Of the three measured soil parameters (volumetric water content (VWC), temperature, and conductivity), only VWC was significantly correlated to a biomarker gene, mcrA (p = 0.0398) but not pmoA or either of the N 2 O cycling genes (p > 0.05 for cnorB and nosZ). 16S rRNA amplicon library sequencing results revealed soil VWC, CH 4 flux and N 2 O flux together explained 64% of the microbial community diversity between samples. Sequencing of mcrA and pmoA amplicon libraries revealed treatment had little effect on diversity of CH 4 cycling organisms. Overall, these results suggest GHG cycling occurs in all soils regardless of whether or not they are associated with a leach field system. Copyright © 2018 Elsevier B.V. All rights reserved.

Coupling of Belowground Carbon Cycling and Stoichiometry from Organisms to Ecosystems along a Soil C Gradient Under Rice Cultivation

NASA Astrophysics Data System (ADS)

Hartman, W.; Ye, R.; Horwath, W. R.; Tringe, S. G.

2015-12-01

Ecological stoichiometry is a framework linking biogeochemical cycles to organism functional traits that has been widely applied in aquatic ecosystems, animals and plants, but is poorly explored in soil microbes. We evaluated relationships among soil stoichiometry, carbon (C) cycling, and microbial community structure and function along a soil gradient spanning ~5-25% C in cultivated rice fields with experimental nitrogen (N) amendments. We found rates of soil C turnover were associated with nutrient stoichiometry and phosphorus (P) availability at ecosystem, community, and organism scales. At the ecosystem scale, soil C turnover was highest in mineral soils with lower C content and N:P ratios, and was positively correlated with soil inorganic P. Effects of N fertilization on soil C cycling also appeared to be mediated by soil P availability, while microbial community composition (by 16S rRNA sequencing) was not altered by N addition. Microbial communities varied along the soil C gradient, corresponding with highly covariant soil %C, N:P ratios, C quality, and carbon turnover. In contrast, we observed unambiguous shifts in microbial community function, imputed from taxonomy and directly assessed by shotgun sequenced metagenomes. The abundance of genes for carbohydrate utilization decreased with increasing soil C (and declining C turnover), while genes for aromatic C uptake, N fixation and P scavenging increased along with potential incorporation of C into biomass pools. Ecosystem and community-scale associations between C and nutrient substrate availability were also reflected in patterns of resource allocation among individual genomes (imputed and assembled). Microbes associated with higher rates of soil C turnover harbored more genes for carbohydrate utilization, fewer genes for obtaining energetically costly forms of C, N and P, more ribosomal RNA gene copies, and potentially lower C use efficiency. We suggest genome clustering by functional gene suites might yield simplified guilds related to biogeochemical cycling, even when function is imputed directly from taxonomy. Our findings in a controlled model wetland ecosystem bolster evidence for the role of P in influencing soil C cycling, and our approach could be leveraged to reduce complex microbial data for trait-based modeling of soil C cycling.

Unusual isotopic composition of C-CO2 from sterilized soil microcosms: a new way to separate intracellular from extracellular respiratory metabolisms.

NASA Astrophysics Data System (ADS)

Kéraval, Benoit; Alvarez, Gaël; Lehours, Anne Catherine; Amblard, Christian; Fontaine, Sebastien

2015-04-01

The mineralization of organic C requires two main steps. First, microorganisms secrete exoenzymes in soil in order to depolymerize plant and microbial cell walls and release soluble substrates for microbial assimilation. The second step of mineralization, during which C is released as CO2, implies the absorption and utilization of solubilized substrates by microbial cells with the aim to produce energy (ATP). In cells, soluble substrates are carried out by a cascade of respiratory enzymes, along which protons and electrons are transferred from a substrate to oxygen. Given the complexity of this oxidative metabolism and the typical fragility of respiratory enzymes, it is traditionally considered that respiration (second step of C mineralization process) is strictly an intracellular metabolism process. The recurrent observations of substantial CO2 emissions in soil microcosms where microbial cells have been reduced to extremely low levels challenges this paradigm. In a recent study where some respiratory enzymes have shown to function in an extracellular context in soils, Maire et al. (2013) suggested that an extracellular oxidative metabolism (EXOMET) substantially contributes to CO2 emission from soils. This idea is supported by the recent publication of Blankinship et al., 2014 who showed the presence of active enzymes involved in the Krebs cycle on soil particles. Many controversies subsist in the scientific community due to the presence of non-proliferating but morphologically intact cells after irradiation that could substantially contribute to those soil CO2 emissions. To test whether a purely extracellular oxidative metabolism contribute to soil CO2 emissions, we combined high doses of gamma irradiations to different time of soil autoclaving. The presence of active and non-active cells in soil was checked by DNA and RNA extraction and by electronic microscopy. None active cells (RNA-containing cells) were detectable after irradiation, but some morphological intact cells were observed by microscopy. These "ghost" cells were completely destroyed by the irradiation-autoclaving combination releasing large amount of soluble C. The soil respiration (O2 consumption and CO2 production) was reduced by irradiation and autoclaving but not stopped, suggesting the presence of an EXOMET. The delta 13C of CO2 released in the irradiated-autoclaved soil was strongly depleted (-70‰) indicating that this extracellular metabolism induced a substantial isotopic fractionation. Our findings suggest that two main oxidative metabolisms co-occur in soils: cell respiration and EXOMET. The isotopic fractionation induced by the EXOMET open perspectives for its quantification in non-sterilized living soils.

Changes in methane emission and microbial community structure in a Phragmites australis-expanding tidal marsh of a temperature region

NASA Astrophysics Data System (ADS)

Kim, J.; Lee, J.; Kang, H.

2017-12-01

Phragmites australis is one of the representative vegetation of coastal wetlands which is distributed in North America, East Asia and European Countries. In North America, P. australis has invaded large areas of coastal wetlands, which causes various ecological problems such as increases in methane emission and reduction in biodiversity. In South Korea, P. australis is rapidly expanded in tidal marshes in Suncheon Bay. The expansion of P. australis enhanced methane emission by increasing dissolved organic carbon and soil moisture, and changing in relative abundances of methanogen, methanotroph, and sulfate reducing bacteria. Microbial community structure might be also shifted and affect methane cycle, but accurate observation on microbial community structure has not been fully illustrated yet. Therefore, we tried to monitor the changing microbial community structure due to P. australis expansion by using Next Generation Sequencing (NGS). NGS results showed that microbial community was substantially changed with the expansion. We also observed seasonal variations and chronosequence of microbial community structures along the expansion of P. australis, which showed distinctive changing patterns. P. australis expansion substantially affected microbial community structure in tidal marsh which may play an important role in methane cycle in tidal marshes.

Innate and cytokine-driven signals, rather than microbial antigens, dominate in natural killer T cell activation during microbial infection.

PubMed

Brigl, Manfred; Tatituri, Raju V V; Watts, Gerald F M; Bhowruth, Veemal; Leadbetter, Elizabeth A; Barton, Nathaniel; Cohen, Nadia R; Hsu, Fong-Fu; Besra, Gurdyal S; Brenner, Michael B

2011-06-06

Invariant natural killer T cells (iNKT cells) are critical for host defense against a variety of microbial pathogens. However, the central question of how iNKT cells are activated by microbes has not been fully explained. The example of adaptive MHC-restricted T cells, studies using synthetic pharmacological α-galactosylceramides, and the recent discovery of microbial iNKT cell ligands have all suggested that recognition of foreign lipid antigens is the main driver for iNKT cell activation during infection. However, when we compared the role of microbial antigens versus innate cytokine-driven mechanisms, we found that iNKT cell interferon-γ production after in vitro stimulation or infection with diverse bacteria overwhelmingly depended on toll-like receptor-driven IL-12. Importantly, activation of iNKT cells in vivo during infection with Sphingomonas yanoikuyae or Streptococcus pneumoniae, pathogens which are known to express iNKT cell antigens and which require iNKT cells for effective protection, also predominantly depended on IL-12. Constitutive expression of high levels of IL-12 receptor by iNKT cells enabled instant IL-12-induced STAT4 activation, demonstrating that among T cells, iNKT cells are uniquely equipped for immediate, cytokine-driven activation. These findings reveal that innate and cytokine-driven signals, rather than cognate microbial antigen, dominate in iNKT cell activation during microbial infections.

Using single-chamber microbial fuel cells as renewable power sources of electro-Fenton reactors for organic pollutant treatment.

PubMed

Zhu, Xiuping; Logan, Bruce E

2013-05-15

Electro-Fenton reactions can be very effective for organic pollutant degradation, but they typically require non-sustainable electrical power to produce hydrogen peroxide. Two-chamber microbial fuel cells (MFCs) have been proposed for pollutant treatment using Fenton-based reactions, but these types of MFCs have low power densities and require expensive membranes. Here, more efficient dual reactor systems were developed using a single-chamber MFC as a low-voltage power source to simultaneously accomplish H2O2 generation and Fe(2+) release for the Fenton reaction. In tests using phenol, 75 ± 2% of the total organic carbon (TOC) was removed in the electro-Fenton reactor in one cycle (22 h), and phenol was completely degraded to simple and readily biodegradable organic acids. Compared to previously developed systems based on two-chamber MFCs, the degradation efficiency of organic pollutants was substantially improved. These results demonstrate that this system is an energy-efficient and cost-effective approach for industrial wastewater treatment of certain pollutants. Copyright © 2013 Elsevier B.V. All rights reserved.

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

DOE PAGES

Roux, Simon; Hawley, Alyse K.; Torres Beltran, Monica; ...

2014-08-29

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186more » microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.« less

Molecular basis of sodium butyrate-dependent proapoptotic activity in cancer cells.

PubMed

Pajak, B; Orzechowski, A; Gajkowska, B

2007-01-01

This review outlines the molecular events that accompany the antitumor action of sodium butyrate (NaBt). Butyrate, a low-molecular weight four-carbon chain volatile fatty acid (VFA) has been previously shown to withdraw cells from cell cycle or to promote cell differentiation, and finally to induce programmed cell death. Recent advances in molecular biology indicate, that this product of large bowel microbial fermentation of dietary fiber, might evoke the above-mentioned effects by indirect action on genes. NaBt was shown to inhibit histone deacetylase activity, allowing DNA binding of several transcription factors. Higher genomic activity leads to the higher expression of proapoptotic genes, higher level of their protein products and elevated sensitivity to death ligand-induced apoptosis. Cancer cells might be arrested in G1 phase of cell cycle in a p21-dependent manner. Proapoptotic activity of NaBt includes higher expression of membrane death receptors (DR4/5), higher level and activation of Smad3 protein in TGF-beta-dependent apoptotic pathway, lower level of antiapoptotic proteins (cFLIP, XIAP) and activation ofproapoptotic tBid protein. Thus, both intrinsic and extrinsic apoptotic pathways are stimulated to ampify the apoptotic signals. These effects are specific for tumor but not for regular cells. Unique properties of NaBt make this agent a promising metabolic inhibitor to retard tumorigenesis to suppress tumor growth.

An innovative approach to bioremediation of mercury contaminated soils from industrial mining operations.

PubMed

McCarthy, Damien; Edwards, Grant C; Gustin, Mae S; Care, Andrew; Miller, Matthieu B; Sunna, Anwar

2017-10-01

Soils contaminated with mercury (Hg) have proved expensive and logistically difficult to remediate. Research continues into finding suitable environmentally-friendly and efficient ways of achieving this end. Bioremediation is an option, which employs the strategies microorganisms have evolved to deal with Hg. One microbial strategy involves uptake and intracellular volatilisation of mercuric ions, which passively diffuse from the cell and back into the atmosphere. In this work, Pseudomonas veronii cells grown to stationary phase were immobilised in a xanthan gum-based biopolymer via encapsulation. The P. veronii-biopolymer mix was then coated onto natural zeolite granules. Zeolite immobilised cells remained viable for at least 16 weeks stored under ambient room temperature. Furthermore, the immobilised cells were shown to retain both viability and Hg volatilisation functionality after transportation from Australia to the USA, where they were applied to Hg contaminated soil. Maximum flux rates exceeded 10 μg Hg m 2  h -1 from mine tailings (≈7 mg kg -1  Hg with 50% v/v water). This was 4 orders of magnitude above background flux levels. It is envisioned that emitted gaseous elemental mercury (GEM) can be readily captured, and transformed back into metallic Hg, which can then be stored appropriately or recycled. This breaks the Hg cycle, as GEM is no longer translocated back to the atmospheric compartment. The immobilising excipients used in this research overcome many logistical issues with delivery of suitable microbial loads to locations of mercury contamination and presents a facile and inexpensive method of augmenting contaminated sites with selected microbial consortia for bioremediation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming

USDA-ARS?s Scientific Manuscript database

This study investigated the activities of ß-glucosidase (C cycling, ß-glucosaminidase (C and N cycling), acid phosphatase (P cycling) and arylsulfatase (S cycling) under lettuce (Lactuca sativa), potato (Solanum Tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall f...

Binding of heavy metal ions in aggregates of microbial cells, EPS and biogenic iron minerals measured in-situ using metal- and glycoconjugates-specific fluorophores

NASA Astrophysics Data System (ADS)

Hao, Likai; Guo, Yuan; Byrne, James M.; Zeitvogel, Fabian; Schmid, Gregor; Ingino, Pablo; Li, Jianli; Neu, Thomas R.; Swanner, Elizabeth D.; Kappler, Andreas; Obst, Martin

2016-05-01

Aggregates consisting of bacterial cells, extracellular polymeric substances (EPS) and Fe(III) minerals formed by Fe(II)-oxidizing bacteria are common at bulk or microscale chemical interfaces where Fe cycling occurs. The high sorption capacity and binding capacity of cells, EPS, and minerals controls the mobility and fate of heavy metals. However, it remains unclear to which of these component(s) the metals will bind in complex aggregates. To clarify this question, the present study focuses on 3D mapping of heavy metals sorbed to cells, glycoconjugates that comprise the majority of EPS constituents, and Fe(III) mineral aggregates formed by the phototrophic Fe(II)-oxidizing bacteria Rhodobacter ferrooxidans SW2 using confocal laser scanning microscopy (CLSM) in combination with metal- and glycoconjugates-specific fluorophores. The present study evaluated the influence of glycoconjugates, microbial cell surfaces, and (biogenic) Fe(III) minerals, and the availability of ferrous and ferric iron on heavy metal sorption. Analyses in this study provide detailed knowledge on the spatial distribution of metal ions in the aggregates at the sub-μm scale, which is essential to understand the underlying mechanisms of microbe-mineral-metal interactions. The heavy metals (Au3+, Cd2+, Cr3+, CrO42-, Cu2+, Hg2+, Ni2+, Pd2+, tributyltin (TBT) and Zn2+) were found mainly sorbed to cell surfaces, present within the glycoconjugates matrix, and bound to the mineral surfaces, but not incorporated into the biogenic Fe(III) minerals. Statistical analysis revealed that all ten heavy metals tested showed relatively similar sorption behavior that was affected by the presence of sorbed ferrous and ferric iron. Results in this study showed that in addition to the mineral surfaces, both bacterial cell surfaces and the glycoconjugates provided most of sorption sites for heavy metals. Simultaneously, ferrous and ferric iron ions competed with the heavy metals for sorption sites on the organic compounds. In summary, the information obtained by the present approach using a microbial model system provides important information to better understand the interactions between heavy metals and biofilms, and microbially formed Fe(III) minerals and heavy metals in complex natural environments.

To what extent do food preferences explain the trophic position of heterotrophic and mixotrophic microbial consumers in a Sphagnum peatland?

PubMed

Jassey, Vincent E J; Meyer, Caroline; Dupuy, Christine; Bernard, Nadine; Mitchell, Edward A D; Toussaint, Marie-Laure; Metian, Marc; Chatelain, Auriel P; Gilbert, Daniel

2013-10-01

Although microorganisms are the primary drivers of biogeochemical cycles, the structure and functioning of microbial food webs are poorly studied. This is the case in Sphagnum peatlands, where microbial communities play a key role in the global carbon cycle. Here, we explored the structure of the microbial food web from a Sphagnum peatland by analyzing (1) the density and biomass of different microbial functional groups, (2) the natural stable isotope (δ(13)C and δ(15)N) signatures of key microbial consumers (testate amoebae), and (3) the digestive vacuole contents of Hyalosphenia papilio, the dominant testate amoeba species in our system. Our results showed that the feeding type of testate amoeba species (bacterivory, algivory, or both) translates into their trophic position as assessed by isotopic signatures. Our study further demonstrates, for H. papilio, the energetic benefits of mixotrophy when the density of its preferential prey is low. Overall, our results show that testate amoebae occupy different trophic levels within the microbial food web, depending on their feeding behavior, the density of their food resources, and their metabolism (i.e., mixotrophy vs. heterotrophy). Combined analyses of predation, community structure, and stable isotopes now allow the structure of microbial food webs to be more completely described, which should lead to improved models of microbial community function.

Microbial community assembly and metabolic function during mammalian corpse decomposition.

PubMed

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-08

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations. Copyright © 2016, American Association for the Advancement of Science.

Biogeochemical cycling at the aquatic-terrestrial interface is linked to parafluvial hyporheic zone inundation history

NASA Astrophysics Data System (ADS)

Goldman, Amy E.; Graham, Emily B.; Crump, Alex R.; Kennedy, David W.; Romero, Elvira B.; Anderson, Carolyn G.; Dana, Karl L.; Resch, Charles T.; Fredrickson, Jim K.; Stegen, James C.

2017-09-01

The parafluvial hyporheic zone combines the heightened biogeochemical and microbial interactions indicative of a hyporheic region with direct atmospheric/terrestrial inputs and the effects of wet-dry cycles. Therefore, understanding biogeochemical cycling and microbial interactions in this ecotone is fundamental to understanding biogeochemical cycling at the aquatic-terrestrial interface and to creating robust hydrobiogeochemical models of dynamic river corridors. We aimed to (i) characterize biogeochemical and microbial differences in the parafluvial hyporheic zone across a small spatial domain (6 lateral meters) that spans a breadth of inundation histories and (ii) examine how parafluvial hyporheic sediments respond to laboratory-simulated re-inundation. Surface sediment was collected at four elevations along transects perpendicular to flow of the Columbia River, eastern WA, USA. The sediments were inundated by the river 0, 13, 127, and 398 days prior to sampling. Spatial variation in environmental variables (organic matter, moisture, nitrate, glucose, % C, % N) and microbial communities (16S and internal transcribed spacer (ITS) rRNA gene sequencing, qPCR) were driven by differences in inundation history. Microbial respiration did not differ significantly across inundation histories prior to forced inundation in laboratory incubations. Forced inundation suppressed microbial respiration across all histories, but the degree of suppression was dramatically different between the sediments saturated and unsaturated at the time of sample collection, indicating a binary threshold response to re-inundation. We present a conceptual model in which irregular hydrologic fluctuations facilitate microbial communities adapted to local conditions and a relatively high flux of CO2. Upon rewetting, microbial communities are initially suppressed metabolically, which results in lower CO2 flux rates primarily due to suppression of fungal respiration. Following prolonged inundation, the microbial community adapts to saturation by shifting composition, and the CO2 flux rebounds to prior levels due to the subsequent change in respiration. Our results indicate that the time between inundation events can push the system into alternate states: we suggest (i) that, above some threshold of inundation interval, re-inundation suppresses respiration to a consistent, low rate and (ii) that, below some inundation interval, re-inundation has a minor effect on respiration. Extending reactive transport models to capture processes that govern such dynamics will provide more robust predictions of river corridor biogeochemical function under altered surface water flow regimes in both managed and natural watersheds.

Different Mechanisms of Soil Microbial Response to Global Change Result in Different Outcomes in the MIMICS-CN Model

NASA Astrophysics Data System (ADS)

Kyker-Snowman, E.; Wieder, W. R.; Grandy, S.

2017-12-01

Microbial-explicit models of soil carbon (C) and nitrogen (N) cycling have improved upon simulations of C and N stocks and flows at site-to-global scales relative to traditional first-order linear models. However, the response of microbial-explicit soil models to global change factors depends upon which parameters and processes in a model are altered by those factors. We used the MIcrobial-MIneral Carbon Stabilization Model with coupled N cycling (MIMICS-CN) to compare modeled responses to changes in temperature and plant inputs at two previously-modeled sites (Harvard Forest and Kellogg Biological Station). We spun the model up to equilibrium, applied each perturbation, and evaluated 15 years of post-perturbation C and N pools and fluxes. To model the effect of increasing temperatures, we independently examined the impact of decreasing microbial C use efficiency (CUE), increasing the rate of microbial turnover, and increasing Michaelis-Menten kinetic rates of litter decomposition, plus several combinations of the three. For plant inputs, we ran simulations with stepwise increases in metabolic litter, structural litter, whole litter (structural and metabolic), or labile soil C. The cumulative change in soil C or N varied in both sign and magnitude across simulations. For example, increasing kinetic rates of litter decomposition resulted in net releases of both C and N from soil pools, while decreasing CUE produced short-term increases in respiration but long-term accumulation of C in litter pools and shifts in soil C:N as microbial demand for C increased and biomass declined. Given that soil N cycling constrains the response of plant productivity to global change and that soils generate a large amount of uncertainty in current earth system models, microbial-explicit models are a critical opportunity to advance the modeled representation of soils. However, microbial-explicit models must be improved by experiments to isolate the physiological and stoichiometric parameters of soil microbes that shift under global change.

Phosphorus cycling in natural and low input soil/plant systems: the role of soil microorganisms

NASA Astrophysics Data System (ADS)

Tamburini, F.; Bünemann, E. K.; Oberson, A.; Bernasconi, S. M.; Frossard, E.

2011-12-01

Availability of phosphorus (as orthophosphate, Pi) limits biological production in many terrestrial ecosystems. During the first phase of soil development, weathering of minerals and leaching of Pi are the processes controlling Pi concentrations in the soil solution, while in mature soils, Pi is made available by desorption of mineral Pi and mineralization of organic compounds. In agricultural soils additional Pi is supplied by fertilization, either with mineral P and/or organic inputs (animal manure or plant residues). Soil microorganisms (bacteria and fungi) mediate several processes, which are central to the availability of Pi to plants. They play a role in the initial release of Pi from the mineral phase, and through extracellular phosphatase enzymes, they decompose and mineralize organic compounds, releasing Pi. On the other hand, microbial immobilization and internal turnover of Pi can decrease the soil available Pi pool, competing in this way with plants. Using radio- and stable isotopic approaches, we show evidence from different soil/plant systems which points to the central role of the microbial activity. In the presented case studies, P contained in the soil microbial biomass is a larger pool than available Pi. In a soil chronosequence after deglaciation, stable isotopes of oxygen associated to phosphate showed that even in the youngest soils microbial activity highly impacted the isotopic signature of available Pi. These results suggested that microorganisms were rapidly taking up and cycling Pi, using it to sustain their community. Microbial P turnover time was faster in the young (about 20 days) than in older soils (about 120 days), reflecting a different functioning of the microbial community. Microbial community crashes, caused by drying/rewetting and freezing/thawing cycles, were most likely responsible for microbial P release to the available P pool. In grassland fertilization experiments with mineral NK and NPK amendments, microbial P turnover was faster in the P-free treatment. Laboratory incubation also showed a more rapid P uptake by microbial biomass in the NK than in the NPK treatment (37% and 6% of added 33P recovered in microbial P after 100 minutes in NK and NPK, respectively). The seasonal microbial P flux in both treatments was 1.5-4 times larger than the annual plant P uptake. In field studies carried out on highly weathered low P soils in Colombia, the comparison between grass-legume and grass-only pastures showed that the presence of legumes had an impact on the overall biological activity. In fact, microbial biomass and phosphatase activity were significantly larger in grass-legume pastures than in the legume-free experiments. Larger release of Pi from the organic P pool improved P availability to plants and pointed at a modified C:N:P stoichiometry along pathways of the nutrient cycle in the soil/plant system. All these data are evidence of a highly dynamic microbial P pool, which controls Pi concentration and, hence, availability for plants in natural and low input agricultural ecosystems.

Origin and analysis of microbial population heterogeneity in bioprocesses.

PubMed

Müller, Susann; Harms, Hauke; Bley, Thomas

2010-02-01

Heterogeneity of industrial production cultures is accepted to a certain degree; however, the underlying mechanisms are seldom perceived or included in the development of new bioprocess control strategies. Population heterogeneity and its basics, perceptible in the diverse proficiency of cells, begins with asymmetric birth and is found to recess during the life cycle. Since inefficient subpopulations have significant impact on the productivity of industrial cultures, cellular heterogeneity needs to be detected and quantified by using high speed detection tools like flow cytometry. Possible origins of population heterogeneity, sophisticated fluorescent techniques for detection of individual cell states, and cutting-edge Omics-technologies for extended information beyond the resolution of fluorescent labelling are highlighted.

In-Field Implementation of a Recombinant Factor C Assay for the Detection of Lipopolysaccharide as a Biomarker of Extant Life within Glacial Environments

PubMed Central

Barnett, Megan J.; Wadham, Jemma L.; Jackson, Miriam; Cullen, David C.

2012-01-01

The discovery over the past two decades of viable microbial communities within glaciers has promoted interest in the role of glaciers and ice sheets (the cryosphere) as contributors to subglacial erosion, global biodiversity, and in regulating global biogeochemical cycles. In situ or in-field detection and characterisation of microbial communities is becoming recognised as an important approach to improve our understanding of such communities. Within this context we demonstrate, for the first time, the ability to detect Gram-negative bacteria in glacial field-environments (including subglacial environments) via the detection of lipopolysaccharide (LPS); an important component of Gram-negative bacterial cell walls. In-field measurements were performed using the recently commercialised PyroGene® recombinant Factor C (rFC) endotoxin detection system and used in conjunction with a handheld fluorometer to measure the fluorescent endpoint of the assay. Twenty-seven glacial samples were collected from the surface, bed and terminus of a low-biomass Arctic valley glacier (Engabreen, Northern Norway), and were analysed in a field laboratory using the rFC assay. Sixteen of these samples returned positive LPS detection. This work demonstrates that LPS detection via rFC assay is a viable in-field method and is expected to be a useful proxy for microbial cell concentrations in low biomass environments. PMID:25585634

Microbial Assimilation of Atmospheric CO2 to Synthesize Organic Matter in Soils

NASA Astrophysics Data System (ADS)

Ge, Tida

2014-05-01

Like higher plants, microbial autotrophs possess photosynthetic systems that enable them to fix CO2. Whilst present in large numbers in soils, the capacity for soil microorganisms to fix CO2 and their importance in terrestrial C cycling has not been quantified. To measure the activities of microbial autotrophs in assimilating atmospheric CO2, seven different soils were incubated with 14C labelled CO2 for 80 d, and the 14C-labelled organic C synthesized was determined. The results indicate that the synthesis rates of 14C-lablled organic C ranged from 0.0134 to 0.103 g C m-2 d-1, and were closely related to RubisCO activities and the abundance of cbbL-genes in the soils, indicating that the synthesis could be attributed to soil microbial autotrophs. This finding suggests that microbial assimilation of atmospheric CO2 is an important process in the sequestration and cycling of terrestrial C that, until now, has been largely ignored.

The global sulfur cycle

NASA Technical Reports Server (NTRS)

Sagan, D. (Editor)

1985-01-01

The results of the planetary biology microbial ecology's 1984 Summer Research Program, which examined various aspects of the global sulfur cycle are summarized. Ways in which sulfur flows through the many living and chemical species that inhabit the surface of the Earth were investigated. Major topics studied include: (1) sulfur cycling and metabolism of phototropic and filamentous sulfur bacteria; (2) sulfur reduction in sediments of marine and evaporite environments; (3) recent cyanobacterial mats; (4) microanalysis of community metabolism in proximity to the photic zone in potential stromatolites; and (5) formation and activity of microbial biofilms on metal sulfides and other mineral surfaces. Relationships between the global sulfur cycle and the understanding of the early evolution of the Earth and biosphere and current processes that affect global habitability are stressed.

Controlling Brochothrix thermosphacta as a spoilage risk using in-package atmospheric cold plasma.

PubMed

Patange, Apurva; Boehm, Daniela; Bueno-Ferrer, Carmen; Cullen, P J; Bourke, Paula

2017-09-01

Brochothrix thermosphacta is the predominant spoilage microorganism in meat and its control in processing environments is important to maintain meat product quality. Atmospheric cold plasma is of interest for control of pathogenic and spoilage microorganisms in foods. This study ascertained the potential of dielectric barrier discharge atmospheric cold plasma (DBD-ACP) for control of B. thermosphacta, taking microbial and food environment factors into consideration, and investigated the shelf-life of lamb chop after in-package plasma treatment in modified atmosphere. Community profiling was used to assess the treatment effects on the lamb microflora. ACP treatment (80 kV) for 30s inactivated B. thermosphacta populations below detection levels in PBS, while 5 min treatment achieved a 2 Log cycle reduction using a complex meat model medium and attached cells. The antimicrobial efficacy of plasma was reduced but still apparent on lamb chop surface-inoculated with high concentrations of B. thermosphacta. Lamb chop treated under modified atmosphere exhibited reduced microbial growth over the product shelf-life and community profiling showed no evident changes to the microbial populations after the treatment. The overall results indicated potential of ACP to enhance microbial control leading to meat storage life extension through adjusting the modality of treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

The genome sequence of Dyella jiangningensis FCAV SCS01 from a lignocellulose-decomposing microbial consortium metagenome reveals potential for biotechnological applications.

PubMed

Desiderato, Joana G; Alvarenga, Danillo O; Constancio, Milena T L; Alves, Lucia M C; Varani, Alessandro M

2018-05-14

Cellulose and its associated polymers are structural components of the plant cell wall, constituting one of the major sources of carbon and energy in nature. The carbon cycle is dependent on cellulose- and lignin-decomposing microbial communities and their enzymatic systems acting as consortia. These microbial consortia are under constant exploration for their potential biotechnological use. Herein, we describe the characterization of the genome of Dyella jiangningensis FCAV SCS01, recovered from the metagenome of a lignocellulose-degrading microbial consortium, which was isolated from a sugarcane crop soil under mechanical harvesting and covered by decomposing straw. The 4.7 Mbp genome encodes 4,194 proteins, including 36 glycoside hydrolases (GH), supporting the hypothesis that this bacterium may contribute to lignocellulose decomposition. Comparative analysis among fully sequenced Dyella species indicate that the genome synteny is not conserved, and that D. jiangningensis FCAV SCS01 carries 372 unique genes, including an alpha-glucosidase and maltodextrin glucosidase coding genes, and other potential biomass degradation related genes. Additional genomic features, such as prophage-like, genomic islands and putative new biosynthetic clusters were also uncovered. Overall, D. jiangningensis FCAV SCS01 represents the first South American Dyella genome sequenced and shows an exclusive feature among its genus, related to biomass degradation.

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust

PubMed Central

Robador, Alberto; Jungbluth, Sean P.; LaRowe, Douglas E.; Bowers, Robert M.; Rappé, Michael S.; Amend, Jan P.; Cowen, James P.

2015-01-01

The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown. Low-temperature (<100°C) fluid samples were investigated from two borehole observatories in the Juan de Fuca Ridge (JFR) flank, representing a range of upper oceanic basement thermal and geochemical properties. Microbial sulfate reduction rates (SRR) were measured in laboratory incubations with 35S-sulfate over a range of temperatures and the identity of the corresponding sulfate-reducing microorganisms (SRM) was studied by analyzing the sequence diversity of the functional marker dissimilatory (bi)sulfite reductase (dsrAB) gene. We found that microbial sulfate reduction was limited by the decreasing availability of organic electron donors in higher temperature, more altered fluids. Thermodynamic calculations indicate energetic constraints for metabolism, which together with relatively higher cell-specific SRR reveal increased maintenance requirements, consistent with novel species-level dsrAB phylotypes of thermophilic SRM. Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling. PMID:25642212

Sporulation and Germination patterns - hedging a bet on long term microbial survivability in dry soil

NASA Astrophysics Data System (ADS)

Claes, N.; Or, D.

2012-04-01

Soil hosts unparalleled diversity of microbial life that is constantly challenged by the vagaries of fluctuating ambient conditions. Desiccation stresses play a key role not only by directly affecting individual bacterial cells, but also by shaping diffusion pathways and cell dispersion. The gradual thinning and fragmentation of the aqueous environment during drying have led to different survival mechanisms including dormancy and sporulation, resulting in a highly resistive state capable of surviving extreme and prolonged environmental stresses until conditions improve in the future. Our aim is to investigate how temporal changes in hydration status shape microbial communities over time, based on simple survival strategy rules for each individual bacterium. The two survival strategies considered are dormancy and sporulation. Dormancy is the state in which bacterial cells significantly reduce their metabolism with minor morphological adaptations. The required energy and time for attaining this state are low relative to sporulation costs. Sporulation involves several morphological and biochemical changes that result in a resistive capsule that endures extreme stresses over long periods of time. The working hypothesis is that different micro-ecological conditions and community compositions would result from temporal patterns and magnitude of desiccation stresses. An Individual Based Model (IBM) considering habitats on rough soil surfaces and local effects of micro-hydrological conditions on dispersion and nutrient diffusion would enable systematic study of emerging communities over extended periods. Different population compositions are expected to emerge based on low and high frequency, duration and amplitudes of wetting-drying cycles reflecting relative success or failure of survival strategy.

Characterization of the Cell Surface Properties of Drinking Water Pathogens by Microbial Adhesion to Hydrocarbon and Electrophoretic Mobility Measurements

EPA Science Inventory

The surface characteristics of microbial cells directly influence their mobility and behavior within aqueous environments. The cell surface hydrophobicity (CSH) and electrophoretic mobility (EPM) of microbial cells impact a number of interactions and processes including aggregati...

Forest soil microbial communities: Using metagenomic approaches to survey permanent plots

Treesearch

Amy L. Ross-Davis; Jane E. Stewart; John W. Hanna; John D. Shaw; Andrew T. Hudak; Theresa B. Jain; Robert J. Denner; Russell T. Graham; Deborah S. Page-Dumroese; Joanne M. Tirocke; Mee-Sook Kim; Ned B. Klopfenstein

2014-01-01

Forest soil ecosystems include some of the most complex microbial communities on Earth (Fierer et al. 2012). These assemblages of archaea, bacteria, fungi, and protists play essential roles in biogeochemical cycles (van der Heijden et al. 2008) and account for considerable terrestrial biomass (Nielsen et al. 2011). Yet, determining the microbial composition of forest...

Oxygenated monoterpenes citral and carvacrol cause oxidative damage in Escherichia coli without the involvement of tricarboxylic acid cycle and Fenton reaction.

PubMed

Chueca, Beatriz; Pagán, Rafael; García-Gonzalo, Diego

2014-10-17

Oxygenated monoterpenes citral and carvacrol are common constituents of many essential oils (EOs) that have been extensively studied as antimicrobial agents but whose mechanisms of microbial inactivation have not been totally elucidated. A recent study described a mechanism of Escherichia coli death for (+)-limonene, a hydrocarbon monoterpene also frequently present in EOs, similar to the common mechanism proposed for bactericidal antibiotics. This mechanism involves the formation of Fenton-mediated hydroxyl radical, a reactive oxygen species (ROS), via tricarboxylic acid (TCA) cycle, which would ultimately inactivate cells. Our objective was to determine whether E. coli MG1655 inactivation by citral and carvacrol follows a similar mechanism of cell death. Challenging experiments with 300μL/L citral and 100μL/L carvacrol inactivated at least 2.5log10cycles of exponentially growing cells in 3h under aerobic conditions. The presence of thiourea (an ROS scavenger) reduced cell inactivation in 2log10cycles, demonstrating the role of ROS in cell death. Decreased resistance of a ΔrecA mutant (deficient in an enzyme involved in SOS response to DNA damage) indicated that citral and carvacrol caused oxidative damage to DNA. Although the mechanism of E. coli inactivation by carvacrol and citral was similarly mediated by ROS, their formation did not follow the same pathways described for (+)-limonene and bactericidal drugs because neither Fenton reaction nor NADH production via the TCA cycle was involved in cell death. Moreover, further experiments demonstrated antimicrobial activity of citral and carvacrol in anaerobic environments without the involvement of ROS. As a consequence, cell death by carvacrol and citral in anaerobiosis follows a different mechanism than that observed under aerobic conditions. These results demonstrated a different mechanism of inactivation by citral and carvacrol with regard to (+)-limonene and bactericidal antibiotics, indicating the complexity of the mechanisms of bacterial inactivation among EO constituents. Advancements in the description of these mechanisms will help in extending and improving the use of these compounds as natural antimicrobials. Copyright © 2014 Elsevier B.V. All rights reserved.

A comparative evaluation of different types of microbial electrolysis desalination cells for malic acid production.

PubMed

Liu, Guangli; Zhou, Ying; Luo, Haiping; Cheng, Xing; Zhang, Renduo; Teng, Wenkai

2015-12-01

The aim of this study was to investigate different microbial electrolysis desalination cells for malic acid production. The systems included microbial electrolysis desalination and chemical-production cell (MEDCC), microbial electrolysis desalination cell (MEDC) with bipolar membrane and anion exchange membrane (BP-A MEDC), MEDC with bipolar membrane and cation exchange membrane (BP-C MEDC), and modified microbial desalination cell (M-MDC). The microbial electrolysis desalination cells performed differently in terms of malic acid production and energy consumption. The MEDCC performed best with the highest malic acid production rate (18.4 ± 0.6 mmol/Lh) and the lowest energy consumption (0.35 ± 0.14 kWh/kg). The best performance of MEDCC was attributable to the neutral pH condition in the anode chamber, the lowest internal resistance, and the highest Geobacter percentage of the anode biofilm population among all the reactors. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ecology and thermal inactivation of microbes in and on interplanetary space vehicle components. [examined with a scanning electron microscope

NASA Technical Reports Server (NTRS)

Campbell, J. E.

1974-01-01

The uses of scanning electron microscopy in assessing changes that occur in spores exposed to wet and dry heat cycles at elevated temperatures were examined. Several species of Bacillus and other nonspore-forming species of organisms were used for the experiment. Surface morphology of viable and nonviable organisms was clearly detectable by this method, making it a potentially useful technique for investigating microbial inactivation on space vehicle surfaces and components. Micrographs of the spores and bacterial cells are provided.

Identifying the role of plant-microbial interactions in driving Arctic carbon cycle changes using a 13C isotope tracer

NASA Astrophysics Data System (ADS)

Hough, M.; Tfaily, M. M.; Blazewicz, S.; Dorrepaal, E.; Crill, P. M.; Rich, V. I.; Saleska, S. R.

2017-12-01

Thawing arctic permafrost (which contains 30-50% of global soil carbon) is expected to drive substantial alterations to carbon (C) cycling that will accelerate climate change. As permafrost thaws, old C may decompose more rapidly and be released as methane (CH4) and carbon dioxide (CO2), but thawing soil can also increase plant productivity as perennial shrub communities transition to faster growing annual wetland plants. The effect of plant community changes on the C cycle is not yet well understood. It could mitigate C loss if C input rates are high enough, or it could increase contributions to CH4 emission (a more potent greenhouse gas than CO2) if it decomposes anaerobically. To investigate the influence of fresh plant litter inputs on peat organic material, microbial communities, and greenhouse gas emissions we traced 13C-enriched plant material from Eriophorum and Sphagnum plants added to arctic peat decomposition incubations into each of these components. High resolution FT-ICR mass spectrometry showed changes in the types of enriched compounds over time indicative of microbial processing. Density fractionation of microbial DNA showed enrichment of the microbial community indicating uptake of 13C-enriched compounds from the plant litter. CO2 and CH4 fluxes were highly 13C enriched and showed three distinct phases of flux after litter addition which were not seen in incubations with no litter added. Together, these lines of evidence indicate that fresh litter inputs may play an important role in structuring microbial decomposition. Future work will explore this influence through closer examination of organic matter and microbial community changes during decomposition.

Temporal Stability of the Microbial Community in Sewage-Polluted Seawater Exposed to Natural Sunlight Cycles and Marine Microbiota

PubMed Central

Sassoubre, Lauren M.; Yamahara, Kevan M.

2015-01-01

Billions of gallons of untreated wastewater enter the coastal ocean each year. Once sewage microorganisms are in the marine environment, they are exposed to environmental stressors, such as sunlight and predation. Previous research has investigated the fate of individual sewage microorganisms in seawater but not the entire sewage microbial community. The present study used next-generation sequencing (NGS) to examine how the microbial community in sewage-impacted seawater changes over 48 h when exposed to natural sunlight cycles and marine microbiota. We compared the results from microcosms composed of unfiltered seawater (containing naturally occurring marine microbiota) and filtered seawater (containing no marine microbiota) to investigate the effect of marine microbiota. We also compared the results from microcosms that were exposed to natural sunlight cycles with those from microcosms kept in the dark to investigate the effect of sunlight. The microbial community composition and the relative abundance of operational taxonomic units (OTUs) changed over 48 h in all microcosms. Exposure to sunlight had a significant effect on both community composition and OTU abundance. The effect of marine microbiota, however, was minimal. The proportion of sewage-derived microorganisms present in the microcosms decreased rapidly within 48 h, and the decrease was the most pronounced in the presence of both sunlight and marine microbiota, where the proportion decreased from 85% to 3% of the total microbial community. The results from this study demonstrate the strong effect that sunlight has on microbial community composition, as measured by NGS, and the importance of considering temporal effects in future applications of NGS to identify microbial pollution sources. PMID:25576619

Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

PubMed Central

Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

2014-01-01

Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE PAGES

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

2017-05-02

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Effect of single- and two-cycle high hydrostatic pressure treatments on water properties, physicochemical and microbial qualities of minimally processed squids (todarodes pacificus).

PubMed

Zhang, Yifeng; Jiao, Shunshan; Lian, Zixuan; Deng, Yun; Zhao, Yanyun

2015-05-01

This study investigated the effect of single- and two-cycle high hydrostatic pressure (HHP) treatments on water properties, physicochemical, and microbial qualities of squids (Todarodes pacificus) during 4 °C storage for up to 10 d. Single-cycle treatments were applied at 200, 400, or 600 MPa for 20 min (S-200, S-400, and S-600), and two-cycle treatments consisted of two 10 min cycles at 200, 400, or 600 MPa, respectively (T-200, T-400, and T-600). HHP-treated samples had higher (P < 0.05) content of P2b (immobilized water) and P21 (myofibril water), but lower P22 (free water) than those of control. The single- and two-cycle HHP treatments at the same pressure level caused no significant difference in water state of squids. The two-cycle HHP treatment was more effective in controlling total volatile basic nitrogen, pH, and total plate counts (TPC) of squids during storage, in which TPC of S-600 and T-600 was 2.9 and 1.8 log CFU/g at 10 d, respectively, compared with 7.5 log CFU/g in control. HHP treatments delayed browning discoloration of the squids during storage, and the higher pressure level and two-cycle HHP were more effective. Water properties highly corresponded with color and texture indices of squids. This study demonstrated that the two-cycle HHP treatment was more effective in controlling microbial growth and quality deterioration while having similar impact on the physicochemical and water properties of squids in comparison with the single-cycle treatment, thus more desirable for extending shelf-life of fresh squids. © 2015 Institute of Food Technologists®

Nutrient Limitation of Microbial Mediated Decomposition and Arctic Soil Chronology

NASA Astrophysics Data System (ADS)

Melle, C. J.; Darrouzet-Nardi, A.; Wallenstein, M. D.

2012-12-01

Soils of northern permafrost regions currently contain twice as much carbon as the entire Earth's atmosphere. Traditionally, environmental constraints have limited microbial activity resulting in restricted decomposition of soil organic matter in these systems and accumulation of massive amounts of soil organic carbon (SOC), however climate change is reducing the constraints of decomposition in arctic permafrost regions. Carbon cycling in nutrient poor, arctic ecosystems is tightly coupled to other biogeochemical cycles. Several studies have suggested strong nitrogen limitations of primary productivity and potentially warm-season microbial activity in these nutrient deficient soils. Nitrogen is required for microbial extracellular enzyme production which drives the decomposition of soil organic matter (SOM). Nitrogen limited arctic soils may also experience limitation via labile carbon availability despite the SOM rich environment due to low extracellular enzyme production. Few studies have directly addressed nutrient induced microbial limitation in SOC rich arctic tundra soils, and even less is known about the potential for nutrient co-limitation. Additionally, through the process of becoming deglaciated, sites within close proximity to one another may have experienced drastic differences in their effective soil ages due to the varied length of their active histories. Many soil properties and nutrient deficiencies are directly related to soil age, however this chronology has not previously been a focus of research on nutrient limitation of arctic soil microbial activity. Understanding of nutrient limitations, as well as potential co-limitation, on arctic soil microbial activity has important implications for carbon cycling and the ultimate fate of the current arctic SOC reservoir. Analyses of nutrient limitation on soils of a single site are not adequate for fully understanding the controls on soil microbial activity across a vast land mass with large variation in effective soil age. My research is focused on addressing the questions of the extent of microbial N limitation in arctic tundra soils, the potential for co-limitation of labile C despite a high SOC environment, and the dependence, if any, nutrient limitation may have on the effective age of the soil. I have addressed these questions by conducting a laboratory soil incubation of factorial design with treatments of amended glucose, amended ammonium nitrate, and a control consisting of an addition of an equivalent volume of deionized water. Moist acid tundra soils possessing similar soil properties from two arctic sites of close proximity yet with varying deglaciation chronologies were utilized in my study. Soil properties of C-mineralization via respiration, microbial biomass, and nitrogen content in the forms of ammonium, nitrate, and total free amino acids and microbial extra-cellular enzyme production were assayed to determine the microbial response to the experimental treatments. Through the results of this work, I hope to better our understanding of biogeochemical cycling within arctic tundra ecosystems and the response to climate change by contributing to existing knowledge of nutrient limitation on microbial mediated decomposition of SOC in the arctic and how this may differ in soils of varying effective age.

Solar energy powered microbial fuel cell with a reversible bioelectrode.

PubMed

Strik, David P B T B; Hamelers, Hubertus V M; Buisman, Cees J N

2010-01-01

The solar energy powered microbial fuel cell is an emerging technology for electricity generation via electrochemically active microorganisms fueled by solar energy via in situ photosynthesized metabolites from algae, cyanobacteria, or living higher plants. A general problem with microbial fuel cells is the pH membrane gradient which reduces cell voltage and power output. This problem is caused by acid production at the anode, alkaline production at the cathode, and the nonspecific proton exchange through the membrane. Here we report a solution for a new kind of solar energy powered microbial fuel cell via development of a reversible bioelectrode responsible for both biocatalyzed anodic and cathodic electron transfer. Anodic produced protons were used for the cathodic reduction reaction which held the formation of a pH membrane gradient. The microbial fuel cell continuously generated electricity and repeatedly reversed polarity dependent on aeration or solar energy exposure. Identified organisms within biocatalyzing biofilm of the reversible bioelectrode were algae, (cyano)bacteria and protozoa. These results encourage application of solar energy powered microbial fuel cells.

Microbial H2 cycling does not affect δ2H values of ground water

USGS Publications Warehouse

Landmeyer, J.E.; Chapelle, F.H.; Bradley, P.M.

2000-01-01

Stable hydrogen-isotope values of ground water (δ2H) and dissolved hydrogen concentrations (H(2(aq)) were quantified in a petroleum-hydrocarbon contaminated aquifer to determine whether the production/consumption of H2 by subsurface microorganisms affects ground water &delta2H values. The range of &delta2H observed in monitoring wells sampled (-27.8 ‰c to -15.5 ‰c) was best explained, however, by seasonal differences in recharge temperature as indicated using ground water δ18O values, rather than isotopic exchange reactions involving the microbial cycling of H2 during anaerobic petroleum-hydrocarbon biodegradation. The absence of a measurable hydrogen-isotope exchange between microbially cycled H2 and ground water reflects the fact that the amount of H2 available from the anaerobic decomposition of petroleum hydrocarbons is small relative to the amount of hydrogen present in water, even though milligram per liter concentrations of readily biodegradable contaminants are present at the study site. Additionally, isotopic fractionation calculations indicate that in order for H2 cycling processes to affect δ2H values of ground water, relatively high concentrations of H2 (>0.080 M) would have to be maintained, considerably higher than the 0.2 to 26 nM present at this site and characteristic of anaerobic conditions in general. These observations suggest that the conventional approach of using δ2H and δ18O values to determine recharge history is appropriate even for those ground water systems characterized by anaerobic conditions and extensive microbial H2 cycling.

Effect of exogenous carbon addition and the freeze-thaw cycle on soil microbes and mineral nitrogen pools1

NASA Astrophysics Data System (ADS)

Hu, Xia; Yin, Peng; Nong, Xiang; Liao, Jinhua

2018-01-01

To elucidate the alpine soil process in winter, the response mechanism of soil mineral nitrogen and soil microbes to exogenous carbon (0 mg C, 1 mg C, 2 mg C, 4 mg C and 8 mg C·g-1 dry soil) and the freeze-thaw cycle (-2 °C, -2 ∼ 2 °C, -20 ∼2°C) were studied by laboratory simulation. The freeze-thaw treatment had no significant effect on microbial biomass nitrogen and the number of bacteria. The soil mineral N pool, the number of fungi, and enzyme activities were obviously affected by the freeze-thaw cycle. A mild freeze-thaw cycle (-2∼2°C) significantly increased the number of fungi and catalase activity, while severe freeze-thaw cycle (-20∼2°C) obviously decreased invertase activity. The results suggested that both the freeze-thaw rate and freeze-thaw temperature amplitudes have a strong effect on soil microbial dynamics in the alpine zone in winter. The results showed that exogenous carbon addition significantly decreased soil NO3-N and NH4 +-N contents, increased soil microbial biomass, the number of microbes, and soil enzyme activities. The results showed that microbial growth in the eastern Tibetan Plateau was somewhat limited by available C. It may represent a larger potential pulse of soil nutrient for alpine plants in the next spring, and may be instrumental for plant community shifts under future climate change predictions due to the possible increased litter addition.

High Carbon Use Efficiency is Not Explained by Production of Storage Compounds

NASA Astrophysics Data System (ADS)

Dijkstra, Paul; van Groenigen, Kees-Jan

2015-04-01

The efficiency with which microbes use substrate to make new microbial biomass (Carbon Use Efficiency or CUE; mol C / mol C) is an important variable in soil and ecosystem C cycling models. Estimates of CUE in soil microbial communities vary widely. It has been hypothesized that high values of CUE are associated with production of storage compounds following a sudden increases in substrate availability during CUE measurements. In that case, these high CUE values would not be representative for balanced microbial growth (i.e. the production of all compounds needed to make new microbial cells). To test this hypothesis, we added position-specific 13C-labeled glucose isotopomers in parallel incubations of a ponderosa pine and piñon-juniper soil. We compared the measured pattern of CO2 release for the six glucose C atoms with patterns of CO2 production expected for balanced growth with a low, medium, or high CUE, and with CO2 production patterns associated with production of storage compounds (glycogen, lipids, or polyhydroxybutyrate). The measured position-specific CO2 production did not match that for production of glycogen, lipids, or polyhydroxybutyrate, but agreed closely with that expected for balanced growth at high CUE and high pentose phosphate pathway activity. We conclude that soil microbial communities utilize glucose substrate for biomass growth with high CUE, and that addition of small amounts of 13C-labeled glucose tracers do not affect CUE or induce storage compounds production. We submit that the measurement of position-specific CO2 production offers a quick and easy way to test biochemically explicit hypotheses concerning microbial growth metabolism.

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

PubMed Central

Imachi, Hiroyuki; Aoi, Ken; Tasumi, Eiji; Saito, Yumi; Yamanaka, Yuko; Saito, Yayoi; Yamaguchi, Takashi; Tomaru, Hitoshi; Takeuchi, Rika; Morono, Yuki; Inagaki, Fumio; Takai, Ken

2011-01-01

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life. PMID:21654849

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor.

PubMed

Imachi, Hiroyuki; Aoi, Ken; Tasumi, Eiji; Saito, Yumi; Yamanaka, Yuko; Saito, Yayoi; Yamaguchi, Takashi; Tomaru, Hitoshi; Takeuchi, Rika; Morono, Yuki; Inagaki, Fumio; Takai, Ken

2011-12-01

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life.

FLUORESCENT IN SITU HYBRIDIZATION AND MICROAUTORADIOGRAPHY APPLIED TO ECOPHYSIOLOGY IN SOIL

EPA Science Inventory

Soil microbial communities perform many important processes, including nutrient cycling, plant-microorganism interactions, and degradation of xenobiotics. The study of microbial communities, however, has been limited by cultural methods, which may greatly underestimate diversity....

Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

PubMed

Huang, Qiuyuan; Briggs, Brandon R; Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China

PubMed Central

Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change. PMID:25365331

Data-model integration to interpret connectivity between biogeochemical cycling, and vegetation phenology and productivity in mountainous ecosystems under changing hydrologic regimes

NASA Astrophysics Data System (ADS)

Brodie, E.; Arora, B.; Beller, H. R.; Bill, M.; Bouskill, N.; Chakraborty, R.; Conrad, M. E.; Dafflon, B.; Enquist, B. J.; Falco, N.; Henderson, A.; Karaoz, U.; Polussa, A.; Sorensen, P.; Steltzer, H.; Wainwright, H. M.; Wang, S.; Williams, K. H.; Wilmer, C.; Wu, Y.

2017-12-01

In mountainous systems, snow-melt is associated with a large pulse of nutrients that originates from under-snow microbial mineralization of organic matter and microbial biomass turnover. Vegetation phenology in these systems is regulated by environmental cues such as air temperature ranges and photoperiod, such that, under typical conditions, vegetation greening and nutrient uptake occur in sync with microbial biomass turnover and nutrient release, closing nutrient cycles and enhancing nutrient retention. However, early snow-melt has been observed with increasing frequency in the mountainous west and is hypothesized to disrupt coupled plant-microbial behavior, potentially resulting in a temporal discontinuity between microbial nutrient release and vegetation greening. As part of the Watershed Function Scientific Focus Area (SFA) at Berkeley Lab we are quantifying below-ground biogeochemistry and above-ground phenology and vegetation chemistry and their relationships to hydrologic events at a lower montane hillslope in the East River catchment, Crested Butte, CO. This presentation will focus on data-model integration to interpret connectivity between biogeochemical cycling of nitrogen and vegetation nitrogen demand. Initial model results suggest that early snow-melt will result in an earlier accumulation and leaching loss of nitrate from the upper soil depths but that vegetation productivity may not decline as traits such as greater rooting depth and resource allocation to stems are favored.

Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

NASA Astrophysics Data System (ADS)

He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

2014-12-01

Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

Soil microbial and nutrient responses to 7 years of seasonally altered precipitation in a Chihuahuan Desert grassland.

PubMed

Bell, Colin W; Tissue, David T; Loik, Michael E; Wallenstein, Matthew D; Acosta-Martinez, Veronica; Erickson, Richard A; Zak, John C

2014-05-01

Soil microbial communities in Chihuahuan Desert grasslands generally experience highly variable spatiotemporal rainfall patterns. Changes in precipitation regimes can affect belowground ecosystem processes such as decomposition and nutrient cycling by altering soil microbial community structure and function. The objective of this study was to determine if increased seasonal precipitation frequency and magnitude over a 7-year period would generate a persistent shift in microbial community characteristics and soil nutrient availability. We supplemented natural rainfall with large events (one/winter and three/summer) to simulate increased precipitation based on climate model predictions for this region. We observed a 2-year delay in microbial responses to supplemental precipitation treatments. In years 3-5, higher microbial biomass, arbuscular mycorrhizae abundance, and soil enzyme C and P acquisition activities were observed in the supplemental water plots even during extended drought periods. In years 5-7, available soil P was consistently lower in the watered plots compared to control plots. Shifts in soil P corresponded to higher fungal abundances, microbial C utilization activity, and soil pH. This study demonstrated that 25% shifts in seasonal rainfall can significantly influence soil microbial and nutrient properties, which in turn may have long-term effects on nutrient cycling and plant P uptake in this desert grassland. © 2013 John Wiley & Sons Ltd.

Understanding soil health by capitalizing on long-term field studies

NASA Astrophysics Data System (ADS)

Tavakkoli, Ehsan; Wang, Zhe; VanZweieten, Lukas; Rose, Michael

2017-04-01

Microbial biodiversity in Australian agricultural soils is of paramount importance as it plays a critical role in regulating soil health, plant productivity, and the cycling of carbon, nitrogen, and other nutrients. Agricultural practices strongly affect soil microbial communities by changing the physical and chemical characteristics of the soil in which microorganisms live, thereby affecting their abundance, diversity, and activity. Despite its importance, the specific responses of various microbial groups to changing environmental conditions (e.g. increased/decreased carbon in response to land management) in agricultural soils are not well understood. This knowledge gap is largely due to previous methodological limitations that, until recently, did not allow microbial diversity and functioning to be meaningfully investigated on large numbers of samples. We sampled soils from a field trial on the effect of strategic tillage in no-till systems to examine the potential impact of tillage and stubble management on soil microbial composition. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used bar-coded high-throughput sequencing. Bioinformatics of the sequencing generated data was performed using a previously scripted and tested pipeline, and involved allocation of the relevant sequences to their samples of origin according to the bar-code. In parallel, changes in soil quality and microbial functionality were determined using multi-enzyme activity assay and multiple substrate-induced respiration. The extracellular enzyme activities that were measured include: β-1,4-glucosidase, β-D-cellobiohydrolase, β-Xylosidase, and α-1,4-glucosidase which are all relevant to the C cycle; β-1,4-N-acetylglucosaminidase and L-leucine aminopeptidase which are both relevant to the N cycle associated and associated with protein catabolism. In this presentation, analyses of soil health and functionality in relation to its response to various agronomic practices and implications for C sequestration and nutrient cycling will be discussed.

Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction.

PubMed

Larsen, Peter; Hamada, Yuki; Gilbert, Jack

2012-07-31

Never has there been a greater opportunity for investigating microbial communities. Not only are the profound effects of microbial ecology on every aspect of Earth's geochemical cycles beginning to be understood, but also the analytical and computational tools for investigating microbial Earth are undergoing a rapid revolution. This environmental microbial interactome, the system of interactions between the microbiome and the environment, has shaped the planet's past and will undoubtedly continue to do so in the future. We review recent approaches for modeling microbial community structures and the interactions of microbial populations with their environments. Different modeling approaches consider the environmental microbial interactome from different aspects, and each provides insights to different facets of microbial ecology. We discuss the challenges and opportunities for the future of microbial modeling and describe recent advances in microbial community modeling that are extending current descriptive technologies into a predictive science. Copyright © 2012 Elsevier B.V. All rights reserved.

Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging

PubMed Central

Greening, Chris; Carere, Carlo R.; Rushton-Green, Rowena; Harold, Liam K.; Hards, Kiel; Taylor, Matthew C.; Morales, Sergio E.; Stott, Matthew B.; Cook, Gregory M.

2015-01-01

The majority of microbial cells in global soils exist in a spectrum of dormant states. However, the metabolic processes that enable them to survive environmental challenges, such as nutrient-limitation, remain to be elucidated. In this work, we demonstrate that energy-starved cultures of Pyrinomonas methylaliphatogenes, an aerobic heterotrophic acidobacterium isolated from New Zealand volcanic soils, persist by scavenging the picomolar concentrations of H2 distributed throughout the atmosphere. Following the transition from exponential to stationary phase due to glucose limitation, the bacterium up-regulates by fourfold the expression of an eight-gene operon encoding an actinobacteria-type H2-uptake [NiFe]-hydrogenase. Whole-cells of the organism consume atmospheric H2 in a first-order kinetic process. Hydrogen oxidation occurred most rapidly under oxic conditions and was weakly associated with the cell membrane. We propose that atmospheric H2 scavenging serves as a mechanism to sustain the respiratory chain of P. methylaliphatogenes when organic electron donors are scarce. As the first observation of H2 oxidation to our knowledge in the Acidobacteria, the second most dominant soil phylum, this work identifies new sinks in the biogeochemical H2 cycle and suggests that trace gas oxidation may be a general mechanism for microbial persistence. PMID:26240343

Hydration dynamics promote bacterial coexistence on rough surfaces

PubMed Central

Wang, Gang; Or, Dani

2013-01-01

Identification of mechanisms that promote and maintain the immense microbial diversity found in soil is a central challenge for contemporary microbial ecology. Quantitative tools for systematic integration of complex biophysical and trophic processes at spatial scales, relevant for individual cell interactions, are essential for making progress. We report a modeling study of competing bacterial populations cohabiting soil surfaces subjected to highly dynamic hydration conditions. The model explicitly tracks growth, motion and life histories of individual bacterial cells on surfaces spanning dynamic aqueous networks that shape heterogeneous nutrient fields. The range of hydration conditions that confer physical advantages for rapidly growing species and support competitive exclusion is surprisingly narrow. The rapid fragmentation of soil aqueous phase under most natural conditions suppresses bacterial growth and cell dispersion, thereby balancing conditions experienced by competing populations with diverse physiological traits. In addition, hydration fluctuations intensify localized interactions that promote coexistence through disproportional effects within densely populated regions during dry periods. Consequently, bacterial population dynamics is affected well beyond responses predicted from equivalent and uniform hydration conditions. New insights on hydration dynamics could be considered in future designs of soil bioremediation activities, affect longevity of dry food products, and advance basic understanding of bacterial diversity dynamics and its role in global biogeochemical cycles. PMID:23051694

Linking the response of bacterial populations to plant development through analysis of rhizosphere-competence traits of soil bacteria

NASA Astrophysics Data System (ADS)

Cho, H. J.; Karaoz, U.; Zhalnina, K.; Firestone, M. K.; Brodie, E.

2016-12-01

A growing plant root exudes changing combinations of compounds including root litter and other detritus throughout its developmental stages, providing a major source of organic C for rhizosphere bacteria. Clear patterns of microbial succession have been observed in the rhizosphere of a number of plants. These patterns of microbial succession are likely key to the processing of soil organic carbon and nutrient recycling. What is less well understood are the microbial traits, or combinations of traits, selected for during plant development. Are these traits or trait-combinations conserved, and is phylogeny a useful integrator of traits? Understanding the mechanisms underlying ecological succession would enable improved prediction of future rhizosphere states and consequences for C and nutrient cycles. In this study, we resolve the responses of rhizosphere bacteria at strain-level during plant (Avena fatua) developmental stages using both isolation and metagenomic approaches. Metagenome reads from bulk and rhizosphere soils were mapped to the genomes of thirty nine bacterial isolates numerically abundant ( 0.5% in relative abundance) and phylogenetically representative of these soils, and also to ninety six metagenome-derived genome bins. Analysis of temporal coverage patterns demonstrate that bacteria can be classified as positive and negative rhizosphere responders, with traits associated with root exudate utilization being important. Significant strain level diversity was observed and variance in the temporal coverage patterns further distinguished closely related strains of the same genera. For example, while a number of strains from the Bradyrhizobia, Mesorhizobia and Mycobacteria all increased in coverage with root growth, suggesting that recently acquired traits are selected for. Candidate traits distinguishing closely related strains included those related to xylose and other plant cell-wall derived sugar utilization, motility and aromatic organic acid utilization. These combinations of traits act together to influence rhizosphere bacterial succession, and developing linkages to other traits related to carbon and nutrient cycling will be key to understanding the feedbacks between plant response to environmental change and soil biogeochemical cycles.

Elevated temperature alters carbon cycling in a model microbial community

NASA Astrophysics Data System (ADS)

Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

2013-12-01

Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other microbial activities. When scaled to more complex ecosystems and integrated into Earth System Models, this approach could significantly improve predictions of global carbon-climate feedbacks. Experiments such as these are a critical first step designed at understanding climate change impacts in order to better predict ecosystem adaptations, assess the viability of mitigation strategies, and inform relevant policy decisions.

Deep sea microbial fuel cell output as a proxy for microbial activity

NASA Astrophysics Data System (ADS)

Richter, K.; George, R.; Hardy, K. R.

2016-02-01

Abstract: Microbial fuel cells (MFCs) work by providing bacteria in anaerobic sediments with an electron acceptor (anode) that stimulates metabolism of organic matter. The buried anode is connected via control circuitry to a cathode exposed to oxygen in the overlying water. During metabolism, bacteria release hydrogen ions into the sediment and transfer electrons extra-cellularly to the anode, which eventually reduce dissolved oxygen at the cathode, forming water. The current is chiefly limited by the rate of microbial metabolism at the anode and serves as a proxy for microbial activity. The Office of Naval Research has encouraged development of microbial fuel cells in the marine environment at a number of academic and naval institutions and studies of important environmental parameters that affect fuel cell performance. Earlier work in shallow sediments of San Diego Bay showed that the most important environmental parameters that control fuel cell power output in San Diego Bay were total organic carbon in the sediment and seasonal water temperature. Current MFC work at SPAWAR includes extension of microbial fuel cell tests to the deep sea environment (>4000 m) and, in parallel, testing microbial fuel cells in the laboratory under deep sea conditions. We are pursuing a field efforts to deploy a microbial fuel cell in progressively deeper water, record in situ power and temperature over several weeks, and retrieve the fuel cell along with sediment samples for analysis. We are also pursuing a laboratory effort to build a matching microbial fuel cell in a pressure vessel capable of matching the pressure and temperature of deep water, and stocking the pressure vessel with deep water sediment in order to take measurements analogous to those in the field. We also hope to determine whether bacteria growing on the anode are different from bacteria growing in the bulk sediment via DNA analysis. The current progress and results from this work at SPAWAR will be presented.

Toward Understanding, Managing, and Protecting Microbial Ecosystems

PubMed Central

Bodelier, Paul L. E.

2011-01-01

Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity–conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology. PMID:21747797

Durability and regeneration of activated carbon air-cathodes in long-term operated microbial fuel cells

NASA Astrophysics Data System (ADS)

Zhang, Enren; Wang, Feng; Yu, Qingling; Scott, Keith; Wang, Xu; Diao, Guowang

2017-08-01

The performance of activated carbon catalyst in air-cathodes in microbial fuel cells was investigated over one year. A maximum power of 1722 mW m-2 was produced within the initial one-month microbial fuel cell operation. The air-cathodes produced a maximum power >1200 mW m-2 within six months, but gradually became a limiting factor for the power output in prolonged microbial fuel cell operation. The maximum power decreased by 55% when microbial fuel cells were operated over one year due to deterioration in activated carbon air-cathodes. While salt/biofilm removal from cathodes experiencing one-year operation increased a limiting performance enhancement in cathodes, a washing-drying-pressing procedure could restore the cathode performance to its original levels, although the performance restoration was temporary. Durable cathodes could be regenerated by re-pressing activated carbon catalyst, recovered from one year deteriorated air-cathodes, with new gas diffusion layer, resulting in ∼1800 mW m-2 of maximum power production. The present study indicated that activated carbon was an effective catalyst in microbial fuel cell cathodes, and could be recovered for reuse in long-term operated microbial fuel cells by simple methods.

Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes

PubMed Central

Andrei, Adrian-Ştefan; Robeson, Michael S; Baricz, Andreea; Coman, Cristian; Muntean, Vasile; Ionescu, Artur; Etiope, Giuseppe; Alexe, Mircea; Sicora, Cosmin Ionel; Podar, Mircea; Banciu, Horia Leonard

2015-01-01

Hypersaline meromictic lakes are extreme environments in which water stratification is associated with powerful physicochemical gradients and high salt concentrations. Furthermore, their physical stability coupled with vertical water column partitioning makes them important research model systems in microbial niche differentiation and biogeochemical cycling. Here, we compare the prokaryotic assemblages from Ursu and Fara Fund hypersaline meromictic lakes (Transylvanian Basin, Romania) in relation to their limnological factors and infer their role in elemental cycling by matching taxa to known taxon-specific biogeochemical functions. To assess the composition and structure of prokaryotic communities and the environmental factors that structure them, deep-coverage small subunit (SSU) ribosomal RNA (rDNA) amplicon sequencing, community domain-specific quantitative PCR and physicochemical analyses were performed on samples collected along depth profiles. The analyses showed that the lakes harbored multiple and diverse prokaryotic communities whose distribution mirrored the water stratification patterns. Ursu Lake was found to be dominated by Bacteria and to have a greater prokaryotic diversity than Fara Fund Lake that harbored an increased cell density and was populated mostly by Archaea within oxic strata. In spite of their contrasting diversity, the microbial populations indigenous to each lake pointed to similar physiological functions within carbon degradation and sulfate reduction. Furthermore, the taxonomy results coupled with methane detection and its stable C isotope composition indicated the presence of a yet-undescribed methanogenic group in the lakes' hypersaline monimolimnion. In addition, ultrasmall uncultivated archaeal lineages were detected in the chemocline of Fara Fund Lake, where the recently proposed Nanohaloarchaeota phylum was found to thrive. PMID:25932617

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism

PubMed Central

Elshahed, Mostafa S.; Najar, Fares Z.; Krumholz, Lee R.

2015-01-01

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring’s source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons. PMID:26417542

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism.

PubMed

Spain, Anne M; Elshahed, Mostafa S; Najar, Fares Z; Krumholz, Lee R

2015-01-01

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring's source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons.

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring

PubMed Central

Ward, Laura; Taylor, Michael W; Power, Jean F; Scott, Bradley J; McDonald, Ian R; Stott, Matthew B

2017-01-01

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40–60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats. PMID:28072418

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring.

PubMed

Ward, Laura; Taylor, Michael W; Power, Jean F; Scott, Bradley J; McDonald, Ian R; Stott, Matthew B

2017-05-01

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats.

Legacy effects overwhelm the short-term effects of exotic plant invasion and restoration on soil microbial community structure, enzyme activities, and nitrogen cycling.

PubMed

Elgersma, Kenneth J; Ehrenfeld, Joan G; Yu, Shen; Vor, Torsten

2011-11-01

Plant invasions can have substantial consequences for the soil ecosystem, altering microbial community structure and nutrient cycling. However, relatively little is known about what drives these changes, making it difficult to predict the effects of future invasions. In addition, because most studies compare soils from uninvaded areas to long-established dense invasions, little is known about the temporal dependence of invasion impacts. We experimentally manipulated forest understory vegetation in replicated sites dominated either by exotic Japanese barberry (Berberis thunbergii), native Viburnums, or native Vacciniums, so that each vegetation type was present in each site-type. We compared the short-term effect of vegetation changes to the lingering legacy effects of the previous vegetation type by measuring soil microbial community structure (phospholipid fatty acids) and function (extracellular enzymes and nitrogen mineralization). We also replaced the aboveground litter in half of each plot with an inert substitute to determine if changes in the soil microbial community were driven by aboveground or belowground plant inputs. We found that after 2 years, the microbial community structure and function was largely determined by the legacy effect of the previous vegetation type, and was not affected by the current vegetation. Aboveground litter removal had only weak effects, suggesting that changes in the soil microbial community and nutrient cycling were driven largely by belowground processes. These results suggest that changes in the soil following either invasion or restoration do not occur quickly, but rather exhibit long-lasting legacy effects from previous belowground plant inputs.

Observation to Theory in Deep Subsurface Microbiology Research: Can We Piece It Together?

NASA Astrophysics Data System (ADS)

Colwell, F. S.; Thurber, A. R.

2016-12-01

Three decades of observations of microbes in deep environments have led to startling discoveries of life in the subsurface. Now, a few theoretical frameworks exist that help to define Stygian life. Temperature, redox gradients, productivity (e.g., in the overlying ocean), and microbial power requirements are thought to determine the distribution of microbes in the subsurface. Still, we struggle to comprehend the spatial and temporal spectra of Earth processes that define how deep microbe communities survive. Stommel diagrams, originally used to guide oceanographic sampling, may be useful in depicting the subsurface where microbial communities are impacted by co-occurring spatial and temporal phenomena that range across exponential scales. Spatially, the geological settings that influence the activity and distribution of microbes range from individual molecules or minerals all the way up to the planetary-scale where geological formations, occupying up to 105 km3, dictate the bio- and functional geography of microbial communities. Temporally, life in the subsurface may respond in time units familiar to humans (e.g., seconds to days) or to events that unfold over hundred millennial time periods. While surface community dynamics are underpinned by solar and lunar cycles, these cycles only fractionally dictate survival underground where phenomena like tectonic activity, isostatic rebound, and radioactive decay are plausible drivers of microbial life. Geological or planetary processes that occur on thousand or million year cycles could be uniquely important to microbial viability in the subsurface. Such an approach aims at a holistic comprehension of the interaction of Earth system dynamics with microbial ecology.

Modelling microbial exchanges between forms of soil nitrogen in contrasting ecosystems

NASA Astrophysics Data System (ADS)

Pansu, M.; Machado, D.; Bottner, P.; Sarmiento, L.

2014-02-01

Although nitrogen (N) is often combined with carbon (C) in organic molecules, C passes from the air to the soil through plant photosynthesis, whereas N passes from the soil to plants through a chain of microbial conversions. However, dynamic models do not fully consider the microorganisms at the centre of exchange processes between organic and mineral forms of N. This study monitored the transfer of 14C and 15N between plant materials, microorganisms, humified compartments, and inorganic forms in six very different ecosystems along an altitudinal transect. The microbial conversions of the 15N forms appear to be strongly linked to the previously modelled C cycle, and the same equations and parameters can be used to model both C and N cycles. The only difference is in the modelling of the flows between microbial and inorganic forms. The processes of mineralization and immobilization of N appear to be regulated by a two-way microbial exchange depending on the C : N ratios of microorganisms and available substrates. The MOMOS (Modelling of Organic Matter of Soils) model has already been validated for the C cycle and also appears to be valid for the prediction of microbial transformations of N forms. This study shows that the hypothesis of microbial homeostasis can give robust predictions at global scale. However, the microbial populations did not appear to always be independent of the external constraints. At some altitudes their C : N ratio could be better modelled as decreasing during incubation and increasing with increasing C storage in cold conditions. The ratio of potentially mineralizable-15N/inorganic-15N and the 15N stock in the plant debris and the microorganisms was modelled as increasing with altitude, whereas the 15N storage in stable humus was modelled as decreasing with altitude. This predicts that there is a risk that mineralization of organic reserves in cold areas may increase global warming.

Winter ecology of a subalpine grassland: Effects of snow removal on soil respiration, microbial structure and function.

PubMed

Gavazov, Konstantin; Ingrisch, Johannes; Hasibeder, Roland; Mills, Robert T E; Buttler, Alexandre; Gleixner, Gerd; Pumpanen, Jukka; Bahn, Michael

2017-07-15

Seasonal snow cover provides essential insulation for mountain ecosystems, but expected changes in precipitation patterns and snow cover duration due to global warming can influence the activity of soil microbial communities. In turn, these changes have the potential to create new dynamics of soil organic matter cycling. To assess the effects of experimental snow removal and advanced spring conditions on soil carbon (C) and nitrogen (N) dynamics, and on the biomass and structure of soil microbial communities, we performed an in situ study in a subalpine grassland in the Austrian Alps, in conjunction with soil incubations under controlled conditions. We found substantial winter C-mineralisation and high accumulation of inorganic and organic N in the topsoil, peaking at snowmelt. Soil microbial biomass doubled under the snow, paralleled by a fivefold increase in its C:N ratio, but no apparent change in its bacteria-dominated community structure. Snow removal led to a series of mild freeze-thaw cycles, which had minor effects on in situ soil CO 2 production and N mineralisation. Incubated soil under advanced spring conditions, however, revealed an impaired microbial metabolism shortly after snow removal, characterised by a limited capacity for C-mineralisation of both fresh plant-derived substrates and existing soil organic matter (SOM), leading to reduced priming effects. This effect was transient and the observed recovery in microbial respiration and SOM priming towards the end of the winter season indicated microbial resilience to short-lived freeze-thaw disturbance under field conditions. Bacteria showed a higher potential for uptake of plant-derived C substrates during this recovery phase. The observed temporary loss in microbial C-mineralisation capacity and the promotion of bacteria over fungi can likely impede winter SOM cycling in mountain grasslands under recurrent winter climate change events, with plausible implications for soil nutrient availability and plant-soil interactions. Copyright © 2017 Elsevier B.V. All rights reserved.

Oxygen Minimum Zones in Miniature: Microbial Community Diversity, Activity, and Assembly Across Oxygen Gradients in Meromictic Marine Lakes, Palau

NASA Astrophysics Data System (ADS)

Beman, J. M.

2016-02-01

Oxygen minimum zones (OMZs) play a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet our understanding of these changes is limited by a lack of systematic analyses of low-oxygen ecosystems. In particular, forecasting biogeochemical feedbacks to deoxygenation requires detailed knowledge of microbial community assembly and activity as oxygen declines. Marine `lakes'—isolated bodies of seawater surrounded by land—are an ideal comparative system, as they provide a pronounced oxygen gradient extending from well-mixed, holomictic lakes to stratified, meromictic lakes that vary in their extent of anoxia. We examined 13 marine lakes using pyrosequencing of 16S rRNA genes, quantitative PCR for nitrogen (N)- and sulfur (S)-cycling functional genes and groups, and N- and carbon (C)-cycling rate measurements. All lakes were inhabited by well-known marine bacteria, demonstrating the broad relevance of this study system. Microbial diversity was typically highest in the anoxic monimolimnion of meromictic lakes, with marine cyanobacteria, SAR11, and other common bacteria replaced by anoxygenic phototrophs, sulfate-reducing bacteria (SRBs), and SAR406 in the monimolimnion. Denitrifier nitrite reductase (nirS) genes were also detected alongside high abundances (>106 ml-1) of dissimilatory sulfite reductase (dsrA) genes from SRBs in the monimolimnion. Sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis=76%) and deterministic processes dominated community assembly at all depths (nearest taxon index values >4). These results indicate that oxygen is a strong, deterministic driver of microbial community assembly. We also observed enhanced N- and C-cycling rates along the transition from hypoxic to anoxic to sulfidic conditions, suggesting that microbial communities form a positive feedback loop that may accelerate deoxygenation and OMZ expansion.

Effects of Bromus tectorum invasion on microbial carbon and nitrogen cycling in two adjacent undisturbed arid grassland communities

USGS Publications Warehouse

Schaeffer, Sean M.; Ziegler, Susan E.; Belnap, Jayne; Evans, R.D.

2012-01-01

Soil nitrogen (N) is an important component in maintaining ecosystem stability, and the introduction of non-native plants can alter N cycling by changing litter quality and quantity, nutrient uptake patterns, and soil food webs. Our goal was to determine the effects of Bromus tectorum (C3) invasion on soil microbial N cycling in adjacent non-invaded and invaded C3 and C4 native arid grasslands. We monitored resin-extractable N, plant and soil δ13C and δ15N, gross rates of inorganic N mineralization and consumption, and the quantity and isotopic composition of microbial phospholipid biomarkers. In invaded C3 communities, labile soil organic N and gross and net rates of soil N transformations increased, indicating an increase in overall microbial N cycling. In invaded C4 communities labile soil N stayed constant, but gross N flux rates increased. The δ13C of phospholipid biomarkers in invaded C4 communities showed that some portion of the soil bacterial population preferentially decomposed invader C3-derived litter over that from the native C4 species. Invasion in C4 grasslands also significantly decreased the proportion of fungal to bacterial phospholipid biomarkers. Different processes are occurring in response to B. tectorum invasion in each of these two native grasslands that: 1) alter the size of soil N pools, and/or 2) the activity of the microbial community. Both processes provide mechanisms for altering long-term N dynamics in these ecosystems and highlight how multiple mechanisms can lead to similar effects on ecosystem function, which may be important for the construction of future biogeochemical process models.

Adaptability in linkage of soil carbon nutrient cycles - the SEAM model

NASA Astrophysics Data System (ADS)

Wutzler, Thomas; Zaehle, Sönke; Schrumpf, Marion; Ahrens, Bernhard; Reichstein, Markus

2017-04-01

In order to understand the coupling of carbon (C) and nitrogen (N) cycles, it is necessary to understand C and N-use efficiencies of microbial soil organic matter (SOM) decomposition. While important controls of those efficiencies by microbial community adaptations have been shown at the scale of a soil pore, an abstract simplified representation of community adaptations is needed at ecosystem scale. Therefore we developed the soil enzyme allocation model (SEAM), which takes a holistic, partly optimality based approach to describe C and N dynamics at the spatial scale of an ecosystem and time-scales of years and longer. We explicitly modelled community adaptation strategies of resource allocation to extracellular enzymes and enzyme limitations on SOM decomposition. Using SEAM, we explored whether alternative strategy-hypotheses can have strong effects on SOM and inorganic N cycling. Results from prototypical simulations and a calibration to observations of an intensive pasture site showed that the so-called revenue enzyme allocation strategy was most viable. This strategy accounts for microbial adaptations to both, stoichiometry and amount of different SOM resources, and supported the largest microbial biomass under a wide range of conditions. Predictions of the SEAM model were qualitatively similar to models explicitly representing competing microbial groups. With adaptive enzyme allocation under conditions of high C/N ratio of litter inputs, N in formerly locked in slowly degrading SOM pools was made accessible, whereas with high N inputs, N was sequestered in SOM and protected from leaching. The finding that adaptation in enzyme allocation changes C and N-use efficiencies of SOM decomposition implies that concepts of C-nutrient cycle interactions should take account for the effects of such adaptations. This can be done using a holistic optimality approach.

Spatial heterogeneity in sulfur isotopes: implications for modern environments and paleoenvironmental reconstructions

NASA Astrophysics Data System (ADS)

Fike, D. A.; Jones, D. S.; Fischer, W. W.

2011-12-01

Sulfur isotope ratio data have been used to provide significant insights into global biogeochemical cycling over Earth history. In addition to providing a framework for the construction of global redox budgets, these observations also provide the primary constraints on the advent and environmental importance of particular microbial metabolisms. As the chemostratigraphic record has become better resolved in space and time, however, reports of coeval discordant data are increasingly common - both within and between individual sedimentary basins. If accurate, this variability challenges our understanding of the first order behavior of the 'global' sulfur biogeochemical cycle. Some of this discordance may be due to spatial gradients in important oceanographic parameters; however, we think that a more likely culprit is ongoing microbial metabolic activity (that impacts the isotopic composition recorded by geological samples) during both syndepositional sediment reworking and early diagenetic lithification. Modern studies have recently highlighted the efficacy with which microbial activity during sediment remobilization can dramatically alter isotopic profiles. Further, the magnitude of local, microbially driven variations in S isotopes in modern sediments is sufficiently large that uneven incorporation of these signatures during deposition and lithification can explain much of the observed discordance in chemostratigraphic reconstructions of sulfur cycling. Here we attempt to link spatial variability in the sedimentary rock record with understanding of modern microbial systems operating in marine sediments. To that end we examine chemostratigraphic records of sulfur isotope (δ34S) data spanning the terminal Neoproterozoic to early Paleozoic eras and assess their scales of spatial reproducibility. We can gain insight into interpreting the observed patterns in these records by examining modern (bio)sedimentary environments. This understanding also allows us to reflect on and refine time series isotope ratio data that constrain the behavior of the sulfur cycle over long timescales.

Microbial Response to Microgravity and Other Low Shear Environments

NASA Technical Reports Server (NTRS)

Nickerson, C.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; Pierson, Duane L.

2004-01-01

Microbial existence and survival requires the ability to sense and respond to environmental changes, including changes in physical forces. This is because microbes inhabit an amazingly diverse range of ecological niches and therefore must constantly adapt to a wide variety of changing environmental conditions, including alterations in temperature, pH, nutrient availability, oxygen levels, and osmotic pressure gradients. Microbes sense their environment through a variety of sensors and receptors which serve to integrate the different signals into the appropriate cellular response(s) that is optimal for survival. While numerous environmental stimuli have been examined for their effect on microorganisms, effects due to changes in mechanical and/or physical forces are also becoming increasingly apparent. Recently, several important studies have demonstrated a key role for microgravity and the low fluid shear dynamics associated with microgravity in the regulation of microbial gene expression, physiology and pathogenesis. The mechanosensory response of microorganisms to these environmental signals, which are relevant to those encountered during microbial life cycles on Earth, may provide insight into their adaptations to physiologically relevant conditions and may ultimately lead to eludicidation of the mechanisms important for mechanosensory transduction in living cells. This review summarizes the recent and potential future research trends aimed at understanding the effect of changes in mechanical forces that occur in microgravity and other low shear environments on different microbial parameters. The results of these studies provide an important step towards understanding how microbes integrate information from multiple mechanical stimuli to an appropriate physiological response.

Surveillance study of bacterial contamination of the parent's cell phone in the NICU and the effectiveness of an anti-microbial gel in reducing transmission to the hands.

PubMed

Beckstrom, A C; Cleman, P E; Cassis-Ghavami, F L; Kamitsuka, M D

2013-12-01

To determine the bacterial contamination rate of the parent's cell phone and the effectiveness of anti-microbial gel in reducing transmission of bacteria from cell phone to hands. Cross-sectional study of cultures from the cell phone and hands before and after applying anti-microbial gel (n=50). All cell phones demonstrated bacterial contamination. Ninety percent had the same bacteria on the cell phone and their cleaned hands. Twenty two percent had no growth on their hands after applying anti-microbial gel after they had the same bacteria on the cell phone and hands. Ninety-two percent of parents were aware that cell phones carried bacteria, but only 38% cleaned their cell phones at least weekly. Bacterial contamination of cell phones may serve as vectors for nosocomial infection in the neonatal intensive care unit. Bacteria transmitted from cell phone to hands may not be eliminated using anti-microbial gel. Development of hand hygiene and cell phone cleaning guidelines are needed regarding bedside cell phone use.

Microbial drivers of spatial heterogeneity of nitrous oxide pulse dynamics following drought in an experimental tropical rainforest

NASA Astrophysics Data System (ADS)

Young, J. C.; Sengupta, A.; U'Ren, J.; Van Haren, J. L. M.; Meredith, L. K.

2017-12-01

Nitrous oxide (N2O) is a long-lived, potent greenhouse gas with increasing atmospheric concentrations. Soil microbes in agricultural and natural ecosystems are the dominant source of N2O, which involves complex interactions between N-cycling microbes, metabolisms, soil properties, and plants. Tropical rainforests are the largest natural source of N2O, however the microbial and environmental drivers are poorly understood as few studies have been performed in these environments. Thus, there is an urgent need for further research to fill in knowledge gaps regarding tropical N-cycling, and the response of soil microbial communities to changes in precipitation patterns, temperature, nitrogen deposition, and land use. To address this data gap, we performed a whole-forest drought in the tropical rainforest biome in Biosphere 2 (B2) and analyzed connections between soil microbes, forest heterogeneity, and N2O emissions. The B2 rainforest is the hottest tropical rainforest on Earth, and is an important model system for studying the response of tropical forests to warming with controlled experimentation. In this study, we measured microbial community abundance and diversity profiles (16S rRNA and ITS2 amplicon sequencing) along with their association with soil properties (e.g. pH, C, N) during the drought and rewetting at five locations (3 depths), including regions that have been previously characterized with high and low N2O drought pulse dynamics (van Haren et al., 2005). In this study, we present the spatial distribution of soil microbial communities within the rainforest at Biosphere 2 and their correlations with edaphic factors. In particular, we focus on microbial, soil, and plant factors that drive high and low N2O pulse zones. As in the past, we found that N2O emissions were highest in response to rewetting in a zone hypothesized to be rich in nutrients from a nearby sugar palm. We will characterize microbial indicator species and nitrogen cycling genes to better resolve N cycling across the forest. Understanding how N2O formation is mediated by soil microbes in response to drought in tropical rainforests is challenging given the great diversity of microbial communities and metabolisms involved, but is critical for understanding the source of global increases in atmospheric N2O.

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

DOE PAGES

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; ...

2017-09-28

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

NASA Astrophysics Data System (ADS)

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; Zhou, Xiaolu; Wang, Meng; Zhang, Kerou; Wang, Gangsheng

2017-10-01

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195 Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated by Xu et al. (2014). We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC), and mineral-associated organic carbon (MOC). However, our work represents the first step toward a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation.

PubMed

Merchant, Sabeeha S; Helmann, John D

2012-01-01

Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. Despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. Limitations for specific elements, either fleeting or persisting over eons, have left an indelible trace on microbial genomes, physiology, and their very atomic composition. We here review the impact of elemental limitation on microbes, with a focus on selected genetic model systems and representative microbes from the ocean ecosystem. Evolutionary adaptations that enhance growth in the face of persistent or recurrent elemental limitations are evident from genome and proteome analyses. These range from the extreme (such as dispensing with a requirement for a hard to obtain element) to the extremely subtle (changes in protein amino acid sequences that slightly, but significantly, reduce cellular carbon, nitrogen, or sulfur demand). One near-universal adaptation is the development of sophisticated acclimation programs by which cells adjust their chemical composition in response to a changing environment. When specific elements become limiting, acclimation typically begins with an increased commitment to acquisition and a concomitant mobilization of stored resources. If elemental limitation persists, the cell implements austerity measures including elemental sparing and elemental recycling. Insights into these fundamental cellular properties have emerged from studies at many different levels, including ecology, biological oceanography, biogeochemistry, molecular genetics, genomics, and microbial physiology. Here, we present a synthesis of these diverse studies and attempt to discern some overarching themes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre.

PubMed

Poretsky, Rachel S; Hewson, Ian; Sun, Shulei; Allen, Andrew E; Zehr, Jonathan P; Moran, Mary Ann

2009-06-01

Metatranscriptomic analyses of microbial assemblages (< 5 microm) from surface water at the Hawaiian Ocean Time-Series (HOT) revealed community-wide metabolic activities and day/night patterns of differential gene expression. Pyrosequencing produced 75 558 putative mRNA reads from a day transcriptome and 75 946 from a night transcriptome. Taxonomic binning of annotated mRNAs indicated that Cyanobacteria contributed a greater percentage of the transcripts (54% of annotated sequences) than expected based on abundance (35% of cell counts and 21% 16S rRNA of libraries), and may represent the most actively transcribing cells in this surface ocean community in both the day and night. Major heterotrophic taxa contributing to the community transcriptome included alpha-Proteobacteria (19% of annotated sequences, most of which were SAR11-related) and gamma-Proteobacteria (4%). The composition of transcript pools was consistent with models of prokaryotic gene expression, including operon-based transcription patterns and an abundance of genes predicted to be highly expressed. Metabolic activities that are shared by many microbial taxa (e.g. glycolysis, citric acid cycle, amino acid biosynthesis and transcription and translation machinery) were well represented among the community transcripts. There was an overabundance of transcripts for photosynthesis, C1 metabolism and oxidative phosphorylation in the day compared with night, and evidence that energy acquisition is coordinated with solar radiation levels for both autotrophic and heterotrophic microbes. In contrast, housekeeping activities such as amino acid biosynthesis, membrane synthesis and repair, and vitamin biosynthesis were overrepresented in the night transcriptome. Direct sequencing of these environmental transcripts has provided detailed information on metabolic and biogeochemical responses of a microbial community to solar forcing.

Elemental Economy: microbial strategies for optimizing growth in the face of nutrient limitation

PubMed Central

Merchant, Sabeeha S.; Helmann, John D.

2014-01-01

Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility at fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. Despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. Limitations for specific elements, either fleeting or persisting over eons, have left an indelible trace on microbial genomes, physiology, and their very atomic composition. We here review the impact of elemental limitation on microbes, with a focus on selected genetic model systems and representative microbes from the ocean ecosystem. Evolutionary adaptations that enhance growth in the face of persistent or recurrent elemental limitations are evident from genome and proteome analyses. These range from the extreme (such as dispensing with a requirement for a hard to obtain element) to the extremely subtle (changes in protein amino acid sequences that slightly, but significantly, reduce cellular carbon, nitrogen, or sulfur demand). One near universal adaptation is the development of sophisticated acclimation programs by which cells adjust their chemical composition in response to a changing environment. When specific elements become limiting, acclimation typically begins with an increased commitment to acquisition and a concomitant mobilization of stored resources. If elemental limitation persists, the cell implements austerity measures including elemental-sparing and elemental-recycling. Insights into these fundamental cellular properties have emerged from studies at many different levels; including ecology, biological oceanography, biogeochemistry, molecular genetics, genomics, and microbial physiology. Here, we present a synthesis of these diverse studies and attempt to discern some overarching themes. PMID:22633059

Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate.

PubMed

Wang, Zejie; Lee, Taekwon; Lim, Bongsu; Choi, Chansoo; Park, Joonhong

2014-01-17

The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were enriched; sulfate from rice straw hydrolysate might be responsible for the large relative abundance of sulfate reducing bacteria.

Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate

PubMed Central

2014-01-01

Background The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. Results The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. Conclusion The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were enriched; sulfate from rice straw hydrolysate might be responsible for the large relative abundance of sulfate reducing bacteria. PMID:24433535

Geobiochemistry: Placing Biochemistry in Its Geochemical Context

NASA Astrophysics Data System (ADS)

Shock, E.; Boyer, G. M.; Canovas, P. A., III; Prasad, A.; Dick, J. M.

2014-12-01

Goals of geobiochemistry include simultaneously evaluating the relative stabilities of microbial cells and minerals, and predicting how the composition of biomolecules can change in response to the progress of geochemical reactions. Recent developments in theoretical geochemistry make it possible to predict standard thermodynamic properties of proteins, nucleotides, lipids, and many metabolites including the constituents of the citric acid cycle, at all temperatures and pressures where life is known to occur, and beyond. Combining these predictions with constraints from geochemical data makes it possible to assess the relative stabilities of biomolecules. Resulting independent predictions of the environmental occurrence of homologous proteins and lipid side-chains can be compared with observations from metagenomic and metalipidomic data to quantify geochemical driving forces that shape the composition of biomolecules. In addition, the energetic costs of generating biomolecules from within a diverse range of habitable environments can be evaluated in terms of prevailing geochemical variables. Comparisons of geochemical bioenergetic calculations across habitats leads to the generalization that the availability of H2 determines the cost of autotrophic biosynthesis relative to the aquatic environment external to microbial cells, and that pH, temperature, pressure, and availability of C, N, P, and S are typically secondary. Increasingly reduced conditions, which are determined by reactions of water with mineral surfaces and mineral assemblages, allow many biosynthetic reactions to shift from costing energy to releasing energy. Protein and lipid synthesis, as well as the reverse citric acid cycle, become energy-releasing processes under these conditions. The resulting energy balances that determine habitability contrast dramatically with assumptions derived from oxic surface conditions, such as those where human biochemistry operates.

Ocean acidification and viral replication cycles: Frequency of lytically infected and lysogenic cells during a mesocosm experiment in the NW Mediterranean Sea

NASA Astrophysics Data System (ADS)

Tsiola, Anastasia; Pitta, Paraskevi; Giannakourou, Antonia; Bourdin, Guillaume; Marro, Sophie; Maugendre, Laure; Pedrotti, Maria Luiza; Gazeau, Frédéric

2017-02-01

The frequency of lytically infected and lysogenic cells (FLIC and FLC, respectively) was estimated during an in situ mesocosm experiment studying the impact of ocean acidification on the plankton community of a low nutrient low chlorophyll (LNLC) system in the north-western Mediterranean Sea (Bay of Villefranche, France) in February/March 2013. No direct effect of elevated partial pressure of CO2 (pCO2) on viral replication cycles could be detected. FLC variability was negatively correlated to heterotrophic bacterial and net community production as well as the ambient bacterial abundance, confirming that lysogeny is a prevailing life strategy under unfavourable-for-the-hosts conditions. Further, the phytoplankton community, assessed by chlorophyll a concentration and the release of >0.4 μm transparent exopolymeric particles, was correlated with the occurrence of lysogeny, indicating a possible link between photosynthetic processes and bacterial growth. Higher FLC was found occasionally at the highest pCO2-treated mesocosm in parallel to subtle differences in the phytoplankton community. This observation suggests that elevated pCO2 could lead to short-term alterations in lysogenic dynamics coupled to phytoplankton-derived processes. Correlation of FLIC with any environmental parameter could have been obscured by the sampling time or the synchronization of lysis to microbial processes not assessed in this experiment. Furthermore, alterations in microbial and viral assemblage composition and gene expression could be a confounding factor. Viral-induced modifications in organic matter flow affect bacterial growth and could interact with ocean acidification with unpredictable ecological consequences.

Application of atomic force microscopy to microbial surfaces: from reconstituted cell surface layers to living cells.

PubMed

Dufrêne, Y F

2001-02-01

The application of atomic force microscopy (AFM) to probe the ultrastructure and physical properties of microbial cell surfaces is reviewed. The unique capabilities of AFM can be summarized as follows: imaging surface topography with (sub)nanometer lateral resolution; examining biological specimens under physiological conditions; measuring local properties and interaction forces. AFM is being used increasingly for: (i) visualizing the surface ultrastructure of microbial cell surface layers, including bacterial S-layers, purple membranes, porin OmpF crystals and fungal rodlet layers; (ii) monitoring conformational changes of individual membrane proteins; (iii) examining the morphology of bacterial biofilms, (iv) revealing the nanoscale structure of living microbial cells, including fungi, yeasts and bacteria, (v) mapping interaction forces at microbial surfaces, such as van der Waals and electrostatic forces, solvation forces, and steric/bridging forces; and (vi) probing the local mechanical properties of cell surface layers and of single cells.

Quantification of Microbial Osmolytes in a Drought Impacted California Grassland

NASA Astrophysics Data System (ADS)

Boot, C. M.; Schaeffer, S. M.; Doyle, A. P.; Schimel, J. P.

2008-12-01

With drought frequency and severity likely increasing in the future, understanding its effect on terrestrial carbon (C) and nitrogen (N) cycling has become essential for accurately modeling ecosystem responses to climate change. Microbes respond to drought stress by accumulating internal solutes, or osmolytes, such as amino acids, betaines and polyols, to balance cell membrane water potential as the soil dries. However, when seasonal rains arrive, internal solutes are released and rapidly mineralized. We have been studying these processes in a California grassland. Beginning in summer 2007, we made monthly measurements of soil moisture, individual amino acid concentration in total soil and in microbial biomass, total dissolved organic carbon and nitrogen (DOC and DON), and microbial biomass carbon and nitrogen (MBC and MBN). We expected microbial concentrations of the known amino acid osmolytes glutamate (glu) and proline (pro) to fluctuate inversely with soil moisture. However, pro was only recovered in Mar 2008 (0.30 μg C g-1 dry soil) and the glu concentration varied proportionally with soil moisture: lowest during summer (0.06 g H2O g-1 dry soil, 2.22 μg glutamate-C g-1 dry soil) and highest in winter (0.27 g H2O g-1 dry soil, 4.43 μg glutamate-C g-1 dry soil). The trend from DOC, MBC, and DON measurements was opposite, however, with all concentrations decreasing as soil moisture shifted from dry to wet, (DOC: 64.61 to 32.49 μg C g-1 dry soil respectively). MBN was the exception to this trend, with concentrations staying nearly constant across seasons. These patterns suggest that the expected amino acids glu and pro are not being used for microbial osmoregulation in the CA grassland, and given the summer to winter decrease in MBC, the primary osmolyte source is likely to be either polyol-type compounds such as mannitol or betaines. The implications for terrestrial carbon cycle are considerable because as the frequency of drought increases, the accumulation and release of osmolytes in response to drought has potential to pump carbon out of the grassland ecosystem.

Above- and belowground linkages in Sphagnum peatland: climate warming affects plant-microbial interactions.

PubMed

Jassey, Vincent E J; Chiapusio, Geneviève; Binet, Philippe; Buttler, Alexandre; Laggoun-Défarge, Fatima; Delarue, Frédéric; Bernard, Nadine; Mitchell, Edward A D; Toussaint, Marie-Laure; Francez, André-Jean; Gilbert, Daniel

2013-03-01

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above- and belowground linkages that regulate soil organic carbon dynamics and C-balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top-predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum-polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above- and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands. © 2012 Blackwell Publishing Ltd.

Microbial community composition explains soil respiration responses to changing carbon inputs along an Andes-to-Amazon elevation gradient

PubMed Central

Whitaker, Jeanette; Ostle, Nicholas; Nottingham, Andrew T; Ccahuana, Adan; Salinas, Norma; Bardgett, Richard D; Meir, Patrick; McNamara, Niall P; Austin, Amy

2014-01-01

1. The Andes are predicted to warm by 3–5 °C this century with the potential to alter the processes regulating carbon (C) cycling in these tropical forest soils. This rapid warming is expected to stimulate soil microbial respiration and change plant species distributions, thereby affecting the quantity and quality of C inputs to the soil and influencing the quantity of soil-derived CO2 released to the atmosphere. 2. We studied tropical lowland, premontane and montane forest soils taken from along a 3200-m elevation gradient located in south-east Andean Peru. We determined how soil microbial communities and abiotic soil properties differed with elevation. We then examined how these differences in microbial composition and soil abiotic properties affected soil C-cycling processes, by amending soils with C substrates varying in complexity and measuring soil heterotrophic respiration (RH). 3. Our results show that there were consistent patterns of change in soil biotic and abiotic properties with elevation. Microbial biomass and the abundance of fungi relative to bacteria increased significantly with elevation, and these differences in microbial community composition were strongly correlated with greater soil C content and C:N (nitrogen) ratios. We also found that RH increased with added C substrate quality and quantity and was positively related to microbial biomass and fungal abundance. 4. Statistical modelling revealed that RH responses to changing C inputs were best predicted by soil pH and microbial community composition, with the abundance of fungi relative to bacteria, and abundance of gram-positive relative to gram-negative bacteria explaining much of the model variance. 5. Synthesis. Our results show that the relative abundance of microbial functional groups is an important determinant of RH responses to changing C inputs along an extensive tropical elevation gradient in Andean Peru. Although we do not make an experimental test of the effects of climate change on soil, these results challenge the assumption that different soil microbial communities will be ‘functionally equivalent’ as climate change progresses, and they emphasize the need for better ecological metrics of soil microbial communities to help predict C cycle responses to climate change in tropical biomes. PMID:25520527

Biogeochemical cycling at the aquatic–terrestrial interface is linked to parafluvial hyporheic zone inundation history

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goldman, Amy E.; Graham, Emily B.; Crump, Alex R.

The parafluvial hyporheic zone combines the heightened biogeochemical and microbial interactions indicative of a hyporheic region with direct atmospheric/terrestrial inputs and the effects of wet–dry cycles. Therefore, understanding biogeochemical cycling and microbial interactions in this ecotone is fundamental to understanding biogeochemical cycling at the aquatic–terrestrial interface and to creating robust hydrobiogeochemical models of dynamic river corridors. We aimed to (i) characterize biogeochemical and microbial differences in the parafluvial hyporheic zone across a small spatial domain (6 lateral meters) that spans a breadth of inundation histories and (ii) examine how parafluvial hyporheic sediments respond to laboratory-simulated re-inundation. Surface sediment was collected at fourmore » elevations along transects perpendicular to flow of the Columbia River, eastern WA, USA. The sediments were inundated by the river 0, 13, 127, and 398 days prior to sampling. Spatial variation in environmental variables (organic matter, moisture, nitrate, glucose, %C, %N) and microbial communities (16S and internal transcribed spacer (ITS) rRNA gene sequencing, qPCR) were driven by differences in inundation history. Microbial respiration did not differ significantly across inundation histories prior to forced inundation in laboratory incubations. Forced inundation suppressed microbial respiration across all histories, but the degree of suppression was dramatically different between the sediments saturated and unsaturated at the time of sample collection, indicating a binary threshold response to re-inundation. We present a conceptual model in which irregular hydrologic fluctuations facilitate microbial communities adapted to local conditions and a relatively high flux of CO 2. Upon rewetting, microbial communities are initially suppressed metabolically, which results in lower CO 2 flux rates primarily due to suppression of fungal respiration. Following prolonged inundation, the microbial community adapts to saturation by shifting composition, and the CO 2 flux rebounds to prior levels due to the subsequent change in respiration. Our results indicate that the time between inundation events can push the system into alternate states: we suggest (i) that, above some threshold of inundation interval, re-inundation suppresses respiration to a consistent, low rate and (ii) that, below some inundation interval, re-inundation has a minor effect on respiration. In conclusion, extending reactive transport models to capture processes that govern such dynamics will provide more robust predictions of river corridor biogeochemical function under altered surface water flow regimes in both managed and natural watersheds.« less

Biogeochemical cycling at the aquatic–terrestrial interface is linked to parafluvial hyporheic zone inundation history

DOE PAGES

Goldman, Amy E.; Graham, Emily B.; Crump, Alex R.; ...

2017-09-21

The parafluvial hyporheic zone combines the heightened biogeochemical and microbial interactions indicative of a hyporheic region with direct atmospheric/terrestrial inputs and the effects of wet–dry cycles. Therefore, understanding biogeochemical cycling and microbial interactions in this ecotone is fundamental to understanding biogeochemical cycling at the aquatic–terrestrial interface and to creating robust hydrobiogeochemical models of dynamic river corridors. We aimed to (i) characterize biogeochemical and microbial differences in the parafluvial hyporheic zone across a small spatial domain (6 lateral meters) that spans a breadth of inundation histories and (ii) examine how parafluvial hyporheic sediments respond to laboratory-simulated re-inundation. Surface sediment was collected at fourmore » elevations along transects perpendicular to flow of the Columbia River, eastern WA, USA. The sediments were inundated by the river 0, 13, 127, and 398 days prior to sampling. Spatial variation in environmental variables (organic matter, moisture, nitrate, glucose, %C, %N) and microbial communities (16S and internal transcribed spacer (ITS) rRNA gene sequencing, qPCR) were driven by differences in inundation history. Microbial respiration did not differ significantly across inundation histories prior to forced inundation in laboratory incubations. Forced inundation suppressed microbial respiration across all histories, but the degree of suppression was dramatically different between the sediments saturated and unsaturated at the time of sample collection, indicating a binary threshold response to re-inundation. We present a conceptual model in which irregular hydrologic fluctuations facilitate microbial communities adapted to local conditions and a relatively high flux of CO 2. Upon rewetting, microbial communities are initially suppressed metabolically, which results in lower CO 2 flux rates primarily due to suppression of fungal respiration. Following prolonged inundation, the microbial community adapts to saturation by shifting composition, and the CO 2 flux rebounds to prior levels due to the subsequent change in respiration. Our results indicate that the time between inundation events can push the system into alternate states: we suggest (i) that, above some threshold of inundation interval, re-inundation suppresses respiration to a consistent, low rate and (ii) that, below some inundation interval, re-inundation has a minor effect on respiration. In conclusion, extending reactive transport models to capture processes that govern such dynamics will provide more robust predictions of river corridor biogeochemical function under altered surface water flow regimes in both managed and natural watersheds.« less

Tropical forest soil microbial communities couple iron and carbon biogeochemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubinsky, E.A.; Silver, W.L.; Firestone, M.K.

2009-10-15

We report that iron-reducing bacteria are primary mediators of anaerobic carbon oxidation in upland tropical soils spanning a rainfall gradient (3500 - 5000 mm yr-1) in northeast Puerto Rico. The abundant rainfall and high net primary productivity of these tropical forests provide optimal soil habitat for iron-reducing and iron-oxidizing bacteria. Spatially and temporally dynamic redox conditions make iron-transforming microbial communities central to the belowground carbon cycle in these wet tropical forests. The exceedingly high abundance of iron-reducing bacteria (up to 1.2 x 10{sup 9} cells per gram soil) indicated that they possess extensive metabolic capacity to catalyze the reduction ofmore » iron minerals. In soils from the higher rainfall sites, measured rates of ferric iron reduction could account for up to 44 % of organic carbon oxidation. Iron reducers appeared to compete with methanogens when labile carbon availability was limited. We found large numbers of bacteria that oxidize reduced iron at sites with high rates of iron reduction and large numbers of iron-reducers. the coexistence of large populations of ironreducing and iron-oxidizing bacteria is evidence for rapid iron cycling between its reduced and oxidized states, and suggests that mutualistic interactions among these bacteria ultimately fuel organic carbon oxidation and inhibit CH4 production in these upland tropical forests.« less

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO 2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. Amore » nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N 2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.« less

Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges.

PubMed

Karimi, Elham; Slaby, Beate M; Soares, André R; Blom, Jochen; Hentschel, Ute; Costa, Rodrigo

2018-06-01

Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceae genome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

DOE PAGES

Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.; ...

2018-01-29

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO 2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. Amore » nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N 2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.« less

Cellular content of biomolecules in sub-seafloor microbial communities

NASA Astrophysics Data System (ADS)

Braun, Stefan; Morono, Yuki; Becker, Kevin W.; Hinrichs, Kai-Uwe; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Lomstein, Bente Aa.

2016-09-01

Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density centrifugation. Amino acids, amino sugars, muramic acid, and intact polar lipids were analyzed in both whole sediment and cell extract, and cell separation was optimized and evaluated in terms of purity, separation efficiency, taxonomic resemblance, and compatibility to high-performance liquid chromatography and mass spectrometry for biomolecule analyses. Because cell extracts from density centrifugation still contained considerable amounts of detrital particles and non-cellular biomolecules, we further purified cells from two samples by fluorescence-activated cell sorting (FACS). Cells from these highly purified cell extracts had an average content of amino acids and lipids of 23-28 fg cell-1 and 2.3 fg cell-1, respectively, with an estimated carbon content of 19-24 fg cell-1. In the sediment, the amount of biomolecules associated with vegetative cells was up to 70-fold lower than the total biomolecule content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates of microbial biomass.

Electricity generation in microbial fuel cells using neutral red as an electronophore

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, D.H.; Zeikus, J.G.

2000-04-01

Neutral red (NR) was utilized as an electron mediator in microbial fuel cells consuming glucose to study both its efficiency during electricity generation and its role in altering anaerobic growth and metabolism of Escherichia coli and Actinobacillus succinogenes. A study of chemical fuel cells in which NADH, NR, and ferricyanide were the electron donor, the electronophore, and the electron acceptor, respectively, showed that electrical current produced from NADH was proportional to the concentration of NADH. Fourfold more current was produced from NADH in chemical fuel cells when NR was the electron mediator than when thionin was the electron mediator. Inmore » microbial fuel cells in which E. coli resting cells were used the amount of current produced from glucose when NR was the electron mediator was 10-fold more than the amount produced when thionin was the electron mediator. The amount of electrical energy generated and the amount of current produced from glucose in NR-mediated microbial fuel cells containing either E. coli or A. succinogenes were about 10- and 2-fold greater, respectively, when resting cells were used than when growing cells were used. Cell growth was inhibited substantially when these microbial fuel cells were making current, and more oxidized end products were formed under these conditions. When sewage sludge was used in the fuel cell, stable and equivalent levels of current were obtained with glucose, as observed in the pure-culture experiments. These results suggest that NR is better than other electron mediators used in microbial fuel cells and that sludge production can be decreased while electricity is produced in fuel cells. Their results are discussed in relation to factors that may improve the relatively low electrical efficiencies obtained with microbial fuel cells.« less

Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

EPA Science Inventory

Multi-anode microbial electrochemical cells (MXCs) are considered as one of the most promising configurations for scale-up of MXCs, but fundamental understanding of anode kinetics governing current density is limited in the MXCs. In this study we first assessed microbial communi...

Direct effects of temperature on forest nitrogen cycling revealed through analysis of long-term watershed records

Treesearch

E.N. Jack Brookshire; Stefan Gerber; Jackson R. Webster; James M. Vose; Wayne T. Swank

2010-01-01

The microbial conversion of organic nitrogen (N) to plant available forms is a critical determinant of plant growth and carbon sequestration in forests worldwide. In temperate zones, microbial activity is coupled to variations in temperature, yet at the ecosystem level, microbial N mineralization seems to play a minor role in determining patterns of N loss. Rather, N...

Long-term carbon exclusion alters soil microbial function but not community structure across forests of contrasting productivity

NASA Astrophysics Data System (ADS)

Hart, S. C.; Dove, N. C.; Stark, J.

2017-12-01

While it is well-documented that distinct heterotrophic microbial communities emerge under different conditions of carbon (C) availability, the response of soil microbial communities and their function to long-term conditions of C exclusion in situ has yet to be investigated. We evaluated the role of C in controlling soil microbial communities and function by experimentally excluding plant C inputs for nine years at four forest sites along a productivity gradient in Oregon, USA. Carbon exclusion treatments were implemented by root trenching to a depth of 30 cm using 25-cm diameter steel pipe, and minimizing aboveground inputs as plant litter by covering the pipe with a 1-mm mesh screen. After nine years, we measured rates of gross and net nitrogen (N) transformations and microbial respiration in situ in the upper 15-cm of mineral soil in both C excluded plots and undisturbed control soils. We measured the soil total C and N concentration and potential extracellular enzyme activities. We used phospholipid fatty acid (PLFA) analysis to determine potential changes in the microbial community structure. Nine years of C exclusion reduced soil total C by about 20%, except at the highest productivity site where no statistically significant change was observed. Although PLFA community structure and microbial C were unchanged, microbial respiration was reduced by 15-45% at all sites. Similarly, specific extracellular enzyme activities for all enzymes increased at these sites with C exclusion, suggesting that the microbial communities were substrate-limited. Although gross N mineralization decreased under C exclusion, decreases in gross N immobilization were greater, resulting in increased net N mineralization rates in all but the lowest productivity site. Furthermore, C exclusion only increased net nitrification in the highest productivity site. Although these field-based results are largely consistent with previous laboratory studies indicating a strong coupling between C and N biogeochemical cycles, they build upon this earlier research by suggesting that the "C connection" to the N cycle depends on the rate of C cycling within the ecosystem.

Gene-centric approach to integrating environmental genomics and biogeochemical models.

PubMed

Reed, Daniel C; Algar, Christopher K; Huber, Julie A; Dick, Gregory J

2014-02-04

Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution, and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models by incorporating genomics data to provide predictions that are readily testable. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modeled to examine key questions about cryptic sulfur cycling and dinitrogen production pathways in OMZs. Simulations support previous assertions that denitrification dominates over anammox in the central Arabian Sea, which has important implications for the loss of fixed nitrogen from the oceans. Furthermore, cryptic sulfur cycling was shown to attenuate the secondary nitrite maximum often observed in OMZs owing to changes in the composition of the chemolithoautotrophic community and dominant metabolic pathways. Results underscore the need to explicitly integrate microbes into biogeochemical models rather than just the metabolisms they mediate. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides a framework for achieving mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

PubMed Central

Wilbanks, Elizabeth G; Jaekel, Ulrike; Salman, Verena; Humphrey, Parris T; Eisen, Jonathan A; Facciotti, Marc T; Buckley, Daniel H; Zinder, Stephen H; Druschel, Gregory K; Fike, David A; Orphan, Victoria J

2014-01-01

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the ‘pink berry’ consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and 34S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0–500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ34S-sulfide decreased from 6‰ to −31‰ from the exterior to interior of the berry. These values correspond to sulfate–sulfide isotopic fractionations (15–53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria. PMID:24428801

N2O and N2 emissions from contrasting soil environments - interactive effects of soil nitrogen, hydrology and microbial communities

NASA Astrophysics Data System (ADS)

Christiansen, Jesper; Elberling, Bo; Ribbons, Relena; Hedo, Javier; José Fernández Alonso, Maria; Krych, Lukasz; Sandris Nielsen, Dennis; Kitzler, Barbara

2016-04-01

Reactive nitrogen (N) in the environment has doubled relative to the natural global N cycle with consequences for biogeochemical cycling of soil N. Also, climate change is expected to alter precipitation patterns and increase soil temperatures which in Arctic environments may accelerate permafrost thawing. The combination of changes in the soil N cycle and hydrological regimes may alter microbial transformations of soil N with unknown impacts on N2O and N2 emissions from temperate and Arctic soils. We present the first results of soil N2O and N2 emissions, chemistry and microbial communities over soil hydrological gradients (upslope, intermediate and wet) across a global N deposition gradient. The global gradient covered an N-limited high Arctic tundra (Zackenberg-ZA), a pacific temperate rain forest (Vancouver Island-VI) and an N saturated forest in Austria (Klausenleopoldsdorf-KL). The N2O and N2 emissions were measured from intact cores at field moisture in a He-atmosphere system. Extractable NH4+ and NO3-, organic and microbial C and N and potential enzyme-activities were determined on soil samples. Soil genomic DNA was subjected to MiSeq-based tag-encoded 16S rRNA and ITS gene amplicon sequencing for the bacterial and fungal community structure. Similar soil moisture levels were observed for the upslope, intermediate and wet locations at ZA, VI and KL, respectively. Extractable NO3- was highest at the N rich KL and lowest at ZA and showed no trend with soil moisture similar to NH4+. At ZA and VI soil NH4+ was higher than NO3- indicating a tighter N cycling. N2O emissions increased with soil moisture at all sites. The N2O emissions for the wet locations ranked similarly to NO3- with the largest response to soil moisture at KL. N2 emissions were remarkably similar across the sites and increased with soil wetness. Microbial C and N also increased with soil moisture and were overall lowest at the N rich KL site. The potential activity of protease enzyme was site dependent indicating different capacities for N turnover of the microbial community. These findings indicate a positive feedback between increased soil N and wetter soils that promotes N2O relative to N2. These interactions may be site specific due to differential functional diversity of the soil microbial community. Future characterization of the community structure will shed light on the link between the role of microbial groups related to soil N cycling pathways and the resultant partitioning of N2O and N2 emissions in these contrasting environments.

Carbonic anhydrase distribution across organisms and environments: genomic predictors for soil enzymatic fluxes of carbon cycle tracers δ18O and COS

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Singer, E.

2016-12-01

Carbonyl sulfide (COS) and the oxygen isotope composition (δ18O) of CO2 are potential tools for differentiating the contributions of photosynthesis and respiration to the balance of global carbon cycling. These processes are coupled at the leaf level via the enzyme carbonic anhydrase (CA), which hydrolyzes CO2 in the first biochemical step of the photosynthetic pathway (CO2 + H2O ⇌ HCO3- + H+) and correspondingly structural analogue COS (COS + H2O → CO2 + H2S). CA also accelerates the exchange of oxygen isotopes between CO2 and H2O leading to a distinct isotopic imprint. The biogeochemical cycles of these tracers include significant, yet poorly characterized soil processes that challenge their utility for probing the carbon cycle. In soils, microbial CA also hydrolyze COS and accelerate O isotope exchange between CO2 and soil water. Genomic predictors of microbial CA activity may help account and predict for these soil fluxes. Using a bioinformatics approach, we assess the distribution of the six known CA classes (α, β, γ, δ, η, ζ) in organisms ranging from fungi and plants to archaea and bacteria, and ask whether CA diversity is linked to soil microbial diversity. We survey the diversity and relative abundance of CA in a wide variety of environments and estimate the sensitivity of CA to biome and land use. Finally, we compare the CA distribution in soils to measurements (oxygen isotope and COS fluxes) and models of CA activity to develop genomic predictors for CA activity. This work provides the first survey of CA in soils, a step towards understanding the significant role of CA in microbial ecology and microbe-mediated biogeochemical cycles.

Poly iron sulfate flocculant as an effective additive for improving the performance of microbial fuel cells.

PubMed

Miyahara, Morio; Sakamoto, Akihiro; Kouzuma, Atsushi; Watanabe, Kazuya

2016-12-01

Laboratory microbial fuel cells were supplied with artificial wastewater and used to examine how supplementation with poly iron sulfate, an inorganic polymer flocculant widely used in wastewater-treatment plants, affects electricity generation and anode microbiomes. It is shown that poly iron sulfate substantially increases electric outputs from microbial fuel cells. Microbiological analyses show that iron and sulfate separately affect anode microbiomes, and the increase in power output is associated with the increases in bacteria affiliated with the families Geobacteraceae and/or Desulfuromonadaceae. We suggest that poly iron sulfate is an effective additive for increasing the electric output from microbial fuel cells. Other utilities of poly iron sulfate in microbial fuel cells are also discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Infection Paradox: High Abundance but Low Impact of Freshwater Benthic Viruses

PubMed Central

Filippini, Manuela; Buesing, Nanna; Bettarel, Yvan; Sime-Ngando, Télesphore; Gessner, Mark O.

2006-01-01

The discovery of an abundant and diverse virus community in oceans and lakes has profoundly reshaped ideas about global carbon and nutrient fluxes, food web dynamics, and maintenance of microbial biodiversity. These roles are exerted through massive viral impact on the population dynamics of heterotrophic bacterioplankton and primary producers. We took advantage of a shallow wetland system with contrasting microhabitats in close proximity to demonstrate that in marked contrast to pelagic systems, viral infection, determined directly by transmission electron microscopy, and consequently mortality of prokaryotes were surprisingly low in benthic habitats in all seasons. This was true even though free viruses were abundant throughout the year and bacterial infection and mortality rates were high in surrounding water. The habitats in which we found this pattern include sediment, decomposing plant litter, and biofilms on aquatic vegetation. Overall, we detected viruses in only 4 of a total of ∼15,000 bacterial cells inspected in these three habitats; for comparison, nearly 300 of ∼5,000 cells suspended in the water column were infected. The strikingly low incidence of impact of phages in the benthos may have important implications, since a major portion of microbial biodiversity and global carbon and nutrient turnover are associated with surfaces. Therefore, if failure to infect benthic bacteria is a widespread phenomenon, then the global role of viruses in controlling microbial diversity, food web dynamics, and biogeochemical cycles would be greatly diminished compared to predictions based on data from planktonic environments. PMID:16820485

Identification and activity of acetate-assimilating bacteria in diffuse fluids venting from two deep-sea hydrothermal systems.

PubMed

Winkel, Matthias; Pjevac, Petra; Kleiner, Manuel; Littmann, Sten; Meyerdierks, Anke; Amann, Rudolf; Mußmann, Marc

2014-12-01

Diffuse hydrothermal fluids often contain organic compounds such as hydrocarbons, lipids, and organic acids. Microorganisms consuming these compounds at hydrothermal sites are so far only known from cultivation-dependent studies. To identify potential heterotrophs without prior cultivation, we combined microbial community analysis with short-term incubations using (13)C-labeled acetate at two distinct hydrothermal systems. We followed cell growth and assimilation of (13)C into single cells by nanoSIMS combined with fluorescence in situ hybridization (FISH). In 55 °C-fluids from the Menez Gwen hydrothermal system/Mid-Atlantic Ridge, a novel epsilonproteobacterial group accounted for nearly all assimilation of acetate, representing the first aerobic acetate-consuming member of the Nautiliales. In contrast, Gammaproteobacteria dominated the (13) C-acetate assimilation in incubations of 37 °C-fluids from the back-arc hydrothermal system in the Manus Basin/Papua New Guinea. Here, 16S rRNA gene sequences were mostly related to mesophilic Marinobacter, reflecting the high content of seawater in these fluids. The rapid growth of microorganisms upon acetate addition suggests that acetate consumers in diffuse fluids are copiotrophic opportunists, which quickly exploit their energy sources, whenever available under the spatially and temporally highly fluctuating conditions. Our data provide first insights into the heterotrophic microbial community, catalyzing an under-investigated part of microbial carbon cycling at hydrothermal vents. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Extracellular Saccharide-Mediated Reduction of Au3+ to Gold Nanoparticles: New Insights for Heavy Metals Biomineralization on Microbial Surfaces.

PubMed

Kang, Fuxing; Qu, Xiaolei; Alvarez, Pedro J J; Zhu, Dongqiang

2017-03-07

Biomineralization is a critical process controlling the biogeochemical cycling, fate, and potential environmental impacts of heavy metals. Despite the indispensability of extracellular polymeric substances (EPS) to microbial life and their ubiquity in soil and aquatic environments, the role played by EPS in the transformation and biomineralization of heavy metals is not well understood. Here, we used gold ion (Au 3+ ) as a model heavy metal ion to quantitatively assess the role of EPS in biomineralization and discern the responsible functional groups. Integrated spectroscopic analyses showed that Au 3+ was readily reduced to zerovalent gold nanoparticles (AuNPs, 2-15 nm in size) in aqueous suspension of Escherichia coli or dissolved EPS extracted from microbes. The majority of AuNPs (95.2%) was formed outside Escherichia coli cells, and the removal of EPS attached to cells pronouncedly suppressed Au 3+ reduction, reflecting the predominance of the extracellular matrix in Au 3+ reduction. XPS, UV-vis, and FTIR analyses corroborated that Au 3+ reduction was mediated by the hemiacetal groups (aldehyde equivalents) of reducing saccharides of EPS. Consistently, the kinetics of AuNP formation obeyed pseudo-second-order reaction kinetics with respect to the concentrations of Au 3+ and the hemiacetal groups in EPS, with minimal dependency on the source of microbial EPS. Our findings indicate a previously overlooked, universally significant contribution of EPS to the reduction, mineralization, and potential detoxification of metal species with high oxidation state.

Solar radiation uncorks the lignin bottleneck on plant litter decomposition in terrestrial ecosystems

NASA Astrophysics Data System (ADS)

Austin, A.; Ballare, C. L.; Méndez, M. S.

2015-12-01

Plant litter decomposition is an essential process in the first stages of carbon and nutrient turnover in terrestrial ecosystems, and together with soil microbial biomass, provide the principal inputs of carbon for the formation of soil organic matter. Photodegradation, the photochemical mineralization of organic matter, has been recently identified as a mechanism for previously unexplained high rates of litter mass loss in low rainfall ecosystems; however, the generality of this process as a control on carbon cycling in terrestrial ecosystems is not known, and the indirect effects of photodegradation on biotic stimulation of carbon turnover have been debated in recent studies. We demonstrate that in a wide range of plant species, previous exposure to solar radiation, and visible light in particular, enhanced subsequent biotic degradation of leaf litter. Moreover, we demonstrate that the mechanism for this enhancement involves increased accessibility for microbial enzymes to plant litter carbohydrates due to a reduction in lignin content. Photodegradation of plant litter reduces the structural and chemical bottleneck imposed by lignin in secondary cell walls. In litter from woody plant species, specific interactions with ultraviolet radiation obscured facilitative effects of solar radiation on biotic decomposition. The generalized positive effect of solar radiation exposure on subsequent microbial activity is mediated by increased accessibility to cell wall polysaccharides, which suggests that photodegradation is quantitatively important in determining rates of mass loss, nutrient release and the carbon balance in a broad range of terrestrial ecosystems.

Variation in antibiotic-induced microbial recolonization impacts on the host metabolic phenotypes of rats.

PubMed

Swann, Jonathan R; Tuohy, Kieran M; Lindfors, Peter; Brown, Duncan T; Gibson, Glenn R; Wilson, Ian D; Sidaway, James; Nicholson, Jeremy K; Holmes, Elaine

2011-08-05

The interaction between the gut microbiota and their mammalian host is known to have far-reaching consequences with respect to metabolism and health. We investigated the effects of eight days of oral antibiotic exposure (penicillin and streptomycin sulfate) on gut microbial composition and host metabolic phenotype in male Han-Wistar rats (n = 6) compared to matched controls. Early recolonization was assessed in a third group exposed to antibiotics for four days followed by four days recovery (n = 6). Fluorescence in situ hybridization analysis of the intestinal contents collected at eight days showed a significant reduction in all bacterial groups measured (control, 10(10.7) cells/g feces; antibiotic-treated, 10(8.4)). Bacterial suppression reduced the excretion of mammalian-microbial urinary cometabolites including hippurate, phenylpropionic acid, phenylacetylglycine and indoxyl-sulfate whereas taurine, glycine, citrate, 2-oxoglutarate, and fumarate excretion was elevated. While total bacterial counts remained notably lower in the recolonized animals (10(9.1) cells/g faeces) compared to the controls, two cage-dependent subgroups emerged with Lactobacillus/Enterococcus probe counts dominant in one subgroup. This dichotomous profile manifested in the metabolic phenotypes with subgroup differences in tricarboxylic acid cycle metabolites and indoxyl-sulfate excretion. Fecal short chain fatty acids were diminished in all treated animals. Antibiotic treatment induced a profound effect on the microbiome structure, which was reflected in the metabotype. Moreover, the recolonization process was sensitive to the microenvironment, which may impact on understanding downstream consequences of antibiotic consumption in human populations.

Proline Availability Regulates Proline-4-Hydroxylase Synthesis and Substrate Uptake in Proline-Hydroxylating Recombinant Escherichia coli

PubMed Central

Falcioni, Francesco; Blank, Lars M.; Frick, Oliver; Karau, Andreas; Schmid, Andreas

2013-01-01

Microbial physiology plays a crucial role in whole-cell biotransformation, especially for redox reactions that depend on carbon and energy metabolism. In this study, regio- and enantio-selective proline hydroxylation with recombinant Escherichia coli expressing proline-4-hydroxylase (P4H) was investigated with respect to its interconnectivity to microbial physiology and metabolism. P4H production was found to depend on extracellular proline availability and on codon usage. Medium supplementation with proline did not alter p4h mRNA levels, indicating that P4H production depends on the availability of charged prolyl-tRNAs. Increasing the intracellular levels of soluble P4H did not result in an increase in resting cell activities above a certain threshold (depending on growth and assay temperature). Activities up to 5-fold higher were reached with permeabilized cells, confirming that host physiology and not the intracellular level of active P4H determines the achievable whole-cell proline hydroxylation activity. Metabolic flux analysis revealed that tricarboxylic acid cycle fluxes in growing biocatalytically active cells were significantly higher than proline hydroxylation rates. Remarkably, a catalysis-induced reduction of substrate uptake was observed, which correlated with reduced transcription of putA and putP, encoding proline dehydrogenase and the major proline transporter, respectively. These results provide evidence for a strong interference of catalytic activity with the regulation of proline uptake and metabolism. In terms of whole-cell biocatalyst efficiency, proline uptake and competition of P4H with proline catabolism are considered the most critical factors. PMID:23455348

Linking Soil Microbial Ecology to Ecosystem Functioning in Integrated Crop-Livestock Systems

USDA-ARS?s Scientific Manuscript database

Enhanced soil stability, nutrient cycling and C sequestration potential are important ecosystem functions driven by soil microbial processes and are directly influenced by agricultural management. Integrated crop-livestock agroecosystems (ICL) can enhance these functions via high-residue returning c...

Soil microbial communities and metabolic function of a Northern Alabama forest ecosystem

USDA-ARS?s Scientific Manuscript database

Thinning, prescribed burning, and their combinations, are common forest management practices to restore degraded forest communities and to prevent uncontrollable wildfires. However, their impacts on soil microbial communities, which are vital to global element cycling, are traditionally overlooked. ...

Evidence of biogeochemical processes in iron duricrust formation

NASA Astrophysics Data System (ADS)

Levett, Alan; Gagen, Emma; Shuster, Jeremiah; Rintoul, Llew; Tobin, Mark; Vongsvivut, Jitraporn; Bambery, Keith; Vasconcelos, Paulo; Southam, Gordon

2016-11-01

Canga is a moderately hard iron-rich duricrust primarily composed of goethite as a result of the weathering of banded iron formations. Canga duricrusts lack a well-developed soil profile and consequently form an innate association with rupestrian plants that may become ferruginised, contributing to canga possessing macroscopic biological features. Examination of polished canga using a field emission scanning electron microscope (FE-SEM) revealed the biological textures associated with canga extended to the sub-millimetre scale in petrographic sections and polished blocks. Laminae that formed by abiotic processes and regions where goethite cements were formed in association with microorganisms were observed in canga. Biological cycling of iron within canga has resulted in two distinct forms of microbial fossilisation: permineralisation of multispecies biofilms and mineralisation of cell envelopes. Goethite permineralised biofilms frequently formed around goethite-rich kaolinite grains in close proximity to goethite bands and were composed of micrometre-scale rod-shaped, cocci and filamentous microfossils. In contrast, the cell envelopes immobilised by authigenic iron oxides were primarily of rod-shaped microorganisms, were not permineralised and occurred in pore spaces within canga. Complete mineralisation of intact rod-shaped casts and the absence of permineralisation suggested mineralised cell envelopes may represent fossilised iron-oxidising bacteria in the canga ecosystem. Replication of these iron-oxidising bacteria appeared to infill the porous regions within canga. Synchrotron-based Fourier transform infrared (FTIR) microspectroscopy demonstrated that organic biomarkers were poorly preserved with only weak bands indicative of aliphatic methylene (CH2) associated with permineralised microbial biofilms. High resolution imaging of microbial fossils in canga that had been etched with oxalic acid supported the poor preservation of organic biomarkers within canga, indicating mineralogical replacement of organic biomarkers.

Possible roles of uncultured archaea in carbon cycling in methane-seep sediments

NASA Astrophysics Data System (ADS)

Yoshinaga, Marcos Y.; Lazar, Cassandre S.; Elvert, Marcus; Lin, Yu-Shih; Zhu, Chun; Heuer, Verena B.; Teske, Andreas; Hinrichs, Kai-Uwe

2015-09-01

Studies on microbial carbon cycling uniformly confirm that anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria represent the dominant and most active fraction of the sedimentary microbial community in methane-seep sediments. However, little is known about other frequently observed and abundant microbial taxa, their role in carbon cycling and association with the anaerobic oxidation of methane (AOM). Here, we provide a comprehensive characterization of stable carbon isotopes (δ13C) from several intact polar lipid (IPL) classes and metabolite pools in a downcore profile at a cold seep within the oxygen minimum zone off Pakistan. We aimed to evaluate microbial carbon metabolism using IPLs in relation to redox conditions, metabolites and 16S rRNA gene libraries. The 13C-depleted signature of carbon pools and microbial metabolites in pore waters (e.g., dissolved inorganic carbon, lactate and acetate) demonstrated high accumulation of AOM-associated biomass and subsequent turnover thereof. ANMEs accounted for a small fraction of the archaeal 16S rRNA gene survey, whereas sequences of other uncultured benthic archaea dominated the clone libraries, particularly the Marine Benthic Group D. On the basis of lipid diversity and carbon isotope information, we suggest that structurally diverse phospho- and glycolipids, including the recently identified unsaturated tetraethers that are particularly abundant in this setting, are likely derived from archaea other than ANMEs. Through the evaluation of δ13C values of individual IPL, our results indicate heterotrophy as a possible metabolic pathway of archaea in these AOM-dominated sediments.

Regime Shift and Microbial Dynamics in a Sequencing Batch Reactor for Nitrification and Anammox Treatment of Urine ▿†

PubMed Central

Bürgmann, Helmut; Jenni, Sarina; Vazquez, Francisco; Udert, Kai M.

2011-01-01

The microbial population and physicochemical process parameters of a sequencing batch reactor for nitrogen removal from urine were monitored over a 1.5-year period. Microbial community fingerprinting (automated ribosomal intergenic spacer analysis), 16S rRNA gene sequencing, and quantitative PCR on nitrogen cycle functional groups were used to characterize the microbial population. The reactor combined nitrification (ammonium oxidation)/anammox with organoheterotrophic denitrification. The nitrogen elimination rate initially increased by 400%, followed by an extended period of performance degradation. This phase was characterized by accumulation of nitrite and nitrous oxide, reduced anammox activity, and a different but stable microbial community. Outwashing of anammox bacteria or their inhibition by oxygen or nitrite was insufficient to explain reactor behavior. Multiple lines of evidence, e.g., regime-shift analysis of chemical and physical parameters and cluster and ordination analysis of the microbial community, indicated that the system had experienced a rapid transition to a new stable state that led to the observed inferior process rates. The events in the reactor can thus be interpreted to be an ecological regime shift. Constrained ordination indicated that the pH set point controlling cycle duration, temperature, airflow rate, and the release of nitric and nitrous oxides controlled the primarily heterotrophic microbial community. We show that by combining chemical and physical measurements, microbial community analysis and ecological theory allowed extraction of useful information about the causes and dynamics of the observed process instability. PMID:21724875

The importance of anabolism in microbial control over soil carbon storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liang, Chao; Schimel, Joshua P.; Jastrow, Julie D.

Studies of the decomposition, transformation and stabilization of soil organic matter (SOM) have dramatically increased in recent years owing to growing interest in studying the global carbon (C) cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic C reservoir in soils depends upon microbial involvement, as soil C dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microorganism-mediated processes lead to soil C stabilization. Here, we define two pathways—ex vivo modification and in vivo turnover—which jointly explain soil C dynamics driven by microbial catabolismmore » and/or anabolism. Accordingly, we use the conceptual framework of the soil ‘microbial carbon pump’ (MCP) to demonstrate how microorganisms are an active player in soil C storage. The MCP couples microbial production of a set of organic compounds to their further stabilization, which we define as the entombing effect. This integration captures the cumulative long-term legacy of microbial assimilation on SOM formation, with mechanisms (whether via physical protection or a lack of activation energy due to chemical composition) that ultimately enable the entombment of microbial-derived C in soils. We propose a need for increased efforts and seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil C dynamics to the responses of the terrestrial C cycle under global change.« less

Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass

PubMed Central

Guo, Xue; Zhou, Xishu; Hale, Lauren; Yuan, Mengting; Feng, Jiajie; Ning, Daliang; Shi, Zhou; Qin, Yujia; Liu, Feifei; Wu, Liyou; He, Zhili; Van Nostrand, Joy D.; Liu, Xueduan; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong

2018-01-01

Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010–2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P < 0.05) increased root and microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P < 0.05) changed by clipping. Clipping significantly (P < 0.05) increased the abundances of labile carbon (C) degrading genes. More importantly, the abundances of recalcitrant C degrading genes were consistently and significantly (P < 0.05) increased by clipping in the last 2 years, which could accelerate recalcitrant C degradation and weaken long-term soil carbon stability. Furthermore, genes involved in nutrient-cycling processes including nitrogen cycling and phosphorus utilization were also significantly increased by clipping. The shifts of microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices. PMID:29904372

Extractable nitrogen and microbial community structure respond to grassland restoration regardless of historical context and soil composition

PubMed Central

Dickens, Sara Jo M.; Allen, Edith B.; Santiago, Louis S.; Crowley, David

2015-01-01

Grasslands have a long history of invasion by exotic annuals, which may alter microbial communities and nutrient cycling through changes in litter quality and biomass turnover rates. We compared plant community composition, soil chemical and microbial community composition, potential soil respiration and nitrogen (N) turnover rates between invaded and restored plots in inland and coastal grasslands. Restoration increased microbial biomass and fungal : bacterial (F : B) ratios, but sampling season had a greater influence on the F : B ratio than did restoration. Microbial community composition assessed by phospholipid fatty acid was altered by restoration, but also varied by season and by site. Total soil carbon (C) and N and potential soil respiration did not differ between treatments, but N mineralization decreased while extractable nitrate and nitrification and N immobilization rate increased in restored compared with unrestored sites. The differences in soil chemistry and microbial community composition between unrestored and restored sites indicate that these soils are responsive, and therefore not resistant to feedbacks caused by changes in vegetation type. The resilience, or recovery, of these soils is difficult to assess in the absence of uninvaded control grasslands. However, the rapid changes in microbial and N cycling characteristics following removal of invasives in both grassland sites suggest that the soils are resilient to invasion. The lack of change in total C and N pools may provide a buffer that promotes resilience of labile pools and microbial community structure. PMID:25555522

Brine assemblages of ultrasmall microbial cells within the ice cover of Lake Vida, Antarctica.

PubMed

Kuhn, Emanuele; Ichimura, Andrew S; Peng, Vivian; Fritsen, Christian H; Trubl, Gareth; Doran, Peter T; Murray, Alison E

2014-06-01

The anoxic and freezing brine that permeates Lake Vida's perennial ice below 16 m contains an abundance of very small (≤0.2-μm) particles mixed with a less abundant population of microbial cells ranging from >0.2 to 1.5 μm in length. Fluorescent DNA staining, electron microscopy (EM) observations, elemental analysis, and extraction of high-molecular-weight genomic DNA indicated that a significant portion of these ultrasmall particles are cells. A continuous electron-dense layer surrounding a less electron-dense region was observed by EM, indicating the presence of a biological membrane surrounding a cytoplasm. The ultrasmall cells are 0.192 ± 0.065 μm, with morphology characteristic of coccoid and diplococcic bacterial cells, often surrounded by iron-rich capsular structures. EM observations also detected the presence of smaller unidentified nanoparticles of 0.020 to 0.140 μm among the brine cells. A 16S rRNA gene clone library from the brine 0.1- to 0.2-μm-size fraction revealed a relatively low-diversity assemblage of Bacteria sequences distinct from the previously reported >0.2-μm-cell-size Lake Vida brine assemblage. The brine 0.1- to 0.2-μm-size fraction was dominated by the Proteobacteria-affiliated genera Herbaspirillum, Pseudoalteromonas, and Marinobacter. Cultivation efforts of the 0.1- to 0.2-μm-size fraction led to the isolation of Actinobacteria-affiliated genera Microbacterium and Kocuria. Based on phylogenetic relatedness and microscopic observations, we hypothesize that the ultrasmall cells in Lake Vida brine are ultramicrocells that are likely in a reduced size state as a result of environmental stress or life cycle-related conditions.

Brine Assemblages of Ultrasmall Microbial Cells within the Ice Cover of Lake Vida, Antarctica

PubMed Central

Kuhn, Emanuele; Ichimura, Andrew S.; Peng, Vivian; Fritsen, Christian H.; Trubl, Gareth; Doran, Peter T.

2014-01-01

The anoxic and freezing brine that permeates Lake Vida's perennial ice below 16 m contains an abundance of very small (≤0.2-μm) particles mixed with a less abundant population of microbial cells ranging from >0.2 to 1.5 μm in length. Fluorescent DNA staining, electron microscopy (EM) observations, elemental analysis, and extraction of high-molecular-weight genomic DNA indicated that a significant portion of these ultrasmall particles are cells. A continuous electron-dense layer surrounding a less electron-dense region was observed by EM, indicating the presence of a biological membrane surrounding a cytoplasm. The ultrasmall cells are 0.192 ± 0.065 μm, with morphology characteristic of coccoid and diplococcic bacterial cells, often surrounded by iron-rich capsular structures. EM observations also detected the presence of smaller unidentified nanoparticles of 0.020 to 0.140 μm among the brine cells. A 16S rRNA gene clone library from the brine 0.1- to 0.2-μm-size fraction revealed a relatively low-diversity assemblage of Bacteria sequences distinct from the previously reported >0.2-μm-cell-size Lake Vida brine assemblage. The brine 0.1- to 0.2-μm-size fraction was dominated by the Proteobacteria-affiliated genera Herbaspirillum, Pseudoalteromonas, and Marinobacter. Cultivation efforts of the 0.1- to 0.2-μm-size fraction led to the isolation of Actinobacteria-affiliated genera Microbacterium and Kocuria. Based on phylogenetic relatedness and microscopic observations, we hypothesize that the ultrasmall cells in Lake Vida brine are ultramicrocells that are likely in a reduced size state as a result of environmental stress or life cycle-related conditions. PMID:24727273

[Isolation and identification of electrochemically active microorganism from micro-aerobic environment].

PubMed

Wu, Song; Xiao, Yong; Zheng, Zhi-Yong; Zheng, Yue; Yang, Zhao-Hui; Zhao, Feng

2014-10-01

Extracellular electron transfer of electrochemically active microorganism plays vital role in biogeochemical cycling of metals and carbon and in biosynthesis of bioenergy. Compared to anaerobic anode, micro-aerobic anode captures more energy from microbial fuel cell. However, most of previous researches focused on functioning bacteria in anaerobic anode, functioning bacteria in micro-aerobic anode was rarely studied. Herein, we used the traditional aerobic screening technology to isolate functioning bacteria from a micro-aerobic anode. Three pure cultures Aeromonas sp. WS-XY2, Citrobacter sp. WS-XY3 and Bacterium strain WS-XY4 were obtained. WS-XY2 and WS-XY3 were belonged to Proteobacteria, whereas WS-XY4 was possibly a new species. Cyclic voltammetry and chronoamperometry analysis demonstrated all of them showed the electrochemical activity by direct extracellular electron transfer, and micro-aerobic anode could select bacteria that have similar electrochemical activity to proliferate on the anode. We further conclude that functioning bacteria in micro-aerobic anode are more efficient than that of anaerobic anode may be the reason that micro-aerobic anode has better performance than anaerobic anode. Therefore, a thorough study of functioning bacteria in micro-aerobic anode will significantly promote the energy recovery from microbial fuel cell.

Novel Self-driven Microbial Nutrient Recovery Cell with Simultaneous Wastewater Purification

PubMed Central

Chen, Xi; Sun, Dongya; Zhang, Xiaoyuan; Liang, Peng; Huang, Xia

2015-01-01

Conventional wastewater purification technologies consume large amounts of energy, while the abundant chemical energy and nutrient resources contained in sewage are wasted in such treatment processes. A microbial nutrient recovery cell (MNRC) has been developed to take advantage of the energy contained in wastewater, in order to simultaneously purify wastewater and recover nutrient ions. When wastewater was circulated between the anode and cathode chambers of the MNRC, the organics (COD) were removed by bacteria while ammonium and phosphate (NH4+-N and PO43−-P) were recovered by the electrical field that was produced using in situ energy in the wastewater without additional energy input. The removal efficiencies from wastewater were >82% for COD, >96% for NH4+-N, and >64% for PO43−-P in all the operational cycles. Simultaneously, the concentrations of NH4+ and PO43− in the recovery chamber increased to more than 1.5 and 2.2 times, respectively, compared with the initial concentrations in wastewater. The MNRC provides proof-of-concept as a sustainable, self-driven approach to efficient wastewater purification and nutrient recovery in a comprehensive bioelectrochemical system. PMID:26503712

Bacterial Flux by Net Precipitation from the Phyllosphere to the Forest Floor.

NASA Astrophysics Data System (ADS)

Pound, P.; Van Stan, J. T., II; Moore, L. D.; Bittar, T.

2016-12-01

Transport pathways of microbes between ecosystem spheres (atmosphere, phyllosphere, and pedosphere) represent major fluxes in nutrient cycles and have the potential to significantly affect microbial ecological processes. We quantified a previously unexamined microbial flux from the phyllosphere to the pedosphere during rainfall and found it to be substantial. Net rainfall bacterial fluxes for throughfall and stemflow were quantified using flow cytometry and a quantitative Polymerase Chain Reaction (qPCR) assay for a Quercus virginiana (Mill., southern live oak) forest with heavy epiphyte cover of Tillandsia usneoides (L., Spanish moss) and Pleopeltis polypodiodes (L., resurrection fern) in coastal Georgia (Southeast USA). Total net precipitation flux of bacteria was 15 quadrillion cells year-1 ha-1, which (assuming a bacterial cell mass of 1 pg) is approximately 15 kg of bacterial biomass supply per year. Stemflow generation was low in this stand (rarely exceeded 10 L storm-1) yet still delivered half the annual net precipitation flux due to high bacterial concentration. The role of this previously unquantified bacterial flux in the forest floor has also been under studied, yet it may be significant by contributing functional community members (if living) or labile lysates (if dead).

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

PubMed Central

Roux, Simon; Hawley, Alyse K; Torres Beltran, Monica; Scofield, Melanie; Schwientek, Patrick; Stepanauskas, Ramunas; Woyke, Tanja; Hallam, Steven J; Sullivan, Matthew B

2014-01-01

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs. DOI: http://dx.doi.org/10.7554/eLife.03125.001 PMID:25171894

Flexible and stretchable microbial fuel cells with modified conductive and hydrophilic textile.

PubMed

Pang, Sumiao; Gao, Yang; Choi, Seokheun

2018-02-15

We built a flexible, stretchable microbial fuel cell (MFC) by laminating two functional components: a bioanode textile with a conductive and hydrophilic polymer coating and a solid-state cathode textile loaded with silver oxide. The textile MFC used Pseudomonas aeruginosa PAO1 as a biocatalyst to generate the maximum power and current density of 1.0µW/cm 2 and 6.3µA/cm 2 , respectively, which are comparable with or even higher than other flexible MFCs such as paper-based devices (~ a few µW/cm 2 ). Additionally, the textile MFC generated consistent power even with repeated 70 cycles of 50% stretching. A simple batch fabrication method simultaneously produced 20 individual 2cm × 2cm devices by using brushing, spraying, ironing, and computerized sewing, a process that will revolutionize the mass production of textile MFCs. This achievement is scientifically meaningful because developing textile MFCs requires integration of both electronic and fluidic components into the textile three-dimensionally. This flexible and stretchable energy harvesting device is expected to be easily integrated with the next generation stretchable electronics for realizing low-power, stand-alone, self-sustainable systems. Copyright © 2017 Elsevier B.V. All rights reserved.

Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific.

PubMed

Hu, Sarah K; Campbell, Victoria; Connell, Paige; Gellene, Alyssa G; Liu, Zhenfeng; Terrado, Ramon; Caron, David A

2016-04-01

Microbial eukaryotes fulfill key ecological positions in marine food webs. Molecular approaches that connect protistan diversity and biogeography to their diverse metabolisms will greatly improve our understanding of marine ecosystem function. The majority of molecular-based studies to date use 18S rRNA gene sequencing to characterize natural microbial assemblages, but this approach does not necessarily discriminate between active and non-active cells. We incorporated RNA sequencing into standard 18S rRNA gene sequence surveys with the purpose of assessing those members of the protistan community contributing to biogeochemical cycling (active organisms), using the ratio of cDNA (reverse transcribed from total RNA) to 18S rRNA gene sequences within major protistan taxonomic groups. Trophically important phytoplankton, such as diatoms and chlorophytes exhibited seasonal trends in relative activity. Additionally, both radiolaria and ciliates displayed previously unreported high relative activities below the euphotic zone. This study sheds new light on the relative metabolic activity of specific protistan groups and how microbial communities respond to changing environmental conditions. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sites.

PubMed

Liang, Yuting; Zhao, Huihui; Zhang, Xu; Zhou, Jizhong; Li, Guanghe

2014-07-15

To compare the functional gene structure and diversity of microbial communities in saline-alkali and slightly acidic oil-contaminated sites, 40 soil samples were collected from two typical oil exploration sites in North and South China and analyzed with a comprehensive functional gene array (GeoChip 3.0). The overall microbial pattern was significantly different between the two sites, and a more divergent pattern was observed in slightly acidic soils. Response ratio was calculated to compare the microbial functional genes involved in organic contaminant degradation and carbon, nitrogen, phosphorus, and sulfur cycling. The results indicated a significantly low abundance of most genes involved in organic contaminant degradation and in the cycling of nitrogen and phosphorus in saline-alkali soils. By contrast, most carbon degradation genes and all carbon fixation genes had similar abundance at both sites. Based on the relationship between the environmental variables and microbial functional structure, pH was the major factor influencing the microbial distribution pattern in the two sites. This study demonstrated that microbial functional diversity and heterogeneity in oil-contaminated environments can vary significantly in relation to local environmental conditions. The limitation of nitrogen and phosphorus and the low degradation capacity of organic contaminant should be carefully considered, particularly in most oil-exploration sites with saline-alkali soils. Copyright © 2014 Elsevier B.V. All rights reserved.

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

PubMed

Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

2017-10-15

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial carbon pump and its significance for carbon sequestration in soils

NASA Astrophysics Data System (ADS)

Liang, Chao

2017-04-01

Studies of the decomposition, transformation and stabilization of soil organic carbon have dramatically increased in recent years due to growing interest in studying the global carbon cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic carbon reservoir in soils depends upon microbial involvement because soil carbon dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microbe-mediated processes lead to soil carbon stabilization. Here, two pathways, ex vivo modification and in vivo turnover, were defined to jointly explain soil carbon dynamics driven by microbial catabolism and/or anabolism. Accordingly, a conceptual framework consisting of the raised concept of the soil "microbial carbon pump" (MCP) was demonstrated to describe how microbes act as an active player in soil carbon storage. The hypothesis is that the long-term microbial assimilation process may facilitate the formation of a set of organic compounds that are stabilized (whether via protection by physical interactions or a reduction in activation energy due to chemical composition), ultimately leading to the sequestration of microbial-derived carbon in soils. The need for increased efforts was proposed to seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil carbon dynamics to the responses of the terrestrial carbon cycle under global change.

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in urban streams

NASA Astrophysics Data System (ADS)

Ledford, S. H.; Price, J. R.; Ryan, M. O.; Toran, L.; Sales, C. M.

2017-12-01

New technologies are allowing for intense scrutiny of the impact of land use on microbial communities in stream networks. We used a combination of analytical chemistry, real-time polymerase chain reaction (qPCR) and targeted amplicon sequencing for a preliminary study on the impact of wastewater treatment plant effluent discharge on urban streams. Samples were collected on two dates above and below treatment plants on the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, PA, USA. As expected, effluent was observed to be a significant source of nutrients and human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources. Antecedent moisture conditions impacted overall microbial community diversity, with higher diversity occurring after rainfall. These findings hint at resilience in stream microbial communities to recover from wastewater treatment plant effluent and are vital to understanding the impacts of urbanization on microbial stream communities.

Response of sediment microbial community structure in a freshwater reservoir to manipulations in oxygen availability.

PubMed

Bryant, Lee D; Little, John C; Bürgmann, Helmut

2012-04-01

Hypolimnetic oxygenation systems (HOx) are being increasingly used in freshwater reservoirs to elevate dissolved oxygen levels in the hypolimnion and suppress sediment-water fluxes of soluble metals (e.g. Fe and Mn) which are often microbially mediated. We assessed changes in sediment microbial community structure and corresponding biogeochemical cycling on a reservoir-wide scale as a function of HOx operations. Sediment microbial biomass as quantified by DNA concentration was increased in regions most influenced by the HOx. Following an initial decrease in biomass in the upper sediment while oxygen concentrations were low, biomass typically increased at all depths as the 4-month-long oxygenation season progressed. A distinct shift in microbial community structure was only observed at the end of the season in the upper sediment near the HOx. While this shift was correlated to HOx-enhanced oxygen availability, increased TOC levels and precipitation of Fe- and Mn-oxides, abiotic controls on Fe and Mn cycling, and/or the adaptability of many bacteria to variations in prevailing electron acceptors may explain the delayed response and the comparatively limited changes at other locations. While the sediment microbial community proved remarkably resistant to relatively short-term changes in HOx operations, HOx-induced variation in microbial structure, biomass, and activity was observed after a full season of oxygenation. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Searching for biogeochemical hot spots in three dimensions: Soil C and N cycling in hydropedologic settings in a northern hardwood forest

NASA Astrophysics Data System (ADS)

Morse, J. L.; Werner, S. F.; Gillin, C. P.; Goodale, C. L.; Bailey, S. W.; McGuire, K. J.; Groffman, P. M.

2014-08-01

Understanding and predicting the extent, location, and function of biogeochemical hot spots at the watershed scale is a frontier in environmental science. We applied a hydropedologic approach to identify (1) biogeochemical differences among morphologically distinct hydropedologic settings and (2) hot spots of microbial carbon (C) and nitrogen (N) cycling activity in a northern hardwood forest in Hubbard Brook Experimental Forest, New Hampshire, USA. We assessed variables related to C and N cycling in spodic hydropedologic settings (typical podzols, bimodal podzols, and Bh podzols) and groundwater seeps during August 2010. We found that soil horizons (Oi/Oe, Oa/A, and B) differed significantly for most variables. B horizons (>10 cm) accounted for 71% (±11%) of C pools and 62% (±10%) of microbial biomass C in the sampled soil profile, whereas the surface horizons (Oi/Oe and Oa/A; 0-10 cm) were dominant zones for N-cycle-related variables. Watershed-wide estimates of C and N cycling were higher by 34 to 43% (±17-19%) when rates, horizon thickness, and areal extent of each hydropedologic setting were incorporated, versus conventionally calculated estimates for typical podzols that included only the top 10 cm of mineral soil. Despite the variation in profile development in typical, bimodal, and Bh podzols, we did not detect significant differences in C and N cycling among them. Across all soil horizons and hydropedologic settings, we found strong links between biogeochemical cycling and soil C, suggesting that the accumulation of C in soils may be a robust indicator of microbial C and N cycling capacity in the landscape.

Quantitative Relationships between Photosynthetic, Nitrogen Fixing, and Fermentative H2 Metabolism in a Photosynthetic Microbial Mat

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Albert, Daniel B.; Bebout, Brad M.; Turk, Kendra A.; DesMarais, David J.

2004-01-01

The ultimate potential of any microbial ecosystem to contribute chemically to its environment - and therefore, to impact planetary biogeochemistry or to generate recognizable biosignatures - depends not only on the individual metabolic capabilities of constituent organisms, but also on how those capabilities are expressed through interactions with neighboring organisms. This is particularly important for microbial mats, which compress an extremely broad range of metabolic potential into a small and dynamic system. H2 participates in many of these metabolic processes, including the major elemental cycling processes of photosynthesis, nitrogen fixation, sulfate reduction, and fermentation, and may therefore serve as a mediator of microbial interactions within the mat system. Collectively, the requirements of energy, electron transfer, and biomass element stoichiometry suggest quantitative relationships among the major element cycling processes, as regards H2 metabolism We determined experimentally the major contributions to 32 cycling in hypersaline microbial mats from Baja California, Mexico, and compared them to predicted relationships. Fermentation under dark, anoxic conditions is quantitatively the most important mechanism of H2 production, consistent with expectations for non-heterocystous mats such as those under study. Up to 16% of reducing equivalents fixed by photosynthesis during the day may be released by this mechanism. The direct contribution of nitrogen fixation to H2 production is small in comparison, but this process may indirectly stimulate substantial H2 generation, by requiring higher rates of fermentation. Sulfate reduction, aerobic consumption, diffusive and ebulitive loss, and possibly H2-based photoreduction of CO2 serve as the principal H2 sinks. Collectively, these processes interact to create an orders-of-magnitude daily variation in H2 concentrations and fluxes, and thereby in the oxidation-reduction potential that is imposed on microbial processes occuring within the mat matrix.

Role of microorganisms for cycling of atmospheric constituents, emphasizing the greenhouse gas methane (Invited)

NASA Astrophysics Data System (ADS)

Conrad, R.

2013-12-01

Microorganisms have contributed significantly to the formation of the atmosphere and the habitability of Earth. Microbial methanogenesis probably helped overcoming the faint sun problem on young Earth. Later on, cyanobacterial photosynthesis produced oxygen and thus restricted the life zone of methanogenic microbial communities, which nowadays contribute only about 1% to total carbon cycle. Nevertheless, methanogenesis still dominates the budget of atmospheric methane and contributes significantly to the greenhouse effect. There are numerous habitats, which exchange methane with the atmosphere, and even more in which methane is intensively cycled albeit little emitted. Methane can be a byproduct of chemical reactions in plant leaves, or of aerobic methyl phosphonate consumption in ocean water. Most commonly, however, methane is a stoichiometric catabolic product in the degradation of organic matter by anaerobic microorganisms. The degradation is achieved by a complex microbial community consisting of various species of hydrolytic and fermentative Bacteria that produce hydrogen, carbon dioxide and acetate as major end products, and of methanogenic Archaea that eventually convert these compounds to methane and carbon dioxide. The composition of such methanogenic microbial communities, the rates and paths of methane formation, and the isotopic composition of the produced methane all exhibit quite some variability across the different habitats in which methane is produced from organic matter decomposition, such as flooded soils, lake sediments, peatlands, animal gut systems. The structure of the microbial communities often strongly affects their function. It is a challenging task to understand the environmental and biochemical basis of the interactions of abiotic factors and microorganisms shaping the structure and function of the microbial communities in the different methanogenic habitats.

Microbial Decomposers Not Constrained by Climate History Along a Mediterranean Climate Gradient

NASA Astrophysics Data System (ADS)

Baker, N. R.; Khalili, B.; Martiny, J. B. H.; Allison, S. D.

2017-12-01

The return of organic carbon to the atmosphere through terrestrial decomposition is mediated through the breakdown of complex organic polymers by extracellular enzymes produced by microbial decomposer communities. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. To address this question, we deployed fine-pore nylon mesh "microbial cage" litterbags containing grassland litter with and without local inoculum across five sites in southern California, spanning a gradient of 10.3-22.8° C in mean annual temperature and 100-400+ mm mean annual precipitation. Litterbags were deployed in October 2014 and collected four times over the course of 14 months. Recovered litter was assayed for mass loss, litter chemistry, microbial biomass, extracellular enzymes (Vmax and Km­), and enzyme temperature sensitivities. We hypothesized that grassland litter would decompose most rapidly in the grassland site, and that access to local microbial communities would enhance litter decomposition rates and microbial activity in the other sites along the gradient. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbes were not restricted in their ability to decompose litter under different climate conditions. Although we observed a strong correlation between bacterial biomass and mass loss across the gradient, litter that was inoculated with local microbial communities lost less mass despite having greater bacterial biomass and potentially accumulating more microbial residues. Our results suggest that microbial community composition may not constrain C-cycling rates under climate change in our system. However, there may be community constraints on decomposition if climate change alters litter chemistry, a mechanism only indirectly addressed by our design.

Seasonal changes in microbial community structure and activity imply winter production is linked to summer hypoxia in a large lake.

PubMed

Wilhelm, Steven W; LeCleir, Gary R; Bullerjahn, George S; McKay, Robert M; Saxton, Matthew A; Twiss, Michael R; Bourbonniere, Richard A

2014-02-01

Carbon and nutrient cycles in large temperate lakes such as Lake Erie are primarily driven by phototrophic and heterotrophic microorganisms, although our understanding of these is often constrained to late spring through summer due to logistical constraints. During periods of > 90% ice cover in February of 2008, 2009, and 2010, we collected samples from an icebreaker for an examination of bacterial production as well as microbial community structure. In comparison with summer months (August 2002 and 2010), we tested hypotheses concerning seasonal changes in microbial community diversity and production. Bacterial production estimates were c. 2 orders of magnitude higher (volume normalized) in summer relative to winter. Our observations further demonstrate that the microbial community, including single-celled phototrophs, varied in composition between August and February. Sediment traps deployed and collected over a 3 year period (2008-2011) confirmed that carbon export was ongoing and not limiting winter production. The results support the notion that active primary producers in winter months export carbon to the sediments that is not consumed until the warmer seasons. The establishment of this linkage is a critical observation in efforts to understand the extent and severity of annual summertime formations of a zone of regional hypoxia in Lake Erie. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process

PubMed Central

Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

2016-01-01

Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types. PMID:27485896

Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process

NASA Astrophysics Data System (ADS)

Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

2016-08-01

Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types.

Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process.

PubMed

Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

2016-08-03

Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types.

When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems

PubMed Central

Sauterey, Boris; Ward, Ben A.; Follows, Michael J.; Bowler, Chris; Claessen, David

2015-01-01

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that “Everything is everywhere, but the environment selects”, we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean. PMID:25852217

When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems.

PubMed

Sauterey, Boris; Ward, Ben A; Follows, Michael J; Bowler, Chris; Claessen, David

2015-01-01

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that "Everything is everywhere, but the environment selects", we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean.

Predicting Biological Information Flow in a Model Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Louca, S.; Hawley, A. K.; Katsev, S.; Beltran, M. T.; Bhatia, M. P.; Michiels, C.; Capelle, D.; Lavik, G.; Doebeli, M.; Crowe, S.; Hallam, S. J.

2016-02-01

Microbial activity drives marine biochemical fluxes and nutrient cycling at global scales. Geochemical measurements as well as molecular techniques such as metagenomics, metatranscriptomics and metaproteomics provide great insight into microbial activity. However, an integration of molecular and geochemical data into mechanistic biogeochemical models is still lacking. Recent work suggests that microbial metabolic pathways are, at the ecosystem level, strongly shaped by stoichiometric and energetic constraints. Hence, models rooted in fluxes of matter and energy may yield a holistic understanding of biogeochemistry. Furthermore, such pathway-centric models would allow a direct consolidation with meta'omic data. Here we present a pathway-centric biogeochemical model for the seasonal oxygen minimum zone in Saanich Inlet, a fjord off the coast of Vancouver Island. The model considers key dissimilatory nitrogen and sulfur fluxes, as well as the population dynamics of the genes that mediate them. By assuming a direct translation of biocatalyzed energy fluxes to biosynthesis rates, we make predictions about the distribution and activity of the corresponding genes. A comparison of the model to molecular measurements indicates that the model explains observed DNA, RNA, protein and cell depth profiles. This suggests that microbial activity in marine ecosystems such as oxygen minimum zones is well described by DNA abundance, which, in conjunction with geochemical constraints, determines pathway expression and process rates. Our work further demonstrates how meta'omic data can be mechanistically linked to environmental redox conditions and biogeochemical processes.

Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile.

PubMed

Lara, José; Escudero González, Lorena; Ferrero, Marcela; Chong Díaz, Guillermo; Pedrós-Alió, Carlos; Demergasso, Cecilia

2012-05-01

Microbial populations are involved in the arsenic biogeochemical cycle in catalyzing arsenic transformations and playing indirect roles. To investigate which ecotypes among the diverse microbial communities could have a role in cycling arsenic in salt lakes in Northern Chile and to obtain clues to facilitate their isolation in pure culture, sediment samples from Salar de Ascotán and Salar de Atacama were cultured in diluted LB medium amended with NaCl and arsenic, at different incubation conditions. The samples and the cultures were analyzed by nucleic acid extraction, fingerprinting analysis, and sequencing. Microbial reduction of As was evidenced in all the enrichments carried out in anaerobiosis. The results revealed that the incubation factors were more important for determining the microbial community structure than arsenic species and concentrations. The predominant microorganisms in enrichments from both sediments belonged to the Firmicutes and Proteobacteria phyla, but most of the bacterial ecotypes were confined to only one system. The occurrence of an active arsenic biogeochemical cycle was suggested in the system with the highest arsenic content that included populations compatible with microorganisms able to transform arsenic for energy conservation, accumulate arsenic, produce H(2), H(2)S and acetic acid (potential sources of electrons for arsenic reduction) and tolerate high arsenic levels.

Microbial Potential for Ecosystem N Loss Is Increased by Experimental N Deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freedman, Zachary B.; Upchurch, Rima A.; Zak, Donald R.

Fossil fuel combustion and fertilizer use has increased the amount of biologically available N entering terrestrial ecosystems. Nonetheless, our understanding of how anthropogenic N may alter the physiological mechanisms by which soil microorganisms cycle N in soil is still developing. Here, we applied shotgun metagenomics to a replicated long-term field experiment to determine how two decades of experimental N deposition, at a rate expected by mid-century, has affected the genetic potential of the soil microbial community to cycle N in soils. Experimental N deposition lead to a significant and persistent increase in functional assemblages mediating N cycle transformations associated withmore » ecosystem N loss (i.e., denitrification and nitrification), whereas functional assemblages associated with N input and retention (i.e., N fixation and microbial N assimilation) were less positively affected. Furthermore, the abundance and composition of microbial taxa, as well as functional assemblages involved in housekeeping functions (i.e., DNA replication) were unaffected by experimental N deposition. Here taken together, our results suggest that functional genes and gene pathways associated with ecosystem N loss have been favored by experimental N deposition, which may represent a genetic mechanism fostering increased N loss as anthropogenic N deposition increases in the future.« less

Microbial Potential for Ecosystem N Loss Is Increased by Experimental N Deposition

DOE PAGES

Freedman, Zachary B.; Upchurch, Rima A.; Zak, Donald R.; ...

2016-10-13

Fossil fuel combustion and fertilizer use has increased the amount of biologically available N entering terrestrial ecosystems. Nonetheless, our understanding of how anthropogenic N may alter the physiological mechanisms by which soil microorganisms cycle N in soil is still developing. Here, we applied shotgun metagenomics to a replicated long-term field experiment to determine how two decades of experimental N deposition, at a rate expected by mid-century, has affected the genetic potential of the soil microbial community to cycle N in soils. Experimental N deposition lead to a significant and persistent increase in functional assemblages mediating N cycle transformations associated withmore » ecosystem N loss (i.e., denitrification and nitrification), whereas functional assemblages associated with N input and retention (i.e., N fixation and microbial N assimilation) were less positively affected. Furthermore, the abundance and composition of microbial taxa, as well as functional assemblages involved in housekeeping functions (i.e., DNA replication) were unaffected by experimental N deposition. Here taken together, our results suggest that functional genes and gene pathways associated with ecosystem N loss have been favored by experimental N deposition, which may represent a genetic mechanism fostering increased N loss as anthropogenic N deposition increases in the future.« less

Microbial Heat Recovery Cell (MHRC) System Concept

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

This factsheet describes a project that aimed to develop a microbial heat recovery cell (MHRC) system that combines a microbial reverse electrodialysis technology with waste heat recovery to convert industrial effluents into electricity and hydrogen.

Labile and recalcitrant organic matter utilization by river biofilm under increasing water temperature.

PubMed

Ylla, Irene; Romaní, Anna M; Sabater, Sergi

2012-10-01

Microbial biofilms in rivers contribute to the decomposition of the available organic matter which typically shows changes in composition and bioavailability due to their origin, seasonality, and watershed characteristics. In the context of global warming, enhanced biofilm organic matter decomposition would be expected but this effect could be specific when either a labile or a recalcitrant organic matter source would be available. A laboratory experiment was performed to mimic the effect of the predicted increase in river water temperature (+4 °C above an ambient temperature) on the microbial biofilm under differential organic matter sources. The biofilm microbial community responded to higher water temperature by increasing bacterial cell number, respiratory activity (electron transport system) and microbial extracellular enzymes (extracellular enzyme activity). At higher temperature, the phenol oxidase enzyme explained a large fraction of respiratory activity variation suggesting an enhanced microbial use of degradation products from humic substances. The decomposition of hemicellulose (β-xylosidase activity) seemed to be also favored by warmer conditions. However, at ambient temperature, the enzymes highly responsible for respiration activity variation were β-glucosidase and leu-aminopeptidase, suggesting an enhanced microbial use of polysaccharides and peptides degradation products. The addition of labile dissolved organic carbon (DOC; dipeptide plus cellobiose) caused a further augmentation of heterotrophic biomass and respiratory activity. The changes in the fluorescence index and the ratio Abs(250)/total DOC indicated that higher temperature accelerated the rates of DOC degradation. The experiment showed that the more bioavailable organic matter was rapidly cycled irrespective of higher temperature while degradation of recalcitrant substances was enhanced by warming. Thus, pulses of carbon at higher water temperature might have consequences for DOC processing.

The biogeochemistry of metal cycling

NASA Technical Reports Server (NTRS)

Nealson, Kenneth H. (Editor); Nealson, Molly (Editor); Dutcher, F. Ronald (Editor)

1990-01-01

The results of the Planetary Biology and Microbial Ecology's summer 1987 program are summarized. The purpose of the interdisciplinary PBME program is to integrate, via lectures and laboratory work, the contributions of university and NASA scientists and student interns. The 1987 program examined various aspects of the biogeochemistry of metal cycling, and included such areas as limnology, metal chemistry, metal geochemistry, microbial ecology, and interactions with metals. A particular area of focus was the use of remote sensing in the study of biogeochemistry. Abstracts and bibliographies of the lectures and reports of the laboratory projects are presented.

Engineering biological systems using automated biofoundries.

PubMed

Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, Huimin

2017-07-01

Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Bacterial quorum sensing and nitrogen cycling in rhizosphere soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeAngelis, K.M.; Lindow, S.E.; Firestone, M.K.

2008-10-01

Plant photosynthate fuels carbon-limited microbial growth and activity, resulting in increased rhizosphere nitrogen (N)-mineralization. Most soil organic N is macromolecular (chitin, protein, nucleotides); enzymatic depolymerization is likely rate-limiting for plant N accumulation. Analyzing Avena (wild oat) planted in microcosms containing sieved field soil, we observed increased rhizosphere chitinase and protease specific activities, bacterial cell densities, and dissolved organic nitrogen (DON) compared to bulk soil. Low-molecular weight DON (<3000 Da) was undetectable in bulk soil but comprised 15% of rhizosphere DON. Extracellular enzyme production in many bacteria requires quorum sensing (QS), cell-density dependent group behavior. Because proteobacteria are considered major rhizospheremore » colonizers, we assayed the proteobacterial QS signals acyl-homoserine lactones (AHLs), which were significantly increased in the rhizosphere. To investigate the linkage between soil signaling and N cycling, we characterized 533 bacterial isolates from Avena rhizosphere: 24% had chitinase or protease activity and AHL production; disruption of QS in 7 of 8 eight isolates disrupted enzyme activity. Many {alpha}-Proteobacteria were newly found with QS-controlled extracellular enzyme activity. Enhanced specific activities of N-cycling enzymes accompanied by bacterial density-dependent behaviors in rhizosphere soil gives rise to the hypothesis that QS could be a control point in the complex process of rhizosphere N-mineralization.« less

Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon.

PubMed

Highton, Matthew P; Roosa, Stéphanie; Crawshaw, Josie; Schallenberg, Marc; Morales, Sergio E

2016-01-01

Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH , nirS , nosZI , and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor†

PubMed Central

Orcutt, Beth N.; Sylvan, Jason B.; Knab, Nina J.; Edwards, Katrina J.

2011-01-01

Summary: The majority of life on Earth—notably, microbial life—occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean—the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.—has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats. PMID:21646433

Metabarcoding: a powerful tool to investigate microbial communities and shape future plant protection strategies

USDA-ARS?s Scientific Manuscript database

Microorganisms are the main drivers shaping the functioning and equilibrium of all ecosystems, contributing to nutrient cycling, primary production, litter decomposition, and multi-trophic interactions. Knowledge about the microbial assemblies in specific ecological niches is pivotal to understand ...

Insights on the marine microbial nitrogen cycle from isotopic approaches to nitrification

PubMed Central

Casciotti, Karen L.; Buchwald, Carolyn

2012-01-01

The microbial nitrogen (N) cycle involves a variety of redox processes that control the availability and speciation of N in the environment and that are involved with the production of nitrous oxide (N2O), a climatically important greenhouse gas. Isotopic measurements of ammonium (NH+4), nitrite (NO−2), nitrate (NO−3), and N2O can now be used to track the cycling of these compounds and to infer their sources and sinks, which has lead to new and exciting discoveries. For example, dual isotope measurements of NO−3 and NO−2 have shown that there is NO−3 regeneration in the ocean's euphotic zone, as well as in and around oxygen deficient zones (ODZs), indicating that nitrification may play more roles in the ocean's N cycle than generally thought. Likewise, the inverse isotope effect associated with NO−2 oxidation yields unique information about the role of this process in NO−2 cycling in the primary and secondary NO−2 maxima. Finally, isotopic measurements of N2O in the ocean are indicative of an important role for nitrification in its production. These interpretations rely on knowledge of the isotope effects for the underlying microbial processes, in particular ammonia oxidation and nitrite oxidation. Here we review the isotope effects involved with the nitrification process and the insights provided by this information, then provide a prospectus for future work in this area. PMID:23091468

Insights on the marine microbial nitrogen cycle from isotopic approaches to nitrification.

PubMed

Casciotti, Karen L; Buchwald, Carolyn

2012-01-01

The microbial nitrogen (N) cycle involves a variety of redox processes that control the availability and speciation of N in the environment and that are involved with the production of nitrous oxide (N(2)O), a climatically important greenhouse gas. Isotopic measurements of ammonium (NH(+) (4)), nitrite (NO(-) (2)), nitrate (NO(-) (3)), and N(2)O can now be used to track the cycling of these compounds and to infer their sources and sinks, which has lead to new and exciting discoveries. For example, dual isotope measurements of NO(-) (3) and NO(-) (2) have shown that there is NO(-) (3) regeneration in the ocean's euphotic zone, as well as in and around oxygen deficient zones (ODZs), indicating that nitrification may play more roles in the ocean's N cycle than generally thought. Likewise, the inverse isotope effect associated with NO(-) (2) oxidation yields unique information about the role of this process in NO(-) (2) cycling in the primary and secondary NO(-) (2) maxima. Finally, isotopic measurements of N(2)O in the ocean are indicative of an important role for nitrification in its production. These interpretations rely on knowledge of the isotope effects for the underlying microbial processes, in particular ammonia oxidation and nitrite oxidation. Here we review the isotope effects involved with the nitrification process and the insights provided by this information, then provide a prospectus for future work in this area.

Bacteriophage in polar inland waters

USGS Publications Warehouse

Säwström, Christin; Lisle, John; Anesio, A.M.; Priscu, John C.; Laybourn-Parry, J.

2008-01-01

Bacteriophages are found wherever microbial life is present and play a significant role in aquatic ecosystems. They mediate microbial abundance, production, respiration, diversity, genetic transfer, nutrient cycling and particle size distribution. Most studies of bacteriophage ecology have been undertaken at temperate latitudes. Data on bacteriophages in polar inland waters are scant but the indications are that they play an active and dynamic role in these microbially dominated polar ecosystems. This review summarises what is presently known about polar inland bacteriophages, ranging from subglacial Antarctic lakes to glacial ecosystems in the Arctic. The review examines interactions between bacteriophages and their hosts and the abiotic and biotic variables that influence these interactions in polar inland waters. In addition, we consider the proportion of the bacteria in Arctic and Antarctic lake and glacial waters that are lysogenic and visibly infected with viruses. We assess the relevance of bacteriophages in the microbial loop in the extreme environments of Antarctic and Arctic inland waters with an emphasis on carbon cycling.

Insight from Genomics on Biogeochemical Cycles in a Shallow-Sea Hydrothermal System

NASA Astrophysics Data System (ADS)

Lu, G. S.; Amend, J.

2015-12-01

Shallow-sea hydrothermal ecosystems are dynamic, high-energy systems influenced by sunlight and geothermal activity. They provide accessible opportunities for investigating thermophilic microbial biogeochemical cycles. In this study, we report biogeochemical data from a shallow-sea hydrothermal system offshore Paleochori Bay, Milos, Greece, which is characterized by a central vent covered by white microbial mats with hydrothermally influenced sediments extending into nearby sea grass area. Geochemical analysis and deep sequencing provide high-resolution information on the geochemical patterns, microbial diversity and metabolic potential in a two-meter transect. The venting fluid is elevated in temperature (~70oC), low in pH (~4), and enriched in reduced species. The geochemical pattern shows that the profile is affected by not only seawater dilution but also microbial regulation. The microbial community in the deepest section of vent core (10-12 cm) is largely dominated by thermophilic archaea, including a methanogen and a recently described Crenarcheon. Mid-core (6-8 cm), the microbial community in the venting area switches to the hydrogen utilizer Aquificae. Near the sediment-water interface, anaerobic Firmicutes and Actinobacteria dominate, both of which are commonly associated with subsurface and hydrothermal sites. All other samples are dominated by diverse Proteobacteria. The sulfate profile is strongly correlated with the population size of delta- and episilon-proteobactia. The dramatic decrease in concentrations of As and Mn in pore fluids as a function of distance from the vent suggests that in addition to seawater dilution, microorganisms are likely transforming these and other ions through a combination of detoxification and catabolism. In addition, high concentrations of dissolved Fe are only measurable in the shallow sea grass area, suggesting that iron-transforming microorganisms are controlling Fe mobility, and promoting biomineralization. Taken together, these samples represent the effects of submarine venting on sediment microbial communities both vertically and horizontally in the predicted fluid flow path, and will provide a detailed investigation of genetic potential for biogeochemical cycling at Paleochori Bay.

A single promoter inversion switches Photorhabdus between pathogenic and mutualistic states.

PubMed

Somvanshi, Vishal S; Sloup, Rudolph E; Crawford, Jason M; Martin, Alexander R; Heidt, Anthony J; Kim, Kwi-suk; Clardy, Jon; Ciche, Todd A

2012-07-06

Microbial populations stochastically generate variants with strikingly different properties, such as virulence or avirulence and antibiotic tolerance or sensitivity. Photorhabdus luminescens bacteria have a variable life history in which they alternate between pathogens to a wide variety of insects and mutualists to their specific host nematodes. Here, we show that the P. luminescens pathogenic variant (P form) switches to a smaller-cell variant (M form) to initiate mutualism in host nematode intestines. A stochastic promoter inversion causes the switch between the two distinct forms. M-form cells are much smaller (one-seventh the volume), slower growing, and less bioluminescent than P-form cells; they are also avirulent and produce fewer secondary metabolites. Observations of form switching by individual cells in nematodes revealed that the M form persisted in maternal nematode intestines, were the first cells to colonize infective juvenile (IJ) offspring, and then switched to P form in the IJ intestine, which armed these nematodes for the next cycle of insect infection.

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

DOE PAGES

Staley, Christopher; Ferrieri, Abigail P.; Tfaily, Malak M.; ...

2017-06-24

The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated.Significantly different bacterial community structures ( P = 0.031) were observed inmore » the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles.The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without relevance to time of day may need to be reevaluated with regard to the impact of diurnal cycles on the rhizosphere microbial community.« less

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Staley, Christopher; Ferrieri, Abigail P.; Tfaily, Malak M.

The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated.Significantly different bacterial community structures ( P = 0.031) were observed inmore » the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles.The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without relevance to time of day may need to be reevaluated with regard to the impact of diurnal cycles on the rhizosphere microbial community.« less

Long-Term Evolution Studies of E. Coli under Combined Effects of Simulated Microgravity and Antibiotic.

NASA Astrophysics Data System (ADS)

Karouia, Fathi; Tirumalai, Madhan R.; Ott, Mark C.; Pierson, Duane L.; Fox, George E.; Tran, Quyen

2016-07-01

Multiple spaceflight and simulated microgravity experiments have shown changes in phenotypic microbial characteristics such as microbial growth, morphology, metabolism, genetic transfer, antibiotic and stress susceptibility, and an increase in virulence factors. However, while these studies have contributed to expand our understanding of the short-term effects of spaceflight or simulated microgravity on biological systems, it remains unclear the type of responses subsequent to long-term exposure to space environment and microgravity in particular. As such, organisms exposed to the space environment for extended periods of time may evolve in unanticipated ways thereby negatively impacting long duration space missions. We report here for the first time, an experimental study of microbial evolution in which the effect of long-term exposure to Low Shear Modeled MicroGravity (LSMMG) on microbial gene expression and physiology in Escherichia coli (E. coli) MG1655 was examined using functional genomics, and molecular techniques with and without simultaneous exposure to broad spectrum antibiotic chloramphenicol. E. coli cells were grown under simulated microgravity for 1000 generations in High Aspect Ratio Vessels (HARVs) that were either heat-sterilized (115 deg C, 15 min) or by using/rinsing the HARVs with a saturated solution of the broad-spectrum antibiotic chloramphenicol. In the case of the cells evolved using the antibiotic sterilized HARVs, the expression levels of 357 genes were significantly changed. In particular, fimbriae encoding genes were significantly up-regulated whereas genes encoding the flagellar motor complex were down-regulated. Re-sequencing of the genome revealed that a number of the flagellar genes were actually deleted. The antibiotic resistance levels of the evolved strains were analyzed using VITEK analyzer. The evolved strain was consistently resistant to the antibiotics used (viz., Ampicillin, Cefalotin, Cefurox-ime, Cefuroxime Axetil, Cefoxitin and Tetracycline), even after 11 cycles of 'erasure' of the 'adaptation memory' - this 'erasure' was accomplished by re-growing the evolved cells under shaker flask conditions and 1 cycle equals 10 generations. In the case of the cells evolved using heat sterilized HARVs, no resistance was observed to any of the an-tibiotics used (Ampicillin, Amoxicillin/Clavulanic Acid, Piperacillin/Tazobactam, Cefalotin, Cefazolin, Cefuroxime, Cefuroxime Axetil, Cefoxitin, Cefpodox-ime, Ceftazidime, Ceftriaxone, Cefepime, Gentamicin, Tobramycin, Ciprofloxacin, Levofloxacin, Norfloxacin, Tetracycline, Nitrofurantoin, and Trimethoprim/Sulfamethoxazole), even after 1000 generations of growth under LSMMG. Competition experiments using an isogenic pair revealed that the adaptive advantage of the 1000G strain (in both cases) over an unexposed strain was rapidly eliminated. While this obviously implies that the adaptation was primarily environmental rather than genomic, the levels of antibiotic resistance observed to be consistently maintained, raises the concern of persistent resistance conferred to bacterial communities through exposure to antibiotics on space missions. Supported by grants from the Center for Bionanotechnology and Environmental Research at Texas Southern University (NASA Cooperative Agreement NNX08B4A47A).

Probing Metabolic Activity of Deep Subseafloor Life with NanoSIMS

NASA Astrophysics Data System (ADS)

Morono, Y.; Terada, T.; Itoh, M.; Inagaki, F.

2014-12-01

There are very few natural environments where life is absent in the Earth's surface biosphere. However, uninhabitable region is expected to be exist in the deep subsurface biosphere, of which extent and constraining factor(s) have still remained largly unknown. Scientific ocean drilling have revealed that microbial communities in sediments are generally phylogenetically distinct from known spieces isolated from the Earth's surface biosphere, and hence metabolic functions of the deep subseafloor life remain unknown. In addition, activity of subseafloor microbial cells are thought to be extraordinally slow, as indicated by limited supply of neutrient and energy substrates. To understand the limits of the Earth's subseafloor biosphere and metabolic functions of microbial populations, detection and quantification of the deeply buried microbial cells in geological habitats are fundamentary important. Using newly developed cell separation techniques as well as an discriminative cell detection system, the current quantification limit of sedimentary microbial cells approaches to 102 cells/cm3. These techniques allow not only to assess very small microbial population close to the subsurface biotic fringe, but also to separate and sort the target cells using flow cytometric cell sorter. Once the deep subseafloor microbial cells are detached from mineral grains and sorted, it opens new windows to subsequent molecular ecological and element/isotopic analyses. With a combined use of nano-scale secondary ion masspectrometry (NanoSIMS) and stable isotope-probing techniques, it is possible to detect and measure activity of substrate incorporation into biomass, even for extremely slow metabolic processes such as uncharacteriszed deep subseafloor life. For example, it was evidenced by NanoSIMS that at least over 80% of microbial cells at ~200 meters-deep, 460,000-year-old sedimentary habitat are indeed live, which substrate incooporation was found to be low (10-15 gC/cell/day) even under the lab incubation condition. Also microbial activity in ultraoligotrophic biosphere samples such as the South Pacific Gyre (i.e., IODP Expeditions 329) will be shown. Our results demonstrates metabolic potential of microbes that have been survived for geological timescale in extremely starved condition.

A new method for long-term storage of titred microbial standard solutions suitable for microbiologic quality control activities of pharmaceutical companies.

PubMed

Chiellini, Carolina; Mocali, Stefano; Fani, Renato; Ferro, Iolanda; Bruschi, Serenella; Pinzani, Alessandro

2016-08-01

Commercially available lyophilized microbial standards are expensive and subject to reduction in cell viability due to freeze-drying stress. Here we introduce an inexpensive and straightforward method for in-house microbial standard preparation and cryoconservation that preserves constant cell titre and cell viability over 14 months.

Linking Nitrogen-Cycling Microbial Communities to Environmental Fluctuations and Biogeochemical Activity in a Large, Urban Estuary: the San Francisco Bay-Delta

NASA Astrophysics Data System (ADS)

Francis, C.

2015-12-01

Nitrogen (N) availability is an important factor controlling productivity and thus carbon cycling in estuaries. The fate of N in estuaries depends on the activities of the microbes that carry out the N-cycle, which in turn depend on factors such as organic matter availability, dissolved inorganic N, salinity, oxygen, and temperature. Key microbial N transformations include nitrification (the aerobic oxidation of ammonia to nitrite and nitrate) and denitrification (the anaerobic reduction of nitrate to dinitrogen gas). While denitrification leads to N loss, nitrification is the only link between reduced N (produced by decomposition) and oxidized N (substrates for N loss processes), and both processes are known to produce nitrous oxide (N2O), a potent greenhouse gas. Understanding controls of N-cycling in the San Francisco Bay-Delta (SFBD)—the largest estuary on the west coast of North America—is particularly important, as this urban estuary is massively polluted with N, even compared to classic "eutrophic" systems. Interestingly, the SFBD has been spared the detrimental consequences of nutrient enrichment, largely due to high suspended sediment concentrations (and thus low light penetration) throughout the water column, combined with high grazing pressure. However, the recent "clearing" of SFBD waters due to a sharp decrease in suspended sediments may significantly alter the ecology of the estuary, by increasing phytoplankton growth. Thus, the SFBD may be losing its historical resilience to eutrophication, and may soon be "high-nutrient, low-chlorophyll" no more. Elucidating the environmental factors affecting the community structure, activity, and functioning of N-cycling microbes in SFBD is crucial for determining how changes in turbidity and productivity will be propagated throughout the ecosystem. While substantial ecological research in the SFBD has focused on phytoplankton and food webs, bacterial and archaeal communities have received far less attention. Using a combination of molecular, biogeochemical, and 'omics' approaches, we have been examining how N-cycling microbial communities throughout the SFBD change in relation to environmental fluctuations—a critical step in understanding how microbial populations drive biogeochemical cycling in this estuary.

Extracellular enzymes facilitate electron uptake in biocorrosion and bioelectrosynthesis.

PubMed

Deutzmann, Jörg S; Sahin, Merve; Spormann, Alfred M

2015-04-21

Direct, mediator-free transfer of electrons between a microbial cell and a solid phase in its surrounding environment has been suggested to be a widespread and ecologically significant process. The high rates of microbial electron uptake observed during microbially influenced corrosion of iron [Fe(0)] and during microbial electrosynthesis have been considered support for a direct electron uptake in these microbial processes. However, the underlying molecular mechanisms of direct electron uptake are unknown. We investigated the electron uptake characteristics of the Fe(0)-corroding and electromethanogenic archaeon Methanococcus maripaludis and discovered that free, surface-associated redox enzymes, such as hydrogenases and presumably formate dehydrogenases, are sufficient to mediate an apparent direct electron uptake. In genetic and biochemical experiments, we showed that these enzymes, which are released from cells during routine culturing, catalyze the formation of H2 or formate when sorbed to an appropriate redox-active surface. These low-molecular-weight products are rapidly consumed by M. maripaludis cells when present, thereby preventing their accumulation to any appreciable or even detectable level. Rates of H2 and formate formation by cell-free spent culture medium were sufficient to explain the observed rates of methane formation from Fe(0) and cathode-derived electrons by wild-type M. maripaludis as well as by a mutant strain carrying deletions in all catabolic hydrogenases. Our data collectively show that cell-derived free enzymes can mimic direct extracellular electron transfer during Fe(0) corrosion and microbial electrosynthesis and may represent an ecologically important but so far overlooked mechanism in biological electron transfer. The intriguing trait of some microbial organisms to engage in direct electron transfer is thought to be widespread in nature. Consequently, direct uptake of electrons into microbial cells from solid surfaces is assumed to have a significant impact not only on fundamental microbial and biogeochemical processes but also on applied bioelectrochemical systems, such as microbial electrosynthesis and biocorrosion. This study provides a simple mechanistic explanation for frequently observed fast electron uptake kinetics in microbiological systems without a direct transfer: free, cell-derived enzymes can interact with cathodic surfaces and catalyze the formation of intermediates that are rapidly consumed by microbial cells. This electron transfer mechanism likely plays a significant role in various microbial electron transfer reactions in the environment. Copyright © 2015 Deutzmann et al.

Soil Exometabolomics: An Approach to Investigate Adsorption of Metabolites on Soils and Minerals

NASA Astrophysics Data System (ADS)

Swenson, T.; Nico, P. S.; Northen, T.

2014-12-01

A large fraction of soil organic matter (SOM) is composed of small molecules of microbial origin resulting from lysed cells and released metabolites. However, the cycling of these nutrients by microorganisms, a critical component of the global carbon cycle, remains poorly understood. Although there are many biotic and abiotic factors affecting the accessibility of SOM to microbes, adsorption to mineral surfaces is among the most important. Here, we are developing exometabolomics methods to further understand the types of microbial metabolites remaining in the water extractable fraction of SOM (WEOM). To estimate which compounds adsorb to a sandy loam soil (obtained from the Angelo Coast Range Reserve in Mendocino, CA), an extract was prepared from the soil bacterium Pseudomonas stutzerii RCH2 grown on 13C acetate. This approach produced highly labeled metabolites that were easily discriminated from the endogenous soil metabolites by gas chromatography/ mass spectrometry. Comparison of the composition of the fresh bacteria extract with what was recovered following a 15 min incubation with soil revealed that only 26% of the metabolites showed >50% recovery in the WEOM. Most cations (polyamines) and anions showed <10% recovery. These represent metabolites that may be inaccessible to microbes in this environment and would be most likely to accumulate as SOM presumably due to binding with minerals and negatively-charged clay particles. Ongoing studies are focused on comparing the adsorption capacity of bacteria extract with several minerals (ferrihydrite, goethite, meghemite, lepidocrocite). Varying conditions such as metabolite-mineral contact time (ranging from hours to days) and temperature (4-37°C) will provide insight into how microbial metabolites behave in a given mineral-rich environment under certain climatic conditions.

Synthetic biology for manufacturing chemicals: constraints drive the use of non-conventional microbial platforms.

PubMed

Czajka, Jeffrey; Wang, Qinhong; Wang, Yechun; Tang, Yinjie J

2017-10-01

Genetically modified microbes have had much industrial success producing protein-based products (such as antibodies and enzymes). However, engineering microbial workhorses for biomanufacturing of commodity compounds remains challenging. First, microbes cannot afford burdens with both overexpression of multiple enzymes and metabolite drainage for product synthesis. Second, synthetic circuits and introduced heterologous pathways are not yet as "robust and reliable" as native pathways due to hosts' innate regulations, especially under suboptimal fermentation conditions. Third, engineered enzymes may lack channeling capabilities for cascade-like transport of metabolites to overcome diffusion barriers or to avoid intermediate toxicity in the cytoplasmic environment. Fourth, moving engineered hosts from laboratory to industry is unreliable because genetic mutations and non-genetic cell-to-cell variations impair the large-scale fermentation outcomes. Therefore, synthetic biology strains often have unsatisfactory industrial performance (titer/yield/productivity). To overcome these problems, many different species are being explored for their metabolic strengths that can be leveraged to synthesize specific compounds. Here, we provide examples of non-conventional and genetically amenable species for industrial manufacturing, including the following: Corynebacterium glutamicum for its TCA cycle-derived biosynthesis, Yarrowia lipolytica for its biosynthesis of fatty acids and carotenoids, cyanobacteria for photosynthetic production from its sugar phosphate pathways, and Rhodococcus for its ability to biotransform recalcitrant feedstock. Finally, we discuss emerging technologies (e.g., genome-to-phenome mapping, single cell methods, and knowledge engineering) that may facilitate the development of novel cell factories.

Soil microbial community structure: mechanical disturbance alters soil microbial community

USDA-ARS?s Scientific Manuscript database

Soil microbes are responsible for soil nutrient cycling in both perennial and annual management systems for beef cattle and grain production. In the Southern Plains of Oklahoma, producers plant winter wheat (Triticum aestivum) in rotation with winter canola (Brassica rapa). Producers in the Southern...

Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep

PubMed Central

Lloyd, Karen G.; Albert, Daniel B.; Biddle, Jennifer F.; Chanton, Jeffrey P.; Pizarro, Oscar; Teske, Andreas

2010-01-01

Background Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. Methodology/Principal Findings We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the mat (∼400 cm and ∼10 cm from the mat's edge) contrasted with sharply diminished activity at ∼50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase) and mcrA (methyl coenzyme M reductase) mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae) and methane-cycling archaea (ANME-1 and ANME-2) were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12–20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. Conclusions/Significance The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. In contrast, 12–20 cm deep in the sediments microbial communities performing methane-cycling and sulfate reduction persist at lower metabolic rates regardless of mat cover, and may increase activity rapidly when subsurface flow changes. PMID:20090951

Electricity production from municipal solid waste using microbial fuel cells.

PubMed

Chiu, H Y; Pai, T Y; Liu, M H; Chang, C A; Lo, F C; Chang, T C; Lo, H M; Chiang, C F; Chao, K P; Lo, W Y; Lo, S W; Chu, Y L

2016-07-01

The organic content of municipal solid waste has long been an attractive source of renewable energy, mainly as a solid fuel in waste-to-energy plants. This study focuses on the potential to use microbial fuel cells to convert municipal solid waste organics into energy using various operational conditions. The results showed that two-chamber microbial fuel cells with carbon felt and carbon felt allocation had a higher maximal power density (20.12 and 30.47 mW m(-2) for 1.5 and 4 L, respectively) than those of other electrode plate allocations. Most two-chamber microbial fuel cells (1.5 and 4 L) had a higher maximal power density than single-chamber ones with corresponding electrode plate allocations. Municipal solid waste with alkali hydrolysis pre-treatment and K3Fe(CN)6 as an electron acceptor improved the maximal power density to 1817.88 mW m(-2) (~0.49% coulomb efficiency, from 0.05-0.49%). The maximal power density from experiments using individual 1.5 and 4 L two-chamber microbial fuel cells, and serial and parallel connections of 1.5 and 4 L two-chamber microbial fuel cells, was found to be in the order of individual 4 L (30.47 mW m(-2)) > serial connection of 1.5 and 4 L (27.75) > individual 1.5 L (20.12) > parallel connection of 1.5 and 4 L (17.04) two-chamber microbial fuel cells . The power density using municipal solid waste microbial fuel cells was compared with information in the literature and discussed. © The Author(s) 2016.

Electricity Generation in Microbial Fuel Cells Using Neutral Red as an Electronophore

PubMed Central

Park, Doo Hyun; Zeikus, J. Gregory

2000-01-01

Neutral red (NR) was utilized as an electron mediator in microbial fuel cells consuming glucose to study both its efficiency during electricity generation and its role in altering anaerobic growth and metabolism of Escherichia coli and Actinobacillus succinogenes. A study of chemical fuel cells in which NADH, NR, and ferricyanide were the electron donor, the electronophore, and the electron acceptor, respectively, showed that electrical current produced from NADH was proportional to the concentration of NADH. Fourfold more current was produced from NADH in chemical fuel cells when NR was the electron mediator than when thionin was the electron mediator. In microbial fuel cells in which E. coli resting cells were used the amount of current produced from glucose when NR was the electron mediator (3.5 mA) was 10-fold more than the amount produced when thionin was the electron mediator (0.4 mA). The amount of electrical energy generated (expressed in joules per mole of substrate) and the amount of current produced from glucose (expressed in milliamperes) in NR-mediated microbial fuel cells containing either E. coli or A. succinogenes were about 10- and 2-fold greater, respectively, when resting cells were used than when growing cells were used. Cell growth was inhibited substantially when these microbial fuel cells were making current, and more oxidized end products were formed under these conditions. When sewage sludge (i.e., a mixed culture of anaerobic bacteria) was used in the fuel cell, stable (for 120 h) and equivalent levels of current were obtained with glucose, as observed in the pure-culture experiments. These results suggest that NR is better than other electron mediators used in microbial fuel cells and that sludge production can be decreased while electricity is produced in fuel cells. Our results are discussed in relation to factors that may improve the relatively low electrical efficiencies (1.2 kJ/mol) obtained with microbial fuel cells. PMID:10742202

Microbes mediate carbon and nitrogen retention in shallow photic sediments

NASA Astrophysics Data System (ADS)

Hardison, A.; Anderson, I.; Canuel, E. A.; Tobias, C.; Veuger, B.

2009-12-01

Sediments in shallow coastal bays are sites of intense biogeochemical cycling facilitated by a complex microbial consortium. Unlike deeper coastal environments, much of the benthos is illuminated by sunlight in these bays. As a result, benthic autotrophs such as benthic microalgae (BMA) and macroalgae play an integral role in nutrient cycling. Investigating pathways of carbon (C) and nitrogen (N) flow through individual compartments within the sediment microbial community has previously proved challenging due to methodological difficulties. However, it is now possible using stable isotopes and microbial biomarkers such as fatty acids and amino acids to track C and N flow through individual microbial pools. We investigated the uptake and retention of C and N by bacteria and BMA in a shallow subtidal system. Using bulk and compound specific isotopic analysis, we traced the pathways of dissolved inorganic 13C and 15N under various treatments: 1) in ambient light or dark, 2) from porewater or water column sources, and 3) in the presence or absence of bloom forming nuisance macroalgae. Excess 13C and 15N in THAAs and excess 13C in total PLFAs showed a strong dependence on light. Enrichment of these pools represents uptake by the microbial community, which can include both autotrophic and heterotrophic components. Higher excess 13C in benthic microalgal fatty acids (C20, C22 PUFAs) provides evidence that benthic microalgae were fixing 13C. Aditionally, the ratio of excess 13C in branched fatty acids to microbial fatty acids (BAR) and excess 13C and 15N in D-Ala to L-Ala (D/L-Ala) were low, suggesting dominance by benthic microalgae over bacteria to total label incorporation. Our results support uptake and retention of C and N by the sediment microbial community and indicate a tight coupling between BMA and bacteria in shallow illuminated systems. This uptake is diminished in the presence of macroalgae, likely due to shading and/or nutrient competition. Therefore, macroalgae reduce the retention of C and N within surface sediments, diminishing the role of the microbial community in nutrient cycling processes.

Root phenotypic differences across a historical gradient of wheat genotypes alter soil rhizosphere communities and their impact on nitrogen cycling

NASA Astrophysics Data System (ADS)

Kallenbach, C.; Junaidi, D.; Fonte, S.; Byrne, P. F.; Wallenstein, M. D.

2017-12-01

Plants and soil microorganisms can exhibit coevolutionary relationships where, for example, in exchange for root carbon, rhizosphere microbes enhance plant fitness through improved plant nutrient availability. Organic agriculture relies heavily on these interactions to enhance crop nitrogen (N) availability. However, modern agriculture and breeding under high mineral N fertilization may have disrupted these interactions through alterations to belowground carbon inputs and associated impacts on the soil microbiome. As sustainability initiatives lead to a restoration of agricultural soil organic matter, modern crop cultivars may still be constrained by crop roots' ability to effectively support microbial-mediated N mineralization. We investigated how differences in root traits across a historical gradient of spring wheat genotypes influence the rhizosphere microbial community and effects on soil N and wheat yield. Five genotypes, representing wild (Wild), pre-Green Revolution (Old), and modern (Modern) wheat, were grown under greenhouse conditions in soils with and without compost to also compare genotype response to difference in native soil microbiomes and organic resource availability. We analyzed rhizosphere soils for microbial community composition, enzyme activities, inorganic N, and microbial biomass. Root length density, surface area, fine root volume and root:shoot ratio were higher in the Wild and Old genotype (Gypsum) compared to the two Modern genotypes (P<0.01). The Wild and Old genotype had a more positive response to compost for root length and diameter, N-cycling enzyme activities, microbial biomass, and soil inorganic N, compared to Modern genotypes. However, under unamended soils, the microbial community and soil N were not affected by genotypes. We also relate how root traits and N cycling across genotypes correspond to microbial community composition. Our preliminary data suggest that the older wheat genotypes and their root traits are more effective at enhancing microbial N mineralization under organically managed soils. Thus, to optimize crop N availability from organic sources, breeding efforts should consider incorporating root traits of older genotypes to better support the beneficial interactions between crop roots and their rhizosphere microbiome.

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

PubMed Central

Pjevac, Petra; Meier, Dimitri V.; Markert, Stephanie; Hentschker, Christian; Schweder, Thomas; Becher, Dörte; Gruber-Vodicka, Harald R.; Richter, Michael; Bach, Wolfgang; Amann, Rudolf; Meyerdierks, Anke

2018-01-01

At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin–Benson–Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys. PMID:29696004

Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils

NASA Astrophysics Data System (ADS)

Wang, Haitao; Marshall, Christopher W.; Cheng, Minying; Xu, Huijuan; Li, Hu; Yang, Xiaoru; Zheng, Tianling

2017-03-01

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments

NASA Astrophysics Data System (ADS)

Nixon, Sophie L.; Telling, Jon P.; Wadham, Jemma L.; Cockell, Charles S.

2017-03-01

Subglacial environments are known to harbour metabolically diverse microbial communities. These microbial communities drive chemical weathering of underlying bedrock and influence the geochemistry of glacial meltwater. Despite its importance in weathering reactions, the microbial cycling of iron in subglacial environments, in particular the role of microbial iron reduction, is poorly understood. In this study we address the prevalence of viable iron-reducing microorganisms in subglacial sediments from five geographically isolated glaciers. Iron-reducing enrichment cultures were established with sediment from beneath Engabreen (Norway), Finsterwalderbreen (Svalbard), Leverett and Russell glaciers (Greenland), and Lower Wright Glacier (Antarctica). Rates of iron reduction were higher at 4 °C compared with 15 °C in all but one duplicated second-generation enrichment culture, indicative of cold-tolerant and perhaps cold-adapted iron reducers. Analysis of bacterial 16S rRNA genes indicates Desulfosporosinus were the dominant iron-reducing microorganisms in low-temperature Engabreen, Finsterwalderbreen and Lower Wright Glacier enrichments, and Geobacter dominated in Russell and Leverett enrichments. Results from this study suggest microbial iron reduction is widespread in subglacial environments and may have important implications for global biogeochemical iron cycling and export to marine ecosystems.

Microbial activity in the marine deep biosphere: progress and prospects.

PubMed

Orcutt, Beth N; Larowe, Douglas E; Biddle, Jennifer F; Colwell, Frederick S; Glazer, Brian T; Reese, Brandi Kiel; Kirkpatrick, John B; Lapham, Laura L; Mills, Heath J; Sylvan, Jason B; Wankel, Scott D; Wheat, C Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).

Microbial formation of labile organic carbon in Antarctic glacial environments

USGS Publications Warehouse

Smith, H.J.; Foster, R.; McKnight, D.M.; Lisle, John T.; Littmann, S.; Kuypers, M.M.M.; Foreman, C.M.

2017-01-01

Roughly six petagrams of organic carbon are stored within ice worldwide. This organic carbon is thought to be of old age and highly bioavailable. Along with storage of ancient and new atmospherically deposited organic carbon, microorganisms may contribute substantially to the glacial organic carbon pool. Models of glacial microbial carbon cycling vary from net respiration to net carbon fixation. Supraglacial streams have not been considered in models although they are amongst the largest ecosystems on most glaciers and are inhabited by diverse microbial communities. Here we investigate the biogeochemical sequence of organic carbon production and uptake in an Antarctic supraglacial stream in the McMurdo Dry Valleys using nanometre-scale secondary ion mass spectrometry, fluorescence spectroscopy, stable isotope analysis and incubation experiments. We find that heterotrophic production relies on highly labile organic carbon freshly derived from photosynthetic bacteria rather than legacy organic carbon. Exudates from primary production were utilized by heterotrophs within 24 h, and supported bacterial growth demands. The tight coupling of microbially released organic carbon and rapid uptake by heterotrophs suggests a dynamic local carbon cycle. Moreover, as temperatures increase there is the potential for positive feedback between glacial melt and microbial transformations of organic carbon.

Microbial activity in the marine deep biosphere: progress and prospects

PubMed Central

Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org). PMID:23874326

Single chamber microbial fuel cell with Ni-Co cathode

NASA Astrophysics Data System (ADS)

Włodarczyk, Barbara; Włodarczyk, Paweł P.; Kalinichenko, Antonina

2017-10-01

The possibility of wastewater treatment and the parallel energy production using the Ni-Co alloy as cathode catalyst for single chamber microbial fuel cells is presented in this research. The research included a preparation of catalyst and comparison of COD, NH4+ and NO3- reduction in the reactor without aeration, with aeration and with using a single chamber microbial fuel cell with Ni-Co cathode. The reduction time for COD with the use of microbial fuel cell with the Ni-Co catalyst is similar to the reduction time with aeration. The current density (2.4 A·m-2) and amount of energy (0.48 Wh) obtained in MFC is low, but the obtained amount of energy allows elimination of the energy needed for reactor aeration. It has been shown that the Ni-Co can be used as cathode catalyst in single chamber microbial fuel cells.

Compact Cell Settlers for Perfusion Cultures of Microbial (and Mammalian) Cells.

PubMed

Freeman, Cassandra A; Samuel, Premsingh S D; Kompala, Dhinakar S

2017-07-01

As microbial secretory expression systems have become well developed for microbial yeast cells, such as Saccharomyces cerevisiae and Pichia pastoris, it is advantageous to develop high cell density continuous perfusion cultures of microbial yeast cells to retain the live and productive yeast cells inside the perfusion bioreactor while removing the dead cells and cell debris along with the secreted product protein in the harvest stream. While the previously demonstrated inclined or lamellar settlers can be used for such perfusion bioreactors for microbial cells, the size and footprint requirements of such inefficiently scaled up devices can be quite large in comparison to the bioreactor size. Faced with this constraint, we have now developed novel, patent-pending compact cell settlers that can be used more efficiently with microbial perfusion bioreactors to achieve high cell densities and bioreactor productivities. Reproducible results from numerous month-long perfusion culture experiments using these devices attached to the 5 L perfusion bioreactor demonstrate very high cell densities due to substantial sedimentation of the larger live yeast cells which are returned to the bioreactor, while the harvest stream from the top of these cell settlers is a significantly clarified liquid, containing less than 30% and more typically less than 10% of the bioreactor cell concentration. Size of cells in the harvest is smaller than that of the cells in the bioreactor. Accumulated protein collected from the harvest and rate of protein accumulation is significantly (> 6x) higher than the protein produced in repeated fed-batch cultures over the same culture duration. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:913-922, 2017. © 2017 American Institute of Chemical Engineers.

Simultaneous Recovery of Extracellular and Intracellular DNA Suitable for Molecular Studies from Marine Sediments

PubMed Central

Corinaldesi, Cinzia; Danovaro, Roberto; Dell'Anno, Antonio

2005-01-01

The occurrence of high extracellular DNA concentrations in aquatic sediments (concentrations that are 3 to 4 orders of magnitude greater than those in the water column) might play an important role in biogeochemical cycling, as well as in horizontal gene transfer through natural transformation. Since isolation of extracellular DNA from sediments is a difficult and unsolved task, in this study we developed an efficient procedure to recover simultaneously DNA associated with microbial cells and extracellular DNA from the same sediment sample. This procedure is specifically suitable for studying extracellular DNA because it avoids any contamination with DNA released by cell lysis during handling and extraction. Applying this procedure to different sediment types, we obtained extracellular DNA concentrations that were about 10 to 70 times higher than the intracellular DNA concentrations. Using specific targeted prokaryotic primers, we obtained evidence that extracellular DNA recovered from different sediments did not contain amplifiable 16S rRNA genes. By contrast, using DNA extracted from microbial cells as the template, we always amplified 16S rRNA genes. Although 16S rRNA genes were not detected in extracellular DNA, analyses of the sizes of extracellular DNA indicated the presence of high-molecular-weight fragments that might have contained other gene sequences. This protocol allows investigation of extracellular DNA and its possible participation in natural transformation processes. PMID:15640168

The microbial diversity, distribution, and ecology of permafrost in China: a review.

PubMed

Hu, Weigang; Zhang, Qi; Tian, Tian; Cheng, Guodong; An, Lizhe; Feng, Huyuan

2015-07-01

Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.

Spatio-seasonal variability in dissolved organic matter optical properties and its bioavailability in a subalpine lake

NASA Astrophysics Data System (ADS)

Stadler, Masumi; Ejarque, Elisabet; Kainz, Martin J.

2017-04-01

Allochthonous and autochothonous dissolved organic matter (DOM) in lakes mainly originate from terrestrial and aquatic primary production, respectively. Due to their differing biochemical composition the degradability of DOM by microorganisms is expected to vary. The carbon use efficiency of bacteria and DOM biodegradability determine whether the consumed DOM is incorporated into microbial biomass or respired to CO2 and ultimately emitted into the atmosphere. Thus, understanding the interaction of biodegradable DOM and its consumers is crucial to increase our knowledge on the role of lakes in the global carbon cycling. However, interactions of specific aquatic DOM signatures and the microbial population still remain widely debated. The aim of this study was to explore how DOM biodegradability changes along a stream-lake continuum at different seasons of the year. We monitored DOM quantity and its optical properties, inorganic nutrients, CO2 and bacterial growth over 20 days in dark bioassays with water from the inflow, outflow and at three layers of an oligotrophic subalpine lake. Preliminary results reveal highest microbial abundance in the metalimnion in winter and summer (0.7 106 and 2.5 106 cells mL-1, respectively) and the inflow in spring and autumn (1 106 and 1.4 106 cells mL-1, respectively) after 20 days. Surprisingly, with the exception of winter samples final inflow bacterial abundance results high, despite its lowest initial natural cell concentration, providing evidence for effective utilisation of terrestrial DOM, even with its high humic signature as indicated by the humification index (HIX). Nonetheless, after a microbial biomass peak with the inflow yielding mostly highest after three days, at the final experimental stage microbial biomass does only marginally differ between all sites with the exception of autumn samples where outflow and metalimnion turn out most productive. Even though the DOM of all lake sites and the lake outflow were characterised by lower molecular weight (indicated by the slope ratio (SR)) and a higher autochthonous signature (BIX) in all seasons, rapid growth of inflow bacteria highlight the potential of terrestrially-derived DOM to support bacterial growth, and challenge previous ideas that autchthonously-produced DOM would be more labile than DOM of terrestrial origin.

Determination of Microbial Growth by Protein Assay in an Air-Cathode Single Chamber Microbial Fuel Cell.

PubMed

Li, Na; Kakarla, Ramesh; Moon, Jung Mi; Min, Booki

2015-07-01

Microbial fuel cells (MFCs) have gathered attention as a novel bioenergy technology to simultaneously treat wastewater with less sludge production than the conventional activated sludge system. In two different operations of the MFC and aerobic process, microbial growth was determined by the protein assay method and their biomass yields using real wastewater were compared. The biomass yield on the anode electrode of the MFC was 0.02 g-COD-cell/g- COD-substrate and the anolyte planktonic biomass was 0.14 g-COD-cell/g-COD-substrate. An MFC without anode electrode resulted in the biomass yield of 0.07 ± 0.03 g-COD-cell/g-COD-substrate, suggesting that oxygen diffusion from the cathode possibly supported the microbial growth. In a comparative test, the biomass yield under aerobic environment was 0.46 ± 0.07 g-COD-cell/g-COD-substrate, which was about 3 times higher than the total biomass value in the MFC operation.

The Importance of TLR2 and Macrophages in Modulating a Humoral Response after Encountering Streptococcus pneumoniae

DTIC Science & Technology

2008-03-26

Response after Encountering Streptococcus Pneumoniae" Brian Schae:5 ,Ph.D. Department of Microbi ogy & Immunology Committee Chairperson Masters...presenting cells (APCs), such as macrophages (M ) and dendritic cells (DC) recognize microbial surface components via cell surface receptors (i.e...stimulating factor (GM-CSF). TH1 cells are able to secrete IFN- , which is important in activating M to produce mediators important for microbial

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer.

PubMed

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb 3 - and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.

Plant-soil-microbe interactions regulating soil C storage

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.

2016-12-01

Integration across disciplines is required to identify the emergent microbial scale properties that regulate the release or occlusion of plant inputs in soil organic matter. To investigate how micro-scale processes influence soil carbon cycling, we measured microbial community composition and activity within soil aggregates monthly over two growing seasons of a long-term bioenergy field experiment. Using a biologically sensitive sieving technique, soil aggregates were isolated and microbial community activity and composition were measured. This aggregate approach revealed biogeochemical processes regulating C cycling that are not detected using whole soil approaches. Soil aggregation influenced microbe-substrate interactions, where diversified perennial grassland systems supported greater aggregation and reduced severity of aggregate turnover compared to corn systems. Aggregate turnover and concurrent increases in activity resulted in greater microbial biomass and physical protection of soil organic matter in prairie systems, especially fertilized prairies. Fertilized prairie enhanced microbial biomass, enzyme activity, and soil aggregation despite greater root biomass in unfertilized prairie. Independent of ecosystem or sampling date, N-acetyl-glucosaminidase activity and Nitrospirae abundance was greatest in large macroaggregates (>2000 µm), which harbored the highest C:N; cellobiohydrolase activity and Acidobacteria abundance was greatest in microaggregates (<250 µm) which had the lowest C:N. Aggregate fractions differed in microbial community composition (bacteria, archaea, and fungi) and potential enzyme activity, independent of cropping system. Microaggregates harbored significantly greater microbial diversity and richness across all bioenergy cropping systems. Together these results suggest that by mediating access to substrates, soil structure (aggregates) can influence the microbial community composition and extracellular enzyme activity to regulate ecosystem scale decomposition of soil organic matter.

Outward electron transfer by Saccharomyces cerevisiae monitored with a bi-cathodic microbial fuel cell-type activity sensor.

PubMed

Ducommun, Raphaël; Favre, Marie-France; Carrard, Delphine; Fischer, Fabian

2010-03-01

A Janus head-like bi-cathodic microbial fuel cell was constructed to monitor the electron transfer from Saccharomyces cerevisiae to a woven carbon anode. The experiments were conducted during an ethanol cultivation of 170 g/l glucose in the presence and absence of yeast-peptone medium. First, using a basic fuel-cell type activity sensor, it was shown that yeast-peptone medium contains electroactive compounds. For this purpose, 1% solutions of soy peptone and yeast extract were subjected to oxidative conditions, using a microbial fuel cell set-up corresponding to a typical galvanic cell, consisting of culture medium in the anodic half-cell and 0.5 M K(3)Fe(CN)(6) in the cathodic half-cell. Second, using a bi-cathodic microbial fuel cell, it was shown that electrons were transferred from yeast cells to the carbon anode. The participation of electroactive compounds in the electron transport was separated as background current. This result was verified by applying medium-free conditions, where only glucose was fed, confirming that electrons are transferred from yeast cells to the woven carbon anode. Knowledge about the electron transfer through the cell membrane is of importance in amperometric online monitoring of yeast fermentations and for electricity production with microbial fuel cells. Copyright (c) 2009 John Wiley & Sons, Ltd.

Bacterioplankton carbon cycling along the Subtropical Frontal Zone off New Zealand

NASA Astrophysics Data System (ADS)

Baltar, Federico; Stuck, Esther; Morales, Sergio; Currie, Kim

2015-06-01

Marine heterotrophic bacterioplankton (Bacteria and Archaea) play a central role in ocean carbon cycling. As such, identifying the factors controlling these microbial populations is crucial to fully understanding carbon fluxes. We studied bacterioplankton activities along a transect crossing three water masses (i.e., Subtropical waters [STW], Sub-Antarctic waters [SAW] and neritic waters [NW]) with contrasting nutrient regimes across the Subtropical Frontal Zone. In contrast to bacterioplankton production and community respiration, bacterioplankton respiration increased in the offshore SAW, causing a seaward increase in the contribution of bacteria to community respiration (from 7% to 100%). Cell-specific bacterioplankton respiration also increased in SAW, but cell-specific production did not, suggesting that prokaryotic cells in SAW were investing more energy towards respiration than growth. This was reflected in a 5-fold decline in bacterioplankton growth efficiency (BGE) towards SAW. One way to explain this decrease in BGE could be due to the observed reduction in phytoplankton biomass (and presumably organic matter concentration) towards SAW. However, this would not explain why bacterioplankton respiration was highest in SAW, where phytoplankton biomass was lowest. Another factor affecting BGE could be the iron limitation characteristic of high-nutrient low-chlorophyll (HNLC) regions like SAW. Our field-study based evidences would agree with previous laboratory experiments in which iron stress provoked a decrease in BGE of marine bacterial isolates. Our results suggest that there is a strong gradient in bacterioplankton carbon cycling rates along the Subtropical Frontal Zone, mainly due to the HNLC conditions of SAW. We suggest that Fe-induced reduction of BGE in HNLC regions like SAW could be relevant in marine carbon cycling, inducing bacterioplankton to act as a link or a sink of organic carbon by impacting on the quantity of organic carbon they incorporate into biomass or respire as CO2.

SPRUCE Small Differences in Ombrotrophy Control Regional-Scale Variation in Methane Cycling among Sphagnum-Dominated Peatlands: Supporting Data

DOE Data Explorer

Zalman, C.; Keller, J.K.; Tfaily, M.; Kolton, M.; Pfeifer-Meister, L.; Wilson, R.M.; Lin, X.; Chanton, J.; Kostka, J.E.; Gill, A.; Finzi, A.; Hopple, A. M.; Bohanna, B.J.M.; Bridgham, S.D.

2018-01-01

These data are provided in support of the SPRUCE publication: Small Differences in Ombrotrophy Control Regional-Scale Variation in Methane Cycling among Sphagnum-Dominated Peatlands (Zalman et al., 2018) Reports the examination of the mechanisms controlling C cycling rates and greenhouse gas emissions using a combination of biogeochemical and microbial approaches in three low pH, Sphagnum-dominated peatlands in northern Minnesota. In particular, we investigated biogeochemical parameters (CH4 and CO2 production potentials, porewater and gas CH4 and CO2 concentrations and associated isotopic signatures), soil chemistry (organic acids and phenolics), and microbial community characteristics (quantification of methanogen and methanotroph abundance and activity) over a 1-year period in these three peatlands. The objective of this intensive study was to analyze biogeochemical and microbial characteristics of three outwardly similar low pH, Sphagnum-dominated peatlands to determine key characteristics that could explain differences in anaerobic C cycling and net CH4 flux despite their close geographical proximity and similar soil pH and plant communities. The supporting data provided include the measurement data for samples from the Minnesota locations, site characteristics, and the summarized and aggregated data used to generate the figures in the main text of the paper and the supplementary data figures for the Minnesota locations.

Metagenetic analysis of the bacterial communities of edible insects from diverse production cycles at industrial rearing companies.

PubMed

Vandeweyer, D; Crauwels, S; Lievens, B; Van Campenhout, L

2017-11-16

Despite the continuing development of new insect-derived food products, microbial research on edible insects and insect-based foods is still very limited. The goal of this study was to increase the knowledge on the microbial quality of edible insects by comparing the bacterial community composition of mealworms (Tenebrio molitor) and crickets (Acheta domesticus and Gryllodes sigillatus) from several production cycles and rearing companies. Remarkable differences in the bacterial community composition were found between different mealworm rearing companies and mealworm production cycles from the same company. In comparison with mealworms, the bacterial community composition of the investigated crickets was more similar among different companies, and was highly similar between both cricket species investigated. Mealworm communities were dominated by Spiroplasma and Erwinia species, while crickets were abundantly colonised by (Para)bacteroides species. With respect to food safety, only a few operational taxonomic units could be associated with potential human pathogens such as Cronobacter or spoilage bacteria such as Pseudomonas. In summary, our results implicate that at least for cricket rearing, production cycles of constant and good quality in terms of bacterial composition can be obtained by different rearing companies. For mealworms however, more variation in terms of microbial quality occurs between companies. Copyright © 2017 Elsevier B.V. All rights reserved.

Life cycle of soil sggregates: from root residue to microbial and physical hotspots

NASA Astrophysics Data System (ADS)

Ghezzehei, T. A.; Or, D.

2017-12-01

Soil aggregation is a physical state of soil in which clumps of primary soil particles are held together by biological and/or chemical cementing agents. Aggregations plays important role in storage and movement of water and essential gases, nutrient cycling, and ultimately supporting microbial and plant life. It is also one of the most dynamic and sensitive soil qualities, which readily responds to disturbances such as cultivation, fire, drought, flooding, and changes in vegetation. Soil aggregation that is primarily controlled by organic matter generally exhibits hierarchical organization of soil constituents into stable units that range in size from a few microns to centimeters. However, this conceptual model of soil aggregation as the key unifying mechanism remains poorly quantified and is rarely included in predictive soil models. Here we provide a biophysical framework for quantitative and predictive modeling of soil aggregation and its attendant soil characteristics. The framework treats aggregates as hotspots of biological, chemical and physical processes centered around roots and root residue. We keep track of the life cycle of an individual aggregate from it genesis in the rhizosphere, fueled by rhizodeposition and mediated by vigorous microbial activity, until its disappearance when the root-derived resources are depleted. The framework synthesizes current understanding of microbial life in porous media; water holding and soil binding capacity of biopolymers; and environmental controls on soil organic matter dynamics. The framework paves a way for integration of processes that are presently modeled as disparate or poorly coupled processes, including storage and protection of carbon, microbial activity, greenhouse gas fluxes, movement and storage of water, resistance of soils against erosion.

Microbial communities and greenhouse gas emissions associated with the biodegradation of specified risk material in compost

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Shanwei; Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1; Reuter, Tim

Highlights: ► Addition of feathers altered bacterial and fungal communities in compost. ► Microbial communities degrading SRM and compost matrix were distinct. ► Addition of feathers may enrich for microbial communities that degrade SRM. ► Inclusion of feather in compost increased both CH{sub 4} and N{sub 2}O emissions from compost. ► Density of methanogens and methanotrophs were weakly associated with CH{sub 4} emissions. - Abstract: Provided that infectious prions (PrP{sup Sc}) are inactivated, composting of specified risk material (SRM) may be a viable alternative to rendering and landfilling. In this study, bacterial and fungal communities as well as greenhouse gasmore » emissions associated with the degradation of SRM were examined in laboratory composters over two 14 day composting cycles. Chicken feathers were mixed into compost to enrich for microbial communities involved in the degradation of keratin and other recalcitrant proteins such as prions. Feathers altered the composition of bacterial and fungal communities primarily during the first cycle. The bacterial genera Saccharomonospora, Thermobifida, Thermoactinomycetaceae, Thiohalospira, Pseudomonas, Actinomadura, and Enterobacter, and the fungal genera Dothideomycetes, Cladosporium, Chaetomium, and Trichaptum were identified as candidates involved in SRM degradation. Feathers increased (P < 0.05) headspace concentrations of CH{sub 4} primarily during the early stages of the first cycle and N{sub 2}O during the second. Although inclusion of feathers in compost increases greenhouse gas emissions, it may promote the establishment of microbial communities that are more adept at degrading SRM and recalcitrant proteins such as keratin and PrP{sup Sc}.« less

Comparative Ecology of H2 Cycling in Organotrophic and Phototrophic Ecosystems

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Bebout, Brad M.; Martens, Christopher S.; DesMarais, David J.; DeVincenzi, Don (Technical Monitor)

2001-01-01

The simple biochemistry of H2 is critical to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. The sensitivity of these many processes to H2 can be described quantitatively, at a basic thermodynamic level. This shared dependence on H2 may provide a means for interpreting the ecology and system-level biogeochemistry of widely variant microbial ecosystems on a common (and quantitative) level. Understanding the factors that control H2 itself is a critical prerequisite. Here, we examine two ecosystems that vary widely with respect to H2 cycling. In anoxic, 'organotrophic' sediments from Cape Lookout Bight (North Carolina, USA), H2 partial pressures are strictly maintained at low, steady-state levels by H2-consuming organisms, in a fashion that can be quantitatively predicted by simple thermodynamic calculations. In phototrophic microbial mats from Baja, Mexico, H2 partial pressures are instead controlled by the activity of light-sensitive H2-producing organisms. In consequence, H2 partial pressures within the system fluctuate by orders of magnitude on hour-long time scales. The differences in H2 cycling subsequently impact H2-sensitive microbial processes, such as methanogenesis. For example, the presence of sulfate in the organotrophic system always yielded low levels of H2 that were inhibitory to methanogenesis; however, the elevated levels of H2 in the phototrophic system favored methane production at significant levels, even in the presence of high sulfate concentrations. The myriad of other H2-sensitive microbial processes are expected to exhibit similar behavior.

Geochemical evidence for cryptic sulfur cycling in salt marsh sediments

NASA Astrophysics Data System (ADS)

Mills, Jennifer V.; Antler, Gilad; Turchyn, Alexandra V.

2016-11-01

Cryptic sulfur cycling is an enigmatic process in which sulfate is reduced to some lower-valence state sulfur species and subsequently quantitatively reoxidized; the rate and microbial energetics of this process and how prevalent it may be in the environment remain controversial. Here we investigate sulfur cycling in salt marsh sediments from Norfolk, England where we observe high ferrous iron concentrations with no depletion of sulfate or change in the sulfur isotope ratio of that sulfate, but a 5‰ increase in the oxygen isotope ratio in sulfate, indicating that sulfate has been through a reductive cycle replacing its oxygen atoms. This cryptic sulfur cycle was replicated in laboratory incubations using 18O-enriched water, demonstrating that the field results do not solely result from mixing processes in the natural environment. Numerical modeling of the laboratory incubations scaled to represent the salt marsh sediments suggests that the uptake rate of sulfate during this cryptic sulfur cycling is similar to the uptake rate of sulfate during the fastest microbial sulfate reduction that has been measured in the natural environment. The difference is that during cryptic sulfur cycling, all of the sulfur is subsequently reoxidized to sulfate. We discuss mechanisms for this pathway of sulfur cycling including the possible link to the subsurface iron cycle.

MICROBIAL INDICATORS OF AQUATIC ECOSYSTEM CHANGE: CURRENT APPLICATIONS TO EUTROPHICATION STUDIES. (R828677C001)

EPA Science Inventory

Human encroachment on aquatic ecosystems is increasing at an unprecedented rate. The impacts of human pollution and habitat alteration are most evident and of greatest concern at the microbial level, where a bulk of production and nutrient cycling takes place. Aquatic ecosyste...

Biogeochemistry of three small Eutrophic Lakes Differentially Influenced by Marine Waters from Bayou Chico Bay, Pensacola, Florida

EPA Science Inventory

Biogeochemical models predict microbial mediated pathways but generally do not account for microorganisms. This study was undertaken to better understand relationships among microbial communities and N, S, Fe and C cycling in three lakes. Jackson Lakes formed from abandoned sand...

An Open-Ended Investigative Microbial Ecology Laboratory for Introductory Biology

ERIC Educational Resources Information Center

Jones-Held, Susan; Paoletti, Robert; Glick, David; Held, Michael E.

2010-01-01

In this article we describe a multi-week investigative laboratory in microbial ecology/diversity and nitrogen cycling that we have used in our introductory biology course. This module encourages active student involvement in experimental design, using the scientific literature and quantitative analysis of large data sets. Students analyze soil…

Long term stability of microbial diversity and activity potential in severely disturbed arid lands of the southwest

USDA-ARS?s Scientific Manuscript database

Arid land cryptobiotic soil crusts govern water infiltration, soil aggregate stability and nutrient cycling between soil microbial communities and vascular plants. Surface mining involves removal of topsoil and associated crust and storage in mixed mounds for extended periods. The exposed subsoil an...

FATTY ACID STABLE ISOTOPE INDICATORS OF MICROBIAL CARBON SOURCE IN TROPICAL SOILS

EPA Science Inventory

The soil microbial community plays an important role in tropical ecosystem functioning because of its importance in the soil organic matter (SOM) cycle. We have measured the stable carbon isotopic ratio (delta13C) of individual phospholipid fatty acids (PLFAs) in a variety of tr...