Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

DOE PAGES

Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; ...

2015-04-30

The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy numbermore » of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.« less

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

PubMed Central

Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

2015-01-01

The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below −10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface. PMID:25983731

NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

PubMed Central

Penton, C. Ryan; Yang, Caiyun; Wu, Liyou; Wang, Qiong; Zhang, Jin; Liu, Feifei; Qin, Yujia; Deng, Ye; Hemme, Christopher L.; Zheng, Tianling; Schuur, Edward A. G.; Tiedje, James; Zhou, Jizhong

2016-01-01

Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites. PMID:27933054

NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

DOE PAGES

Penton, C. Ryan; Yang, Caiyun; Wu, Liyou; ...

2016-11-24

Since nitrogen (N) is often limiting in permafrost soils, we investigated the N 2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlatedmore » to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N 2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.« less

NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

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

Penton, C. Ryan; Yang, Caiyun; Wu, Liyou

Since nitrogen (N) is often limiting in permafrost soils, we investigated the N 2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlatedmore » to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N 2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.« less

Effects of long-term simulated martian conditions on a freeze-dried and homogenized bacterial permafrost community.

PubMed

Hansen, Aviaja A; Jensen, Lars L; Kristoffersen, Tommy; Mikkelsen, Karina; Merrison, Jonathan; Finster, Kai W; Lomstein, Bente Aa

2009-03-01

Indigenous bacteria and biomolecules (DNA and proteins) in a freeze-dried and homogenized Arctic permafrost were exposed to simulated martian conditions that correspond to about 80 days on the surface of Mars with respect to the accumulated UV dose. The simulation conditions included UV radiation, freeze-thaw cycles, the atmospheric gas composition, and pressure. The homogenized permafrost cores were subjected to repeated cycles of UV radiation for 3 h followed by 27 h without irradiation. The effects of the simulation conditions on the concentrations of biomolecules; numbers of viable, dead, and cultured bacteria; as well as the community structure were determined. Simulated martian conditions resulted in a significant reduction of the concentrations of DNA and amino acids in the uppermost 1.5 mm of the soil core. The total number of bacterial cells was reduced in the upper 9 mm of the soil core, while the number of viable cells was reduced in the upper 15 mm. The number of cultured aerobic bacteria was reduced in the upper 6 mm of the soil core, whereas the community structure of cultured anaerobic bacteria was relatively unaffected by the exposure conditions. As explanations for the observed changes, we propose three causes that might have been working on the biological material either individually or synergistically: (i) UV radiation, (ii) UV-generated reactive oxygen species, and (iii) freeze-thaw cycles. Currently, the production and action of reactive gases is only hypothetical and will be a central subject in future investigations. Overall, we conclude that in a stable environment (no wind-/pressure-induced mixing) biological material is efficiently shielded by a 2 cm thick layer of dust, while it is relatively rapidly destroyed in the surface layer, and that biomolecules like proteins and polynucleotides are more resistant to destruction than living biota.

Effects of Long-Term Simulated Martian Conditions on a Freeze-Dried and Homogenized Bacterial Permafrost Community

NASA Astrophysics Data System (ADS)

Hansen, Aviaja A.; Jenson, Lars L.; Kristoffersen, Tommy; Mikkelsen, Karina; Merrison, Jonathan; Finster, Kai W.; Lomstein, Bente Aa.

2009-03-01

Indigenous bacteria and biomolecules (DNA and proteins) in a freeze-dried and homogenized Arctic permafrost were exposed to simulated martian conditions that correspond to about 80 days on the surface of Mars with respect to the accumulated UV dose. The simulation conditions included UV radiation, freeze-thaw cycles, the atmospheric gas composition, and pressure. The homogenized permafrost cores were subjected to repeated cycles of UV radiation for 3 h followed by 27 h without irradiation. The effects of the simulation conditions on the concentrations of biomolecules; numbers of viable, dead, and cultured bacteria; as well as the community structure were determined. Simulated martian conditions resulted in a significant reduction of the concentrations of DNA and amino acids in the uppermost 1.5 mm of the soil core. The total number of bacterial cells was reduced in the upper 9 mm of the soil core, while the number of viable cells was reduced in the upper 15 mm. The number of cultured aerobic bacteria was reduced in the upper 6 mm of the soil core, whereas the community structure of cultured anaerobic bacteria was relatively unaffected by the exposure conditions. As explanations for the observed changes, we propose three causes that might have been working on the biological material either individually or synergistically: (i) UV radiation, (ii) UV-generated reactive oxygen species, and (iii) freeze-thaw cycles. Currently, the production and action of reactive gases is only hypothetical and will be a central subject in future investigations. Overall, we conclude that in a stable environment (no wind-/pressure-induced mixing) biological material is efficiently shielded by a 2 cm thick layer of dust, while it is relatively rapidly destroyed in the surface layer, and that biomolecules like proteins and polynucleotides are more resistant to destruction than living biota.

Anaerobic methanotrophic communities thrive in deep submarine permafrost.

PubMed

Winkel, Matthias; Mitzscherling, Julia; Overduin, Pier P; Horn, Fabian; Winterfeld, Maria; Rijkers, Ruud; Grigoriev, Mikhail N; Knoblauch, Christian; Mangelsdorf, Kai; Wagner, Dirk; Liebner, Susanne

2018-01-22

Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in anaerobic oxidation of methane (AOM) we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota. Methane concentrations and δ 13 C-methane signatures distinguish horizons of potential AOM coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescence in situ hybridization (FISH) corroborate potential activity of AOM communities in submarine permafrost sediments at low temperatures. Modeled potential AOM consumes 72-100% of submarine permafrost methane and up to 1.2 Tg of carbon per year for the total expected area of submarine permafrost. This is comparable with AOM habitats such as cold seeps. We thus propose that AOM is active where submarine permafrost thaws, which should be included in global methane budgets.

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.

PubMed

Wurzbacher, Christian; Nilsson, R Henrik; Rautio, Milla; Peura, Sari

2017-08-01

In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.

Methane dynamics regulated by microbial community response to permafrost thaw.

PubMed

McCalley, Carmody K; Woodcroft, Ben J; Hodgkins, Suzanne B; Wehr, Richard A; Kim, Eun-Hae; Mondav, Rhiannon; Crill, Patrick M; Chanton, Jeffrey P; Rich, Virginia I; Tyson, Gene W; Saleska, Scott R

2014-10-23

Permafrost contains about 50% of the global soil carbon. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ(13)C signature (10-15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus 'Methanoflorens stordalenmirensis' is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.

Permafrost knowledge to serve as foundation for Inuit community planning

NASA Astrophysics Data System (ADS)

Gibéryen, T.; Allard, M.

2011-12-01

With the recent announcement of Québec's provincial government's Plan Nord, Nunavik will see a 500 new houses sweep onto it's territory over the next 5 years. The local Inuit communities are confronted with the pressuring need to find suitable land to safely accommodate the new infrastructures in the long term. Additional to human and environmental constraints are those related to warming permafrost. Intensive studies on four Nunavik communities (Inukjuak, Puvirnituq, Akulivik, Kangirsuk) have allowed us to extensively consult local and regional authorities on their planning and management considerations. Recent and archived drilling data have been used to corroborate air photo interpretation, surficial geology and permafrost mapping. All collected information are integrated into aggregated maps that will eventually serve as community master plans. General recommendations on how to best manage and plan for community expansions on warming permafrost are made. Appropriate engineering techniques assuring long-term stable foundations are outlined and additionally mapped, taking into consideration the variable terrain conditions and simulated changes in permafrost temperature and active layer thickness according to climate change scenarios. The final purpose of our results is for them to support local and regional governments in their community planning process towards the best possible climate change adaptation strategies.

Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland

PubMed Central

Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Schnecker, Jörg; Wild, Birgit; Čapek, Petr; Kaiser, Christina; Torsvik, Vigdis L.; Richter, Andreas; Schleper, Christa; Urich, Tim

2014-01-01

Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation (“buried topsoils”), resulting from a decrease in fungal abundance compared to recent (“unburied”) topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation. PMID

Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau.

PubMed

Hu, Weigang; Zhang, Qi; Tian, Tian; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; An, Lizhe; Feng, Huyuan

2016-05-01

Permafrost on the Qinghai-Tibet Plateau is one of the most sensitive regions to climate warming, thus characterizing its microbial diversity and community composition may be important for understanding their potential responses to climate changes. Here, we investigated the prokaryotic diversity in a 10-m-long permafrost core from the Qinghai-Tibet Plateau by restriction fragment length polymorphism analysis targeting the 16S rRNA gene. We detected 191 and 17 bacterial and archaeal phylotypes representing 14 and 2 distinct phyla, respectively. Proteobacteria was the dominant bacterial phylum, while archaeal communities were characterized by a preponderance of Thaumarchaeota. Some of prokaryotic phylotypes were closely related to characterized species involved in carbon and nitrogen cycles, including nitrogen fixation, methane oxidation and nitrification. However, the majority of the phylotypes were only distantly related to known taxa at order or species level, suggesting the potential of novel diversity. Additionally, both bacterial α diversity and community composition changed significantly with sampling depth, where these communities mainly distributed according to core horizons. Arthrobacter-related phylotypes presented at high relative abundance in two active layer soils, while the deeper permafrost soils were dominated by Psychrobacter-related clones. Changes in bacterial community composition were correlated with most measured soil variables, such as carbon and nitrogen contents, pH, and conductivity.

Microbial Functional Potential and Community Composition in Permafrost-Affected Soils of the NW Canadian Arctic

PubMed Central

Frank-Fahle, Béatrice A.; Yergeau, Étienne; Greer, Charles W.; Lantuit, Hugues; Wagner, Dirk

2014-01-01

Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic. PMID:24416279

Microbial Community Dynamics from Permafrost Across the Pleistocene-Holocene Boundary and Response to Abrupt Climate Change

NASA Astrophysics Data System (ADS)

Hammad, A.; Mahony, M.; Froese, D. G.; Lanoil, B. D.

2014-12-01

Earth is currently undergoing rapid warming similar to that observed about 10,000 years ago at the end of the Pleistocene. We know a considerable amount about the adaptations and extinctions of mammals and plants at the Pleistocene/Holocene (P/H) boundary, but relatively little about changes at the microbial level. Due to permafrost soils' freezing anoxic conditions, they act as microbial diversity archives allowing us to determine how microbial communities adapted to the abrupt warming at the end of P. Since microbial community composition only helps differentiate viable and extant microorganisms in frozen permafrost, microbial activity in thawing permafrost must be investigated to provide a clear understanding of microbial response to climate change. Current increased temperatures will result in warming and potential thaw of permafrost and release of stored organic carbon, freeing it for microbial utilization; turning permafrost into a carbon source. Studying permafrost viable microbial communities' diversity and activity will provide a better understanding of how these microorganisms respond to soil edaphic variability due to climate change across the P/H boundary, providing insight into the changes that the soil community is currently undergoing in this modern era of rapid climate change. Modern soil, H and P permafrost cores were collected from Lucky Lady II site outside Dawson City, Yukon. 16S rRNA high throughput sequencing of permafrost DNA showed the same trends for total and viable community richness and diversity with both decreasing with permafrost depth and only the richness increasing in mid and early P. The modern, H and P soils had 50.9, 33.9, and 27.3% unique viable species and only 14% of the total number of viable species were shared by all soils. Gas flux measurements of thawed permafrost showed metabolic activity in modern and permafrost soils, aerobic CH­­4 consumption in modern, some H and P soils, and anaerobic CH­­4 production in one H

Permafrost soil characteristics and microbial community structure across a boreal forest watershed vary over short spatial scales and dictate community responses to thaw.

NASA Astrophysics Data System (ADS)

Stegen, J.; Bottos, E. M.; Kennedy, D.; Romero, E. B.; Fansler, S.; Chu, R. K.; Tfaily, M.; Jansson, J.; Bernstein, H. C.; Brown, J. M.; Markillie, L. M.

2017-12-01

Understanding drivers of permafrost microbial community structure and function is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw; however, studies describing ecological controls on these communities are lacking. We hypothesize that permafrost communities are uniquely shaped by constraints imposed by prolonged freezing, and decoupled from the selective factors that influence non-permafrost soil communities, but that pre-thaw environmental and community characteristics will be strong determinants of community structure and function post-thaw. We characterized patterns of environmental variation and microbial community composition in sixty permafrost samples spanning landscape gradients in a boreal forest watershed, and monitored community responses to thaw. Consistent with our hypothesis, we found that, proportionally, the strongest process influencing permafrost community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21) and variable selection (0.16), and that deterministic selection arose primarily from energetic constraints of the permafrost environment. Our data supported a structural equation model in which organic carbon thermodynamics and organic acid content, influenced redox conditions and total selection. Post-thaw community composition was found to be driven primarily by pre-thaw community composition, indicating a strong influence of historical conditions. Together, these results suggest that community responses to thaw may be highly varied over short distances and that changes in community structure and function are likely to be drastic, as changes to system hydrology mobilize organisms and nutrients, thereby relieving the primary constraints on the system. These findings are being integrated with metabolomic and metatranscriptomic analyses to improve understanding of how pre-thaw conditions can be used to predict microbial activity post-thaw.

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.

The transcriptional response of microbial communities in thawing Alaskan permafrost soils.

PubMed

Coolen, Marco J L; Orsi, William D

2015-01-01

Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw.

The transcriptional response of microbial communities in thawing Alaskan permafrost soils

PubMed Central

Coolen, Marco J. L.; Orsi, William D.

2015-01-01

Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw. PMID:25852660

Metagenomics Reveals Microbial Community Composition And Function With Depth In Arctic Permafrost Cores

NASA Astrophysics Data System (ADS)

Jansson, J.; Tas, N.; Wu, Y.; Ulrich, C.; Kneafsey, T. J.; Torn, M. S.; Hubbard, S. S.; Chakraborty, R.; Graham, D. E.; Wullschleger, S. D.

2013-12-01

The Arctic is one of the most climatically sensitive regions on Earth and current surveys show that permafrost degradation is widespread in arctic soils. Biogeochemical feedbacks of permafrost thaw are expected to be dominated by the release of currently stored carbon back into the atmosphere as CO2 and CH4. Understanding the dynamics of C release from permafrost requires assessment of microbial functions from different soil compartments. To this end, as part of the Next Generation Ecosystem Experiment in the Arctic, we collected two replicate permafrost cores (1m and 3m deep) from a transitional polygon near Barrow, AK. At this location, permafrost starts from 0.5m in depth and is characterized by variable ice content and higher pH than surface soils. Prior to sectioning, the cores were CT-scanned to determine the physical heterogeneity throughout the cores. In addition to detailed geochemical characterization, we used Illumina MiSeq technology to sequence 16SrRNA genes throughout the depths of the cores at 1 cm intervals. Selected depths were also chosen for metagenome sequencing of total DNA (including phylogenetic and functional genes) using the Illumina HiSeq platform. The 16S rRNA gene sequence data revealed that the microbial community composition and diversity changed dramatically with depth. The microbial diversity decreased sharply below the first few centimeters of the permafrost and then gradually increased in deeper layers. Based on the metagenome sequence data, the permafrost microbial communities were found to contain members with a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. The surface active layers had more representatives of Verrucomicrobia (potential methane oxidizers) whereas the deep permafrost layers were dominated by several different species of Actinobacteria. The latter are known to have a diverse metabolic capability and are able to adapt to stress by entering a dormant yet

Climate Change and Thawing Permafrost in Two Iñupiaq Communities of Alaska's Arctic: Observations, Implications, and Resilience

NASA Astrophysics Data System (ADS)

Woodward, A.; Kofinas, G.

2013-12-01

For thousands of years the Iñupiat of northern Alaska have relied on ecosystems underlain by permafrost for material and cultural resources. As permafrost thaws across the Arctic, these social-ecological systems are changing rapidly. Community-based research and extensive local knowledge of Iñupiaq villagers offer unique and valuable contributions to understanding permafrost change and its implications for humans. We partnered with two Iñupiaq communities in Alaska's Arctic to investigate current and potential effects of thawing permafrost on social-ecological systems. Anaktuvuk Pass is situated on thaw-stable consolidated gravel in the Brooks Range, while Selawik rests on ice-rich permafrost in Beringia lowland tundra. Using the transdisciplinary approach of resilience theory and mixed geophysical and ethnographic methods, we measured active layer thaw depths and documented local knowledge about climate and permafrost change. Thaw depths were greater overall in Selawik. Residents of both communities reported a variety of changes in surface features, hydrology, weather, flora, and fauna that they attribute to thawing permafrost and / or climate change. Overall, Selawik residents described more numerous and extreme examples of such changes, expressed higher degrees of certainty that change is occurring, and anticipated more significant and negative implications for their way of life than did residents of Anaktuvuk Pass. Of the two villages, Selawik faces greater and more immediate challenges to the resilience of its social-ecological system as permafrost thaws.

Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes.

PubMed

Wei, Shiping; Cui, Hongpeng; Zhu, Youhai; Lu, Zhenquan; Pang, Shouji; Zhang, Shuai; Dong, Hailiang; Su, Xin

2018-05-01

Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition, data also show the soil texture and features change as a result of microbial reproduction and activity induced by this permafrost thaw. Those data indicate that microbial ecology under warming permafrost has potential impacts on ecosystem and methane emissions.

Allochthonous carbon is a major regulator to bacterial growth and community composition in subarctic freshwaters

PubMed Central

Roiha, Toni; Peura, Sari; Cusson, Mathieu; Rautio, Milla

2016-01-01

In the subarctic region, climate warming and permafrost thaw are leading to emergence of ponds and to an increase in mobility of catchment carbon. As carbon of terrestrial origin is increasing in subarctic freshwaters the resource pool supporting their microbial communities and metabolism is changing, with consequences to overall aquatic productivity. By sampling different subarctic water bodies for a one complete year we show how terrestrial and algal carbon compounds vary in a range of freshwaters and how differential organic carbon quality is linked to bacterial metabolism and community composition. We show that terrestrial drainage and associated nutrients supported higher bacterial growth in ponds and river mouths that were influenced by fresh terrestrial carbon than in large lakes with carbon from algal production. Bacterial diversity, however, was lower at sites influenced by terrestrial carbon inputs. Bacterial community composition was highly variable among different water bodies and especially influenced by concentrations of dissolved organic carbon (DOC), fulvic acids, proteins and nutrients. Furthermore, a distinct preference was found for terrestrial vs. algal carbon among certain bacterial tribes. The results highlight the contribution of the numerous ponds to cycling of terrestrial carbon in the changing subarctic and arctic regions. PMID:27686416

Allochthonous carbon is a major regulator to bacterial growth and community composition in subarctic freshwaters.

PubMed

Roiha, Toni; Peura, Sari; Cusson, Mathieu; Rautio, Milla

2016-09-30

In the subarctic region, climate warming and permafrost thaw are leading to emergence of ponds and to an increase in mobility of catchment carbon. As carbon of terrestrial origin is increasing in subarctic freshwaters the resource pool supporting their microbial communities and metabolism is changing, with consequences to overall aquatic productivity. By sampling different subarctic water bodies for a one complete year we show how terrestrial and algal carbon compounds vary in a range of freshwaters and how differential organic carbon quality is linked to bacterial metabolism and community composition. We show that terrestrial drainage and associated nutrients supported higher bacterial growth in ponds and river mouths that were influenced by fresh terrestrial carbon than in large lakes with carbon from algal production. Bacterial diversity, however, was lower at sites influenced by terrestrial carbon inputs. Bacterial community composition was highly variable among different water bodies and especially influenced by concentrations of dissolved organic carbon (DOC), fulvic acids, proteins and nutrients. Furthermore, a distinct preference was found for terrestrial vs. algal carbon among certain bacterial tribes. The results highlight the contribution of the numerous ponds to cycling of terrestrial carbon in the changing subarctic and arctic regions.

Microbial communities of the deep unfrozen: Do microbes in taliks increase permafrost carbon vulnerability? (Invited)

NASA Astrophysics Data System (ADS)

Waldrop, M. P.; Blazewicz, S.; Jones, M.; Mcfarland, J. W.; Harden, J. W.; Euskirchen, E. S.; Turetsky, M.; Hultman, J.; Jansson, J.

2013-12-01

The vast frozen terrain of northern latitude ecosystems is typically thought of as being nearly biologically inert for the winter period. Yet deep within the frozen ground of northern latitude soils reside microbial communities that can remain active during the winter months. As we have shown previously, microbial communities may remain active in permafrost soils just below the freezing point of water. Though perhaps more importantly, microbial communities persist in unfrozen areas of water, soil, and sediment beneath water bodies the entire year. Microbial activity in taliks may have significant impacts on biogeochemical cycling in northern latitude ecosystems because their activity is not limited by the winter months. Here we present compositional and functional data, including long term incubation data, for microbial communities within permafrost landscapes, in permafrost and taliks, and the implications of these activities on permafrost carbon decomposition and the flux of CO2 and CH4. Our experiment was conducted at the Alaska Peatland Experiment (APEX) within the Bonanza Creek LTER in interior Alaska. Our site consists of a black spruce forest on permafrost that has degraded into thermokarst bogs at various times over the last five hundred years. We assume the parent substrate of the deep (1-1.5m) thermokarst peat was similar to the nearby forest soil and permafrost C before thaw. At this site, flux tower and autochamber data show that the thermokarst bog is a sink of CO2 , but a significant source of CH4. Yet this does not tell the whole story as these data do not fully capture microbial activity within the deep unfrozen talik layer. There is published evidence that within thermokarst bogs, relatively rapid decomposition of old forest floor material may be occurring. There are several possible mechanisms for this pattern; one possible mechanism for accelerated decomposition is the overwintering activities of microbial communities in taliks of thermokarst

The Permafrost Young Researchers Network (PYRN): Contribution to IPY's "Thermal State of Permafrost"

NASA Astrophysics Data System (ADS)

Johansson, M.; Lantuit, H.; Frauenfeld, O. W.

2007-12-01

The Permafrost Young Researchers Network (PYRN, www.pyrn.org) is a unique resource for students, young scientists, and engineers studying permafrost. It is an international organization fostering innovative collaboration, seeking to recruit, retain, and promote future generations of permafrost scientists and engineers. Initiated for and during IPY, PYRN directs the multi-disciplinary talents of its membership toward global awareness, knowledge, and response to permafrost-related challenges in a changing climate. Created as an education and outreach component of the International Permafrost Association (IPA), PYRN is a central database of permafrost information and science for more than 350 young researchers from 33 countries. PYRN distributes a newsletter, recognizes outstanding permafrost research by its members through an annual awards program, organizes training workshops (2007 in Abisko, Sweden and St. Petersburg, Russia), and contributes to the growth and future of the permafrost community. While networking forms the basis of PYRN's activities, the organization also seeks to establish itself as a driver of permafrost research for the IPY and beyond. We recently launched a series of initiatives on several continents aimed at providing young scientists and engineers with the means to conduct ground temperature monitoring in under-investigated permafrost regions. Focusing on sites not currently covered by the IPA's "Thermal State of Permafrost" project, the young investigators of PYRN will provide and use lightweight drills and temperature sensors to instrument shallow boreholes in those regions. The data and results will be incorporated in the global database on permafrost temperatures and made freely available to the scientific community, thereby contributing to the advance of permafrost science and the strengthening of the next generation of permafrost researchers.

Exploring Viral Mediated Carbon Cycling in Thawing Permafrost Microbial Communities

NASA Astrophysics Data System (ADS)

Trubl, G. G.; Solonenko, N.; Moreno, M.; Sullivan, M. B.; Rich, V. I.

2014-12-01

Viruses are the most abundant biological entities on Earth and their impact on carbon cycling in permafrost habitats is poorly understood. Arctic C cycling is particularly important to interpret due to the rapid climate change occurring and the large amount of C stockpiled there (~1/3 of global soil C is stored in permafrost). Viruses of microbes (i.e. phages) play central roles in C cycling in the oceans, through cellular lysis (phage drive the largest ocean C flux about 150 Gt yr-1, dwarfing all others by >5-fold), production of associated DOC, as well as transport and expression during infection (1029 transduction events day-1). C cycling in thawing permafrost systems is critical in understanding the climate trajectory and phages may be as important for C cycling here as they are in the ocean. The thawed C may become a food source for microbes, producing CO2 and potentially CH4, both potent greenhouse gases. To address the potential role of phage in C cycling in these dynamic systems, we are examining phage from an arctic permafrost thaw gradient in northern Sweden. We have developed a protocol for successfully extracting phage from peat soils and are quantifying phage in 15 peat and 2 lake sediment cores, with the goal of sequencing viromes. Preliminary data suggest that phage are present at 109 g-1 across the permafrost thaw gradient (compared to the typical marine count ~105 ml-1), implying a potentially robust phage-host interaction web in these changing environments. We are examining phage from 11 depth intervals (covering the active and permafrost layer) in the cores to assess phage-host community dynamics. Phage morphology and abundance for each layer and environment are being determined using qTEM and EFM. Understanding the phage that infect bacteria and archaea in these rapidly changing habitats will provide insight into the controls on current and future CH4 and CO2 emissions in permafrost habitats.

Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient.

PubMed

Mondav, Rhiannon; McCalley, Carmody K; Hodgkins, Suzanne B; Frolking, Steve; Saleska, Scott R; Rich, Virginia I; Chanton, Jeff P; Crill, Patrick M

2017-08-01

Biogenic production and release of methane (CH 4 ) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa site (intact permafrost and low radiative forcing signature) had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog (thawing permafrost and low radiative forcing signature) had lower alpha diversity and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering. Hydrogenotrophic methanogens and Acidobacteria dominated the bog shifting from palsa-like to fen-like at the waterline. The fen (no underlying permafrost, high radiative forcing signature) had the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota and was significantly enriched in methanogens. The Mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Vegetation-Associated Impacts on Arctic Tundra Bacterial and Microeukaryotic Communities

PubMed Central

Shi, Yu; Xiang, Xingjia; Shen, Congcong; Neufeld, Josh D.; Walker, Virginia K.

2014-01-01

The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H′) were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. PMID:25362064

Methane flux and carbon isotope composition correlate to shifting plant and microbial communities along a permafrost thaw gradient

NASA Astrophysics Data System (ADS)

McCalley, C. K.; Mondav, R.; Chanton, J.; Crill, P. M.; Hodgkins, S. B.; Kim, E.; Rich, V. I.; Wehr, R.; Woodcroft, B. J.; Tyson, G. W.; Saleska, S. R.

2012-12-01

Methane flux from high latitude wetlands is a critical component of the global carbon budget and is highly sensitive to climate change, with observed and predicted increases as permafrost thaws. Microorganisms mediate wetland methane cycling, but connections between ecosystem-scale flux and underlying microbial dynamics are poorly understood. To address this gap we used isotopic (laser absorption spectrometry) and molecular (16S rRNA gene amplicon sequencing) techniques in a high latitude (68° N) wetland to investigate the relationship between microbial community composition and methane emissions across a permafrost thaw gradient. The transition from permafrost dominated, well drained palsas, through intermediate thaw sites dominated by Sphagnum spp., to wet sites with no underlying permafrost dominated by Eriophorum angustifolium is associated with substantial increases in methane emission. Across this thaw progression the carbon isotopic composition of emitted methane increased from -79.5 ‰ in the intermediate-thawing site to -66.4 ‰ in the thawed site, indicating a relative shift from CO2-reductive towards acetoclastic methanogenesis. Increases in methane flux under thaw were correlated with increasing abundance of methane-producing archaeal clades and increases in methane isotopic composition were associated with shifts in the archaeal community. While CO2 reducing methanogens were found throughout thawing and thawed sites, methanogens of the Methanosarcina (the order of Archaea that contains all known acetoclastic methanogens) were most associated with the fully thawed site. These results directly link microbial community composition to ecosystem scale changes in the magnitude and isotopic composition of methane emissions under permafrost thaw. If isotopic shifts of this magnitude are characteristic of methane dynamics under permafrost loss they should also become detectable in global atmospheric methane observations, providing a global scale tracer of

Permafrost Young Researchers Get Their Hands Dirty: The PYRN-Thermal State of Permafrost IPY Project

NASA Astrophysics Data System (ADS)

Johansson, M.; Lantuit, H.

2009-04-01

The Permafrost Young Researchers Network (PYRN) (www.pyrn.org) is a unique resource for students and young scientists and engineers studying permafrost. It is an international organization fostering innovative collaboration, seeking to recruit, retain, and promote future generations of permafrost scientists and engineers. Initiated for and during IPY, PYRN directs the multi-disciplinary talents of its membership toward global awareness, knowledge, and response to permafrost-related challenges in a changing climate. Created as an education and outreach component of the International Permafrost Association (IPA), PYRN is a central database of permafrost information and science for more than 500 young researchers from over 40 countries. PYRN distributes a newsletter, recognizes outstanding permafrost research by its members through an annual awards program, organizes training workshops (2007 in Abisko, Sweden and St. Petersburg, Russia, 2008 in Fairbanks, Alaska and St. Petersburg, Russia), and contributes to the growth and future of the permafrost community. While networking forms the basis of PYRN's activities, the organization also seeks to establish itself as a driver of permafrost research for the IPY and beyond. We recently launched a series of initiatives on several continents aimed at providing young scientists and engineers with the means to conduct ground temperature monitoring in under investigated permafrost regions. Focusing on sites not currently covered by the IPA's "Thermal State of Permafrost" project, the young investigators of PYRN successfully launched and funded the PYRN-TSP project. They use lightweight drills and temperature sensors to instrument shallow boreholes in those regions. The first phase of the project was started in the spring of 2008 at Scandinavian sites. The data and results will be incorporated in the global database on permafrost temperatures and made freely available to the scientific community, thereby contributing to the

GlobPermafrost- How Space-BasedEarth Observation Supports Understanding of Permafrost

NASA Astrophysics Data System (ADS)

Bartsch, Annett; Grosse, Guido; Kaab, Andreas; Westermann, Sebastian; Strozzi, Tazio; Wiesmann, Andreas; Duguay, Claude; Seifert, Frank Martin; Obu, Jaroslav; Goler, Robert

2016-08-01

The GlobPermafrost project develops, validates and implements Earth Observation (EO) products to support research communities and international organisations in their work on better understanding permafrost characteristics and dynamics. To facilitate usability of these products by the target audience, user requirements with respect to the planned products have been requested and collected through an online community survey as well as by interview. This paper provides an overview on the planned thematic EO products as well as results of the user requirement survey.

Vegetation-associated impacts on arctic tundra bacterial and microeukaryotic communities.

PubMed

Shi, Yu; Xiang, Xingjia; Shen, Congcong; Chu, Haiyan; Neufeld, Josh D; Walker, Virginia K; Grogan, Paul

2015-01-01

The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H') were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. Copyright © 2015, American Society for Microbiology. All Rights

Soil Redox Conditions Are a Strong Determinant of Microbial Community Composition and the Fate of Carbon Following Permafrost Thaw.

NASA Astrophysics Data System (ADS)

Bottos, E. M.; Bramer, L.; Kim, Y. M.; Fansler, S.; Nicora, C.; Zink, E.; Chu, R. K.; Tfaily, M. M.; Metz, T. O.; Jansson, J.; Stegen, J.

2016-12-01

Permafrost-affected soils contain enormous stocks of carbon, which are becoming increasingly available to microbial transformation as permafrost regions warm; however, how this warming will influence the permafrost microbiome and the transformation of soil carbon remains unclear. We hypothesize that the redox conditions that arise following permafrost thaw will dictate the structure and function of the microbial community, and strongly influence the nature of carbon transformations. To examine this, permafrost-affected soils from Caribou Poker Creek Research Watershed, Alaska were incubated at 4 °C under aerobic and anaerobic conditions for periods of 9 and 94 days. Over the incubation period, rates of CO2 and CH4 production were measured by gas chromatography, shifts in microbial community structure were characterized by 16S rRNA gene sequencing, and changes in metabolite and organic matter composition were analyzed by GC-MS and ESI-FTICR MS, respectively. CO2 production rates were significantly higher in aerobic treatments in 9-day and 94-day incubations, by 3-times and 12-times, respectively. Rates of CH4 production were not significantly different between treatments in 9-day incubations, but were 1.6-times higher in anaerobic treatments in 94-day incubations. The community composition remained largely unchanged in the incubated samples, with the exception of the 94-day aerobic incubations, which shifted strongly to become dominated by a single OTU, Rhodoferax ferrireducens. Metabolite profiles also shifted most strongly in the 94-day aerobic incubations, with the abundance of phosphorylated carbon compounds overrepresented in these samples. This work suggests that the redox conditions that arise following permafrost thaw will be a strong determinant of community composition and will govern the ultimate fate of carbon stocks in permafrost-affected soils. Our results are currently being integrated with numerical models aimed at predicting the coupled microbiome

Permafrost in the Yukon-Kuskokwim Delta, Alaska: a case for a holistic and integrated view of permafrost degradation

NASA Astrophysics Data System (ADS)

Herman-Mercer, N. M.; Schuster, P. F.; Laituri, M.; Elder, K.; Mutter, E. A.; Massey, M.; Matkin, E.; Toohey, R.

2016-12-01

The Yukon-Kuskokwim Delta (YKD) region of Alaska is a vast, marshy, lowland plain, underlain by discontinuous permafrost vulnerable to degradation. This region has been home to the Yup'ik and Cup'ik people, subsisting on local resources for centuries. Permafrost thaw in northern latitudes has become the focus of extensive scientific research in recent decades. However, the indigenous residents that live in these areas of degrading permafrost have been largely left out of scientific discussion and studies. More than fifty semi-structured interviews were conducted in four YKD communities. Interview questions were focused on the broad themes of seasonality of subsistence systems and observations of weather and landscape change. Responses revealed the myriad ways people interact with and observe permafrost in their day to day lives. For instance, permafrost is still utilized for food storage, people encounter permafrost when digging graves, and observe permafrost thaw in damage to their homes and other infrastructure in their communities. Yup'ik and Cup'ik residents have an intimate knowledge of the landscape owing to their subsistence based lifestyle and have reported observations of slumping ground, eroding river banks and coast lines as well as land that seems to be rising. Indigenous knowledge and observations complement broader scientific studies and should be used to inform permafrost research and assist in reconstructing historical baselines of permafrost distribution and active layer depth. Further, results of scientific research must be communicated to the people that may be impacted by present and future changes to permafrost that will likely result in changes to hydrologic flowpaths and ultimately ecosystem dynamics that may impact subsistence. Over millennia, northern indigenous communities have developed flexibility in resource harvesting and have exhibited adaptability to a variable and harsh environment. However, changes are being experienced at an

Permafrost Meta-Omics and Climate Change

NASA Astrophysics Data System (ADS)

Mackelprang, Rachel; Saleska, Scott R.; Jacobsen, Carsten Suhr; Jansson, Janet K.; Taş, Neslihan

2016-06-01

Permanently frozen soil, or permafrost, covers a large portion of the Earth's terrestrial surface and represents a unique environment for cold-adapted microorganisms. As permafrost thaws, previously protected organic matter becomes available for microbial degradation. Microbes that decompose soil carbon produce carbon dioxide and other greenhouse gases, contributing substantially to climate change. Next-generation sequencing and other -omics technologies offer opportunities to discover the mechanisms by which microbial communities regulate the loss of carbon and the emission of greenhouse gases from thawing permafrost regions. Analysis of nucleic acids and proteins taken directly from permafrost-associated soils has provided new insights into microbial communities and their functions in Arctic environments that are increasingly impacted by climate change. In this article we review current information from various molecular -omics studies on permafrost microbial ecology and explore the relevance of these insights to our current understanding of the dynamics of permafrost loss due to climate change.

Geomicrobial characterization of a 60 m long permafrost core from Svalbard

NASA Astrophysics Data System (ADS)

Fromreide, Siren; Tore Mørkved, Pål; Gilbert, Graham Lewis; Christiansen, Hanne H.; Reigstad, Laila

2014-05-01

In connection with a planned CO2 storage pilot project in the Arctic, a 60 m long permafrost core was drilled in Adventdalen, Svalbard. The on-shore drilling was performed through mainly marine and deltafront sediments, ending at the bedrock. The core has undergone detailed analyses of sedimentary stratigraphy, age, as well as the permafrost ice and carbon content at The University Centre in Svalbard (UNIS), and at the Center for Permafrost (CENPERM), Copenhagen. The main aim of the study presented here is to link the geochemical properties of the permafrost to the microbial community structure and its potential functions. As little is known about microbial life in permafrost at such depths this study will contribute to the understanding of these inaccessible ecosystems. A baseline geomicrobial description of 7 different depths in the 3 - 60 m interval of the permafrost core was done by culture independent methods such as 16S rRNA amplicon 454 pyrosequencing and functional and ribosomal gene quantifications. Additionally, geochemical analyses of the extracted pore water have been performed, as well as measurements of carbon content and major elements. The enumeration of the total prokaryotic community indicated similar numbers of bacteria and archaea down to approximately 50 m depth, while below this depth there was a dominance of archaeal cells. The bacterial 16S rRNA copy numbers ranged between 108 copies per gram sediment at 3 m depth to 104 copies per gram at the bedrock. Concerning the archaeal cells, the 16S rRNA copy numbers per gram sediment were in the range of 107 at the top of the core, ending at 105in the top of the bedrock. Detection and quantification of selected functional marker genes indicated high numbers of sulphate reducing bacteria at certain sediment depths, and a significant potential for microbial methanogenic activity throughout the core. Correlations studies between geochemical data and microbial community composition are currently ongoing.

Diversity and distribution of archaea community along a stratigraphic permafrost profile from Qinghai-Tibetan Plateau, China.

PubMed

Wei, Shiping; Cui, Hongpeng; He, Hao; Hu, Fei; Su, Xin; Zhu, Youhai

2014-01-01

Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by Crenarchaeota and Euryarchaeota. The active layer contained a proportion of Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis. OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively, were widely distributed in all sediment layers. However, OTU5 affiliated to Group 1.3b/MCG-A was primarily distributed in the active layers. Sequence analysis of the DGGE bands from the 16S rRNAs of methanogenic archaea showed that the majority of methanogens belonged to Methanosarcinales and Methanomicrobiales affiliated to Euryarchaeota and the uncultured ZC-I cluster affiliated to Methanosarcinales distributed in all the depths along the permafrost profile, which indicated a dominant group of methanogens occurring in the cold ecosystems.

Diversity and Distribution of Archaea Community along a Stratigraphic Permafrost Profile from Qinghai-Tibetan Plateau, China

PubMed Central

Cui, Hongpeng; He, Hao; Hu, Fei; Su, Xin; Zhu, Youhai

2014-01-01

Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by Crenarchaeota and Euryarchaeota. The active layer contained a proportion of Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis. OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively, were widely distributed in all sediment layers. However, OTU5 affiliated to Group 1.3b/MCG-A was primarily distributed in the active layers. Sequence analysis of the DGGE bands from the 16S rRNAs of methanogenic archaea showed that the majority of methanogens belonged to Methanosarcinales and Methanomicrobiales affiliated to Euryarchaeota and the uncultured ZC-I cluster affiliated to Methanosarcinales distributed in all the depths along the permafrost profile, which indicated a dominant group of methanogens occurring in the cold ecosystems. PMID:25525409

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

USGS Publications Warehouse

MacKelprang, R.; Waldrop, M.P.; Deangelis, K.M.; David, M.M.; Chavarria, K.L.; Blazewicz, S.J.; Rubin, E.M.; Jansson, J.K.

2011-01-01

Permafrost contains an estimated 1672????????Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 ??C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost. ?? 2011 Macmillan Publishers Limited. All rights reserved.

Examining Environmental Gradients with satellite data in permafrost regions - the current state of the ESA GlobPermafrost initative

NASA Astrophysics Data System (ADS)

Grosse, G.; Bartsch, A.; Kääb, A.; Westermann, S.; Strozzi, T.; Wiesmann, A.; Duguay, C. R.; Seifert, F. M.; Obu, J.; Nitze, I.; Heim, B.; Haas, A.; Widhalm, B.

2017-12-01

Permafrost cannot be directly detected from space, but many surface features of permafrost terrains and typical periglacial landforms are observable with a variety of EO sensors ranging from very high to medium resolution at various wavelengths. In addition, landscape dynamics associated with permafrost changes and geophysical variables relevant for characterizing the state of permafrost, such as land surface temperature or freeze-thaw state can be observed with spaceborne Earth Observation. Suitable regions to examine environmental gradients across the Arctic have been defined in a community white paper (Bartsch et al. 2014, hdl:10013/epic.45648.d001). These transects have been revised and adjusted within the DUE GlobPermafrost initiative of the European Space Agency. The ESA DUE GlobPermafrost project develops, validates and implements Earth Observation (EO) products to support research communities and international organisations in their work on better understanding permafrost characteristics and dynamics. Prototype product cases will cover different aspects of permafrost by integrating in situ measurements of subsurface and surface properties, Earth Observation, and modelling to provide a better understanding of permafrost today. The project will extend local process and permafrost monitoring to broader spatial domains, support permafrost distribution modelling, and help to implement permafrost landscape and feature mapping in a GIS framework. It will also complement active layer and thermal observing networks. Both lowland (latitudinal) and mountain (altitudinal) permafrost issues are addressed. The status of the Permafrost Information System and first results will be presented. Prototypes of GlobPermafrost datasets include: Modelled mean annual ground temperature by use of land surface temperature and snow water equivalent from satellites Land surface characterization including shrub height, land cover and parameters related to surface roughness Trends from

Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra.

PubMed

Kim, Hye Min; Lee, Min Jin; Jung, Ji Young; Hwang, Chung Yeon; Kim, Mincheol; Ro, Hee-Myong; Chun, Jongsik; Lee, Yoo Kyung

2016-11-01

The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.

Diversity and community structure of fungi through a permafrost core profile from the Qinghai-Tibet Plateau of China.

PubMed

Hu, Weigang; Zhang, Qi; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; An, Lizhe; Feng, Huyuan

2014-12-01

While a vast number of studies have addressed the prokaryotic diversity in permafrost, characterized by subzero temperatures, low water activity, and extremely low rates of nutrient and metabolite transfer, fungal patterns have received surprisingly limited attention. Here, the fungal diversity and community structure were investigated by culture-dependent technique combined with cloning-restriction fragment length polymorphism (RFLP) analysis of sediments in a 10-m-long permafrost core from the Qinghai-Tibet Plateau of China. A total of 62 fungal phylotypes related to 10 distinct classes representing three phyla were recovered from 5031 clones generated in 13 environmental gene libraries. A large proportion of the phylotypes (25/62) that were distantly related to described fungal species appeared to be novel diversity. Ascomycota was the predominant group of fungi, with respect to both clone and phylotype number. Our results suggested there was the existence of cosmopolitan psychrophilic or psychrotolerant fungi in permafrost sediments, the community composition of fungi varied with increasing depth, while these communities largely distributed according to core layers. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assessing hazard risk, cost of adaptation and traditional land use activities in the context of permafrost thaw in communities in Yukon and the Northwest Territories, Canada

NASA Astrophysics Data System (ADS)

Benkert, B.; Perrin, A.; Calmels, F.

2015-12-01

Together with its partners, the Northern Climate ExChange (NCE, part of the Yukon Research Centre at Yukon College) has been mapping permafrost-related hazard risk in northern communities since 2010. By integrating geoscience and climate project data, we have developed a series of community-scale hazard risk maps. The maps depict hazard risk in stoplight colours for easy interpretation, and support community-based, future-focused adaptation planning. Communities, First Nations, consultants and local regulatory agencies have used the hazard risk maps to site small-scale infrastructure projects, guide land planning processes, and assess suitability of land development applications. However, we know that assessing risk is only one step in integrating the implications of permafrost degradation in societal responses to environmental change. To build on our permafrost hazard risk maps, we are integrating economic principles and traditional land use elements. To assess economic implications of adaptation to permafrost change, we are working with geotechnical engineers to identify adaptation options (e.g., modified building techniques, permafrost thaw mitigation approaches) that suit the risks captured by our existing hazard risk maps. We layer this with an economic analysis of the costs associated with identified adaptation options, providing end-users with a more comprehensive basis upon which to make decisions related to infrastructure. NCE researchers have also integrated traditional land use activities in assessments of permafrost thaw risk, in a project led by Jean Marie River First Nation in the Northwest Territories. Here, the implications of permafrost degradation on food security and land use priorities were assessed by layering key game and gathering areas on permafrost thaw vulnerability maps. Results indicated that close to one quarter of big and small game habitats, and close to twenty percent of key furbearer and gathering areas within the First Nation

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia.

PubMed

Kumar, Manoj; van Elsas, Jan Dirk; Nissinen, Riitta

2017-01-01

Arctic and alpine biomes are most often strongly nitrogen-limited, and hence biological nitrogen fixation is a strong driver of these ecosystems. Both biomes are characterized by low temperatures and short growing seasons, but they differ in seasonality of solar radiation and in soil water balance due to underlying permafrost in the Arctic. Arcto-alpine plant species are well-adapted to the low temperatures that prevail in their habitats, and plant growth is mainly limited by the availability of nutrients, in particular nitrogen, due to slow mineralization. Nitrogen fixing bacteria are likely important for plant growth in these habitats, but very little is known of these bacteria or forces shaping their communities. In this study, we characterized the potential nitrogen fixing bacterial (PNFB) communities associated with two arcto-alpine pioneer plant species, Oxyria digyna (mountain sorrel) and Saxifraga oppositifolia (blue saxifrage), in three climate regions. Both of these plants readily colonize low nutrient mineral soils. Our goal was to investigate how climate (region) and, on the other hand, host plant and plant species shape these communities. To our knowledge, this is the first comprehensive study describing PNFB communities associated with pioneer plants in different arcto-alpine biomes. Replicate samples were taken from two arctic regions, Kilpisjärvi and Ny-Ålesund, and one alpine region, Mayrhofen. In these, the PNFB communities in the bulk and rhizosphere soils and the plant endospheres were characterized by nifH -targeted PCR and massive parallel sequencing. The data revealed strong effects of climatic region on the dominating nitrogen fixers. Specifically, nifH sequences related to Geobacter (δ- Proteobacteria ) were present in high relative abundances in the nitrogen-fixing communities in the Mayrhofen and Kilpisjärvi regions, while members of the Clostridiales prevailed in the Kilpisjärvi and Ny-Ålesund regions. The bulk and rhizosphere soil

Diversity and survivability of microbial community in ancient permafrost sediment of northeast Siberia

NASA Astrophysics Data System (ADS)

Liang, R.; Lau, M.; Vishnivetskaya, T. A.; Lloyd, K. G.; Pfiffner, S. M.; Rivkina, E.; Onstott, T. C.

2017-12-01

The prevalence of microorganisms in frozen permafrost has been well documented in ancient sediment up to several million years old. However, the long term survivability and metabolic activity of microbes over geological timespans remain underexplored. Siberian permafrost sediment was collected at various depths (1.4m, 11.8 m and 24.8m) to represent a wide range of geological time from thousands to millions of years. Extracellular (eDNA) and intracellular DNA (iDNA) was simultaneously recovered for sequencing to characterize the potentially extinct and extant microbial community. Additionally, aspartic acid racemization assay (D/L Asp) was used to infer the metabolic activity of microbes in ancient permafrost. As compared with the young sample (1.4m), DNA yield and content of aspartic acid dramatically decreased in old samples (11.8m and 24.8m). However, D/L Asp and eDNA/iDNA significantly increased with the geological age. Such findings suggested that ancient microbiomes might be subjected to racemization or even DNA/proteins degradation at subzero temperature over the wide geological time scale. Preliminary characterization of microbial community indicated that the majority of sequences in old samples were identified as bacteria and only a small fraction was identified as archaea from the iDNA pool. While the eDNA and iDNA fractions shared similar dominant taxa at phylum level, the relative abundance of Proteobacteria in eDNA library was much higher than iDNA. By contrast, the phylum affiliated with Firmicutes was more numerically abundant in the iDNA fraction. More dramatic differences were observed between eDNA and iDNA library at lower taxonomic levels. Particularly, the microbial lineages affiliated with the genera Methanoregula, Desulfosporosinus and Syntrophomonas were only detected in the iDNA library. Such taxonomic difference between the relic eDNA and iDNA suggested that numerous species become locally "extinct" whereas many other taxa might survive in

Evaluation of Offline Models Used to Simulate Components of the Permafrost Carbon Feedback: Experience from the Permafrost Carbon Network Model Integration Group

NASA Astrophysics Data System (ADS)

McGuire, A. D.

2016-12-01

The Model Integration Group of the Permafrost Carbon Network (see http://www.permafrostcarbon.org/) has conducted studies to evaluate the sensitivity of offline terrestrial permafrost and carbon models to both historical and projected climate change. These studies indicate that there is a wide range of (1) initial states permafrost extend and carbon stocks simulated by these models and (2) responses of permafrost extent and carbon stocks to both historical and projected climate change. In this study, we synthesize what has been learned about the variability in initial states among models and the driving factors that contribute to variability in the sensitivity of responses. We conclude the talk with a discussion of efforts needed by (1) the modeling community to standardize structural representation of permafrost and carbon dynamics among models that are used to evaluate the permafrost carbon feedback and (2) the modeling and observational communities to jointly develop data sets and methodologies to more effectively benchmark models.

PYRN-Bib: The Permafrost Young Researchers Network Bibliography of Permafrost-Related Degree-Earning Theses

NASA Astrophysics Data System (ADS)

Grosse, Guido; Lantuit, Hugues; Gärtner-Roer, Isabelle

2010-05-01

PYRN-Bib is an international bibliographical database aiming at collecting and distributing information on all theses submitted for earning a scientific degree in permafrost-related research. PYRN-Bib is hosted by the Permafrost Young Researchers Network (PYRN, http://pyrn.ways.org), an international network of early career students and young scientists in permafrost related research with currently more than 750 members. The fully educational, non-profit project PYRN-Bib is published under the patronage of the International Permafrost Association (IPA). The bibliography covers all theses as long as they clearly treat aspects of permafrost research from such diverse fields as: Geophysics, Geology, Cryolithology, Biology, Biogeochemistry, Microbiology, Astrobiology, Chemistry, Engineering, Geomorphology, Remote Sensing, Modeling, Mineral and Hydrocarbon Exploration, and Science History and Education. The specific goals of PYRN-Bib are (1) to generate a comprehensive database that includes all degree-earning theses (e.g. Diploma, Ph.D., Master, etc.), coming from any country and any scientific field, under the single condition that the thesis is strongly related to research on permafrost and/or periglacial processes; (2) to reference unique but buried sources of information including theses published in languages other than English; (3) to make the database widely available to the scientific community and the general public; (4) to solicit PYRN membership; and (5) to provide a mean to map the evolution of permafrost research over the last decades, including regional trends, shifts in research direction, and/or the place of permafrost research in society. PYRN-Bib is available online and maintained by PYRN. The complete bibliography can be downloaded at no cost and is offered in different file formats: tagged Endnote library, XML, BibTex, and PDF. New entries are continuously provided by PYRN members and the scientific community. PYRN-Bib currently contains more than

In situ permafrost thaw due to climate change drives holistic microbial community shifts with implications for methane cycling

NASA Astrophysics Data System (ADS)

Mondav, Rhiannon; McCalley, Carmody; Hodgkins, Suzanne; Rich, Virginia; Frolking, Steve; Saleska, Scott; Barnes, Andrew; Chanton, Jeff; Crill, Patrick

2014-05-01

Thawing permafrost is a potentially significant source of radiative forcing feedback due to increased emissions of methane, a biogenic greenhouse gas (GHG). This study investigated changes in the microbial community along a permafrost thaw gradient at Stordalen Mire, Sweden using 16S rRNA gene amplicon and metagenomic methods. In situ measurements of geochemical parameters, including CH4 and C isotopes, enabled linkage of community dynamics to significant shifts in C balance. The thaw gradient ranged from intact at a palsa (low productivity and GHG emissions), through partially thawed in a bog (high productivity, low GHG emissions) to a completely thawed fen (high productivity and GHG emissions). Microbial assemblages in both the palsa and fen were highly diverse (in both richness and evenness), consistent with climax communities. The microbial community in the bog had distinctly lower diversity, characteristic of ecosystem disturbance. The palsa community was dominated by Acidobacteria and Proteobacteria, as is typical of a range of soils including permafrost. Methanogens dominated both the bog and fen and were most abundant within the zone of water table fluctuation. Inferring methanogens' production pathway from phylogeny showed a shift from mostly hydrogenotrophic methanogens in the bog towards acetotrophic methanogens in the fen. This corroborated porewater and flux emitted CH4 and CO2 carbon isotopic 13C signatures of CH4 and CO2. The fen, where the highest CH4 flux was recorded, was significantly richer in methanogenic archaea. A novel archaea, Candidatus Methanoflorens stordalenmirensis, was present at up to 70% relative abundance in the bog, enabling recovery of a population genome. The genome (and associated metaproteome) of 'M. stordalenmirensis' indicates that hydrogenotrophic methane production is its main energy conservation pathway. 'Methanoflorens' may be an indicator species of permafrost thaw, it is globally ubiquitous, and appears a major

Permafrost conditions at the Upper Kuskokwim river area and its influence on local communities.

NASA Astrophysics Data System (ADS)

Kholodov, A. L.; Panda, S. K.; Hanson, T.

2017-12-01

layer thickness will lead to permafrost degradation and initiate thermokarst process or dryness of the area that increases risk of wild fires. Also, shallow soil freezing within wetlands makes shorter the safe period of snow machines operation. Current research should help local communities make more informed decisions in adaptation of resources management and land use.

Development of a Permafrost Modeling Cyberinfrastructure

NASA Astrophysics Data System (ADS)

Overeem, I.; Jafarov, E. E.; Piper, M.; Schaefer, K. M.

2016-12-01

Permafrost is seen as an essential Arctic climate indicator, and feedback of thawing permafrost to the global climate system through the impacts on the global carbon cycle remain an important research topic. Observations can assess the current state of permafrost, but models are eventually essential to make predictions of future permafrost extent. The purpose of our project, which we call PermaModel, is to develop an easy-to-access and comprehensive cyberinfrastructure aimed at promoting and improving permafrost modeling. The PermaModel Integrated Modeling Toolbox (IMT) includes three permafrost models of increasing complexity. The IMT will be housed within the existing cyberinfrastructure of the Community Surface Dynamics Modeling System (CSDMS), and made publically accessible through the CSDMS Web Modeling Tool (WMT). The WMT will provide easy online access to students, scientists, and stakeholders who want to use permafrost models, but lack the expertise. We plan to include multiple sets of sample inputs, representing a variety of conditions and locations, to enable immediate use of the IMT. We present here the first permafrost model, which is envisioned to be the most suitable for teaching purposes. The model promotes understanding of a 1D heat equation and permafrost active layer dynamics under monthly temperature/climate drivers in an online environment. Modeling labs are presented through the CSDMS Educational Repository and we solicit feedback from faculty for further design of these resources.

Bacterial Community Succession in Pine-Wood Decomposition.

PubMed

Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

Bacterial Community Succession in Pine-Wood Decomposition

PubMed Central

Kielak, Anna M.; Scheublin, Tanja R.; Mendes, Lucas W.; van Veen, Johannes A.; Kuramae, Eiko E.

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities. PMID:26973611

Bacterial communities in floral nectar.

PubMed

Fridman, Svetlana; Izhaki, Ido; Gerchman, Yoram; Halpern, Malka

2012-02-01

Floral nectar is regarded as the most important reward available to animal-pollinated plants to attract pollinators. Despite the vast amount of publications on nectar properties, the role of nectar as a natural bacterial habitat is yet unexplored. To gain a better understanding of bacterial communities inhabiting floral nectar, culture-dependent and -independent (454-pyrosequencing) methods were used. Our findings demonstrate that bacterial communities in nectar are abundant and diverse. Using culture-dependent method we showed that bacterial communities of nectar displayed significant variation among three plant species: Amygdalus communis, Citrus paradisi and Nicotiana glauca. The dominant class in the nectar bacterial communities was Gammaproteobacteria. About half of the isolates were novel species (< 97% similarities of the 16S rRNA gene with known species). Using 454-pyrosequencing we demonstrated that nectar microbial community are distinct for each of the plant species while there are no significant differences between nectar microbial communities within nectars taken from different plants of the same species. Primary selection of the nectar bacteria is unclear; it may be affected by variations in the chemical composition of the nectar in each plant. The role of the rich and diverse nectar microflora in the attraction-repulsion relationships between the plant and its nectar consumers has yet to be explored. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Community-acquired bacterial meningitis.

PubMed

van de Beek, Diederik; Brouwer, Matthijs; Hasbun, Rodrigo; Koedel, Uwe; Whitney, Cynthia G; Wijdicks, Eelco

2016-11-03

Meningitis is an inflammation of the meninges and subarachnoid space that can also involve the brain cortex and parenchyma. It can be acquired spontaneously in the community - community-acquired bacterial meningitis - or in the hospital as a complication of invasive procedures or head trauma (nosocomial bacterial meningitis). Despite advances in treatment and vaccinations, community-acquired bacterial meningitis remains one of the most important infectious diseases worldwide. Streptococcus pneumoniae and Neisseria meningitidis are the most common causative bacteria and are associated with high mortality and morbidity; vaccines targeting these organisms, which have designs similar to the successful vaccine that targets Haemophilus influenzae type b meningitis, are now being used in many routine vaccination programmes. Experimental and genetic association studies have increased our knowledge about the pathogenesis of bacterial meningitis. Early antibiotic treatment improves the outcome, but the growing emergence of drug resistance as well as shifts in the distribution of serotypes and groups are fuelling further development of new vaccines and treatment strategies. Corticosteroids were found to be beneficial in high-income countries depending on the bacterial species. Further improvements in the outcome are likely to come from dampening the host inflammatory response and implementing preventive measures, especially the development of new vaccines.

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.

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest.

PubMed

Taş, Neslihan; Prestat, Emmanuel; McFarland, Jack W; Wickland, Kimberley P; Knight, Rob; Berhe, Asmeret Asefaw; Jorgenson, Torre; Waldrop, Mark P; Jansson, Janet K

2014-09-01

Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the dynamics of C release from these soils requires us to account for the impact of wildfires, which are increasing in frequency as the climate changes. Boreal wildfires contribute to global emission of greenhouse gases (GHG-CO2, CH4 and N2O) and indirectly result in the thawing of near-surface permafrost. In this study, we aimed to define the impact of fire on soil microbial communities and metabolic potential for GHG fluxes in samples collected up to 1 m depth from an upland black spruce forest near Nome Creek, Alaska. We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing. We found that soil moisture, C content and the potential for respiration were reduced by fire, as were microbial community diversity and metabolic potential. There were shifts in dominance of several microbial community members, including a higher abundance of candidate phylum AD3 after fire. The metagenome data showed that fire had a pervasive impact on genes involved in carbohydrate metabolism, methanogenesis and the nitrogen cycle. Although fire resulted in an immediate release of CO2 from surface soils, our results suggest that the potential for emission of GHG was ultimately reduced at all soil depths over the longer term. Because of the size of the permafrost C reservoir, these results are crucial for understanding whether fire produces a positive or negative feedback loop contributing to the global C cycle.

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest

PubMed Central

Taş, Neslihan; Prestat, Emmanuel; McFarland, Jack W; Wickland, Kimberley P; Knight, Rob; Berhe, Asmeret Asefaw; Jorgenson, Torre; Waldrop, Mark P; Jansson, Janet K

2014-01-01

Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the dynamics of C release from these soils requires us to account for the impact of wildfires, which are increasing in frequency as the climate changes. Boreal wildfires contribute to global emission of greenhouse gases (GHG—CO2, CH4 and N2O) and indirectly result in the thawing of near-surface permafrost. In this study, we aimed to define the impact of fire on soil microbial communities and metabolic potential for GHG fluxes in samples collected up to 1 m depth from an upland black spruce forest near Nome Creek, Alaska. We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing. We found that soil moisture, C content and the potential for respiration were reduced by fire, as were microbial community diversity and metabolic potential. There were shifts in dominance of several microbial community members, including a higher abundance of candidate phylum AD3 after fire. The metagenome data showed that fire had a pervasive impact on genes involved in carbohydrate metabolism, methanogenesis and the nitrogen cycle. Although fire resulted in an immediate release of CO2 from surface soils, our results suggest that the potential for emission of GHG was ultimately reduced at all soil depths over the longer term. Because of the size of the permafrost C reservoir, these results are crucial for understanding whether fire produces a positive or negative feedback loop contributing to the global C cycle. PMID:24722629

Web-GIS visualisation of permafrost-related Remote Sensing products for ESA GlobPermafrost

NASA Astrophysics Data System (ADS)

Haas, A.; Heim, B.; Schaefer-Neth, C.; Laboor, S.; Nitze, I.; Grosse, G.; Bartsch, A.; Kaab, A.; Strozzi, T.; Wiesmann, A.; Seifert, F. M.

2016-12-01

The ESA GlobPermafrost (www.globpermafrost.info) provides a remote sensing service for permafrost research and applications. The service comprises of data product generation for various sites and regions as well as specific infrastructure allowing overview and access to datasets. Based on an online user survey conducted within the project, the user community extensively applies GIS software to handle remote sensing-derived datasets and requires preview functionalities before accessing them. In response, we develop the Permafrost Information System PerSys which is conceptualized as an open access geospatial data dissemination and visualization portal. PerSys will allow visualisation of GlobPermafrost raster and vector products such as land cover classifications, Landsat multispectral index trend datasets, lake and wetland extents, InSAR-based land surface deformation maps, rock glacier velocity fields, spatially distributed permafrost model outputs, and land surface temperature datasets. The datasets will be published as WebGIS services relying on OGC-standardized Web Mapping Service (WMS) and Web Feature Service (WFS) technologies for data display and visualization. The WebGIS environment will be hosted at the AWI computing centre where a geodata infrastructure has been implemented comprising of ArcGIS for Server 10.4, PostgreSQL 9.2 and a browser-driven data viewer based on Leaflet (http://leafletjs.com). Independently, we will provide an `Access - Restricted Data Dissemination Service', which will be available to registered users for testing frequently updated versions of project datasets. PerSys will become a core project of the Arctic Permafrost Geospatial Centre (APGC) within the ERC-funded PETA-CARB project (www.awi.de/petacarb). The APGC Data Catalogue will contain all final products of GlobPermafrost, allow in-depth dataset search via keywords, spatial and temporal coverage, data type, etc., and will provide DOI-based links to the datasets archived in the

Microorganisms Trapped Within Permafrost Ice In The Fox Permafrost Tunnel, Alaska

NASA Astrophysics Data System (ADS)

Katayama, T.; Tanaka, M.; Douglas, T. A.; Cai, Y.; Tomita, F.; Asano, K.; Fukuda, M.

2008-12-01

Several different types of massive ice are common in permafrost. Ice wedges are easily recognized by their shape and foliated structure. They grow syngenetically or epigenetically as a result of repeated cycles of frost cracking followed by the infiltration of snow, melt water, soil or other material into the open frost cracks. Material incorporated into ice wedges becomes frozen and preserved. Pool ice, another massive ice type, is formed by the freezing of water resting on top of frozen thermokarst sediment or melting wedges and is not foliated. The Fox Permafrost Tunnel in Fairbanks was excavated within the discontinuous permafrost zone of central Alaska and it contains permafrost, ice wedges, and pool ice preserved at roughly -3°C. We collected samples from five ice wedges and three pool ice structures in the Fox Permafrost Tunnel. If the microorganisms were incorporated into the ice during its formation, a community analysis of the microorganisms could elucidate the environment in which the ice was formed. Organic material from sediments in the tunnel was radiocarbon-dated between 14,000 and 30,000 years BP. However, it is still not clear when the ice wedges were formed or subsequently deformed because they are only partially exposed and their upper surfaces are above the tunnel walls. The objectives of our study were to determine the biogeochemical conditions during massive ice formation and to analyze the microbial community within the ices by incubation-based and DNA-based analyses. The geochemical profile and the PCR-DGGE band patterns of bacteria among five ice wedge and 3 portions of pool ice samples were markedly different. The DGGE band patterns of fungi were simple with a few bands of fungi or yeast. The dominant bands of ice wedge and pool ice samples were affiliated with the genus Geomyces and Doratomyces, respectively. Phylogenetic analysis using rRNA gene ITS regions indicated isolates of Geomyces spp. from different ice wedges were affiliated

Examining Environmental Gradients with Remotely Sensed Data - the ESA GlobPermafrost project

NASA Astrophysics Data System (ADS)

Bartsch, Annett; Grosse, Guido; Kääb, Andreas; Westermann, Sebastian; Strozzi, Tazio; Wiesmann, Andreas; Duguay, Claude; Seifert, Frank Martin; Obu, Jaroslav; Nitze, Ingmar; Heim, Birgit; Haas, Antoni; Widhalm, Barbara

2017-04-01

Permafrost cannot be directly detected from space, but many surface features of permafrost terrains and typical periglacial landforms are observable with a variety of EO sensors ranging from very high to medium resolution at various wavelengths. In addition, landscape dynamics associated with permafrost changes and geophysical variables relevant for characterizing the state of permafrost, such as land surface temperature or freeze-thaw state can be observed with space-based Earth Observation. Suitable regions to examine environmental gradients across the Arctic have been defined in a community white paper (Bartsch et al. 2014). These transects have been updated within the ESA DUE GlobPermafrost project. The ESA DUE GlobPermafrost project develops, validates and implements Earth Observation (EO) products to support research communities and international organisations in their work on better understanding permafrost characteristics and dynamics. Prototype product cases will cover different aspects of permafrost by integrating in situ measurements of subsurface properties and surface properties, Earth Observation, and modelling to provide a better understanding of permafrost today. The project will extend local process and permafrost monitoring to broader spatial domains, support permafrost distribution modelling, and help to implement permafrost landscape and feature mapping in a GIS framework. It will also complement active layer and thermal observing networks. Both lowland (latitudinal) and mountain (altitudinal) permafrost issues are addressed. The selected transects and first results will be presented. This includes identified needs from the user requirements survey, a review of existing land surface products available for the Arctic as well as prototypes of GlobPermafrost datasets, and the permafrost information system through which they can be accessed. Bartsch, Annett; Allard, Michel; Biskaborn, Boris Kolumban; Burba, George; Christiansen, Hanne H; Duguay

Polymicrobial airway bacterial communities in adult bronchiectasis patients

PubMed Central

2014-01-01

Background Chronic airway infection contributes to the underlying pathogenesis of non-cystic fibrosis bronchiectasis (NCFBr). In contrast to other chronic airway infections, associated with COPD and CF bronchiectasis, where polymicrobial communities have been implicated in lung damage due to the vicious circle of recurrent bacterial infections and inflammation, there is sparse information on the composition of bacterial communities in NCFBr. Seventy consecutive patients were recruited from an outpatient adult NCFBr clinic. Bacterial communities in sputum samples were analysed by culture and pyrosequencing approaches. Bacterial sequences were analysed using partial least square discrimination analyses to investigate trends in community composition and identify those taxa that contribute most to community variation. Results The lower airway in NCFBr is dominated by three bacterial taxa Pasteurellaceae, Streptococcaceae and Pseudomonadaceae. Moreover, the bacterial community is much more diverse than indicated by culture and contains significant numbers of other genera including anaerobic Prevotellaceae, Veillonellaceae and Actinomycetaceae. We found particular taxa are correlated with different clinical states, 27 taxa were associated with acute exacerbations, whereas 11 taxa correlated with stable clinical states. We were unable to demonstrate a significant effect of antibiotic therapy, gender, or lung function on the diversity of the bacterial community. However, presence of clinically significant culturable taxa; particularly Pseudomonas aeruginosa and Haemophilus influenzae correlated with a significant change in the diversity of the bacterial community in the lung. Conclusions We have demonstrated that acute exacerbations, the frequency of exacerbation and episodes of clinical stability are correlated, in some patients, with a significantly different bacterial community structure, that are associated with a presence of particular taxa in the NCFBr lung. Moreover

Methanogen community composition and rates of methane consumption in Canadian High Arctic permafrost soils.

PubMed

Allan, J; Ronholm, J; Mykytczuk, N C S; Greer, C W; Onstott, T C; Whyte, L G

2014-04-01

Increasing permafrost thaw, driven by climate change, has the potential to result in organic carbon stores being mineralized into carbon dioxide (CO2) and methane (CH4) through microbial activity. This study examines the effect of increasing temperature on community structure and metabolic activity of methanogens from the Canadian High Arctic, in an attempt to predict how warming will affect microbially controlled CH4 soil flux. In situ CO2 and CH4 flux, measured in 2010 and 2011 from ice-wedge polygons, indicate that these soil formations are a net source of CO2 emissions, but a CH4 sink. Permafrost and active layer soil samples were collected at the same sites and incubated under anaerobic conditions at warmer temperatures, with and without substrate amendment. Gas flux was measured regularly and indicated an increase in CH4 flux after extended incubation. Pyrosequencing was used to examine the effects of an extended thaw cycle on methanogen diversity and the results indicate that in situ methanogen diversity, based on the relative abundance of the 16S ribosomal ribonucleic acid (rRNA) gene associated with known methanogens, is higher in the permafrost than in the active layer. Methanogen diversity was also shown to increase in both the active layer and permafrost soil after an extended thaw. This study provides evidence that although High Arctic ice-wedge polygons are currently a sink for CH4, higher arctic temperatures and anaerobic conditions, a possible result of climate change, could result in this soil becoming a source for CH4 gas flux. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic alaska

DOE PAGES

Kao-Kniffin, J.; Woodcroft, B. J.; Carver, S. M.; ...

2015-12-18

We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus ‘Methanoflorens stordalenmirensis’ were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the activemore » layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus ‘M. stordalenmirensis’ across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures.« less

Characterisation of the Permafrost Carbon Pool

USGS Publications Warehouse

Kuhry, P.; Grosse, G.; Harden, J.W.; Hugelius, G.; Koven, C.D.; Ping, C.-L.; Schirrmeister, L.; Tarnocai, C.

2013-01-01

The current estimate of the soil organic carbon (SOC) pool in the northern permafrost region of 1672 Petagrams (Pg) C is much larger than previously reported and needs to be incorporated in global soil carbon (C) inventories. The Northern Circumpolar Soil Carbon Database (NCSCD), extended to include the range 0–300 cm, is now available online for wider use by the scientific community. An important future aim is to provide quantitative uncertainty ranges for C pool estimates. Recent studies have greatly improved understanding of the regional patterns, landscape distribution and vertical (soil horizon) partitioning of the permafrost C pool in the upper 3 m of soils. However, the deeper C pools in unconsolidated Quaternary deposits need to be better constrained. A general lability classification of the permafrost C pool should be developed to address potential C release upon thaw. The permafrost C pool and its dynamics are beginning to be incorporated into Earth System models, although key periglacial processes such as thermokarst still need to be properly represented to obtain a better quantification of the full permafrost C feedback on global climate change.

Interactive effects of wildfire and permafrost on microbial communities and soil processes in an Alaskan black spruce forest

USGS Publications Warehouse

Waldrop, M.P.; Harden, J.W.

2008-01-01

Boreal forests contain significant quantities of soil carbon that may be oxidized to CO2 given future increases in climate warming and wildfire behavior. At the ecosystem scale, decomposition and heterotrophic respiration are strongly controlled by temperature and moisture, but we questioned whether changes in microbial biomass, activity, or community structure induced by fire might also affect these processes. We particularly wanted to understand whether postfire reductions in microbial biomass could affect rates of decomposition. Additionally, we compared the short-term effects of wildfire to the long-term effects of climate warming and permafrost decline. We compared soil microbial communities between control and recently burned soils that were located in areas with and without permafrost near Delta Junction, AK. In addition to soil physical variables, we quantified changes in microbial biomass, fungal biomass, fungal community composition, and C cycling processes (phenol oxidase enzyme activity, lignin decomposition, and microbial respiration). Five years following fire, organic surface horizons had lower microbial biomass, fungal biomass, and dissolved organic carbon (DOC) concentrations compared with control soils. Reductions in soil fungi were associated with reductions in phenol oxidase activity and lignin decomposition. Effects of wildfire on microbial biomass and activity in the mineral soil were minor. Microbial community composition was affected by wildfire, but the effect was greater in nonpermafrost soils. Although the presence of permafrost increased soil moisture contents, effects on microbial biomass and activity were limited to mineral soils that showed lower fungal biomass but higher activity compared with soils without permafrost. Fungal abundance and moisture were strong predictors of phenol oxidase enzyme activity in soil. Phenol oxidase enzyme activity, in turn, was linearly related to both 13C lignin decomposition and microbial respiration

Why Permafrost Is Thawing, Not Melting

NASA Astrophysics Data System (ADS)

Grosse, Guido; Romanovsky, Vladimir; Nelson, Frederick E.; Brown, Jerry; Lewkowicz, Antoni G.

2010-03-01

As global climate change is becoming an increasingly important political and social issue, it is essential for the cryospheric and global change research communities to speak with a single voice when using basic terminology to communicate research results and describe underlying physical processes. Experienced science communicators have highlighted the importance of using the correct terms to communicate research results to the media and general public [e.g., Akasofu, 2008; Hassol, 2008]. The consequences of scientists using improper terminology are at best oversimplification, but they more likely involve misunderstandings of the facts by the public. A glaring example of scientifically incorrect terminology appearing frequently in scientific and public communication relates to reports on the degradation of permafrost. Numerous research papers have appeared in recent years, broadly echoed in the news media, describing the “melting of permafrost,” its effects in the Arctic, and its feedbacks on climate through the carbon cycle. Although permafrost researchers have attempted to distinguish between the appropriate term “permafrost thawing” and the erroneous “permafrost melting” [e.g., van Everdingen, 2005; French, 2002], the latter is still used widely. A Web-based search using the phrase “permafrost melting” reveals hundreds of occurrences, many from highly regarded news and scientific organizations, including Reuters, New Scientist, ABC, The Guardian, Discovery News, Smithsonian magazine, the National Science Foundation, and others.

Distinct microbial communities associated with buried soils in the Siberian tundra

PubMed Central

Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Mikutta, Robert; Owens, Sarah; Gilbert, Jack; Schnecker, Jörg; Wild, Birgit; Hannisdal, Bjarte; Maerz, Joeran; Lashchinskiy, Nikolay; Čapek, Petr; Šantrůčková, Hana; Gentsch, Norman; Shibistova, Olga; Guggenberger, Georg; Richter, Andreas; Torsvik, Vigdis L; Schleper, Christa; Urich, Tim

2014-01-01

Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze–thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes. PMID:24335828

Dietary and developmental shifts in butterfly-associated bacterial communities

PubMed Central

2018-01-01

Bacterial communities associated with insects can substantially influence host ecology, evolution and behaviour. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analysed bacterial communities of 12 butterfly species across different developmental stages, using amplicon sequencing of the 16S rRNA gene. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, only few species showed significant dietary and developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species and family identity, potentially due to dietary and physiological variation across the host phylogeny. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbour distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities across all butterfly hosts. PMID:29892359

Variability in the sensitivity among model simulations of permafrost and carbon dynamics in the permafrost region between 1960 and 2009

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

McGuire, A. David; Koven, Charles; Lawrence, David M.

A significant portion of the large amount of carbon (C) currently stored in soils of the permafrost region in the Northern Hemisphere has the potential to be emitted as the greenhouse gases CO 2 and CH 4 under a warmer climate. In this study we evaluated the variability in the sensitivity of permafrost and C in recent decades among land surface model simulations over the permafrost region between 1960 and 2009. The 15 model simulations all predict a loss of near-surface permafrost (within 3 m) area over the region, but there are large differences in the magnitude of the simulatedmore » rates of loss among the models (0.2 to 58.8 × 10 3 km 2 yr –1). Sensitivity simulations indicated that changes in air temperature largely explained changes in permafrost area, although interactions among changes in other environmental variables also played a role. All of the models indicate that both vegetation and soil C storage together have increased by 156 to 954 Tg C yr –1 between 1960 and 2009 over the permafrost region even though model analyses indicate that warming alone would decrease soil C storage. Increases in gross primary production (GPP) largely explain the simulated increases in vegetation and soil C. The sensitivity of GPP to increases in atmospheric CO 2 was the dominant cause of increases in GPP across the models, but comparison of simulated GPP trends across the 1982–2009 period with that of a global GPP data set indicates that all of the models overestimate the trend in GPP. Disturbance also appears to be an important factor affecting C storage, as models that consider disturbance had lower increases in C storage than models that did not consider disturbance. Furthermore, to improve the modeling of C in the permafrost region, there is the need for the modeling community to standardize structural representation of permafrost and carbon dynamics among models that are used to evaluate the permafrost C feedback and for the modeling and observational

Variability in the sensitivity among model simulations of permafrost and carbon dynamics in the permafrost region between 1960 and 2009

DOE PAGES

McGuire, A. David; Koven, Charles; Lawrence, David M.; ...

2016-07-08

A significant portion of the large amount of carbon (C) currently stored in soils of the permafrost region in the Northern Hemisphere has the potential to be emitted as the greenhouse gases CO 2 and CH 4 under a warmer climate. In this study we evaluated the variability in the sensitivity of permafrost and C in recent decades among land surface model simulations over the permafrost region between 1960 and 2009. The 15 model simulations all predict a loss of near-surface permafrost (within 3 m) area over the region, but there are large differences in the magnitude of the simulatedmore » rates of loss among the models (0.2 to 58.8 × 10 3 km 2 yr –1). Sensitivity simulations indicated that changes in air temperature largely explained changes in permafrost area, although interactions among changes in other environmental variables also played a role. All of the models indicate that both vegetation and soil C storage together have increased by 156 to 954 Tg C yr –1 between 1960 and 2009 over the permafrost region even though model analyses indicate that warming alone would decrease soil C storage. Increases in gross primary production (GPP) largely explain the simulated increases in vegetation and soil C. The sensitivity of GPP to increases in atmospheric CO 2 was the dominant cause of increases in GPP across the models, but comparison of simulated GPP trends across the 1982–2009 period with that of a global GPP data set indicates that all of the models overestimate the trend in GPP. Disturbance also appears to be an important factor affecting C storage, as models that consider disturbance had lower increases in C storage than models that did not consider disturbance. Furthermore, to improve the modeling of C in the permafrost region, there is the need for the modeling community to standardize structural representation of permafrost and carbon dynamics among models that are used to evaluate the permafrost C feedback and for the modeling and observational

Variability in the sensitivity among model simulations of permafrost and carbon dynamics in the permafrost region between 1960 and 2009

USGS Publications Warehouse

McGuire, A. David; Koven, Charles; Lawrence, David M.; Clein, Joy S.; Xia, Jiangyang; Beer, Christian; Burke, Eleanor J.; Chen, Guangsheng; Chen, Xiaodong; Delire, Christine; Jafarov, Elchin; MacDougall, Andrew H.; Marchenko, Sergey S.; Nicolsky, Dmitry J.; Peng, Shushi; Rinke, Annette; Saito, Kazuyuki; Zhang, Wenxin; Alkama, Ramdane; Bohn, Theodore J.; Ciais, Philippe; Decharme, Bertrand; Ekici, Altug; Gouttevin, Isabelle; Hajima, Tomohiro; Hayes, Daniel J.; Ji, Duoying; Krinner, Gerhard; Lettenmaier, Dennis P.; Luo, Yiqi; Miller, Paul A.; Moore, John C.; Romanovsky, Vladimir; Schädel, Christina; Schaefer, Kevin; Schuur, Edward A.G.; Smith, Benjamin; Sueyoshi, Tetsuo; Zhuang, Qianlai

2016-01-01

A significant portion of the large amount of carbon (C) currently stored in soils of the permafrost region in the Northern Hemisphere has the potential to be emitted as the greenhouse gases CO2and CH4 under a warmer climate. In this study we evaluated the variability in the sensitivity of permafrost and C in recent decades among land surface model simulations over the permafrost region between 1960 and 2009. The 15 model simulations all predict a loss of near-surface permafrost (within 3 m) area over the region, but there are large differences in the magnitude of the simulated rates of loss among the models (0.2 to 58.8 × 103 km2 yr−1). Sensitivity simulations indicated that changes in air temperature largely explained changes in permafrost area, although interactions among changes in other environmental variables also played a role. All of the models indicate that both vegetation and soil C storage together have increased by 156 to 954 Tg C yr−1between 1960 and 2009 over the permafrost region even though model analyses indicate that warming alone would decrease soil C storage. Increases in gross primary production (GPP) largely explain the simulated increases in vegetation and soil C. The sensitivity of GPP to increases in atmospheric CO2 was the dominant cause of increases in GPP across the models, but comparison of simulated GPP trends across the 1982–2009 period with that of a global GPP data set indicates that all of the models overestimate the trend in GPP. Disturbance also appears to be an important factor affecting C storage, as models that consider disturbance had lower increases in C storage than models that did not consider disturbance. To improve the modeling of C in the permafrost region, there is the need for the modeling community to standardize structural representation of permafrost and carbon dynamics among models that are used to evaluate the permafrost C feedback and for the modeling and observational communities to

Microbial diversity in European alpine permafrost and active layers.

PubMed

Frey, Beat; Rime, Thomas; Phillips, Marcia; Stierli, Beat; Hajdas, Irka; Widmer, Franco; Hartmann, Martin

2016-03-01

Permafrost represents a largely understudied genetic resource. Thawing of permafrost with global warming will not only promote microbial carbon turnover with direct feedback on greenhouse gases, but also unlock an unknown microbial diversity. Pioneering metagenomic efforts have shed light on the permafrost microbiome in polar regions, but temperate mountain permafrost is largely understudied. We applied a unique experimental design coupled to high-throughput sequencing of ribosomal markers to characterize the microbiota at the long-term alpine permafrost study site 'Muot-da-Barba-Peider' in eastern Switzerland with an approximate radiocarbon age of 12 000 years. Compared to the active layers, the permafrost community was more diverse and enriched with members of the superphylum Patescibacteria (OD1, TM7, GN02 and OP11). These understudied phyla with no cultured representatives proposedly feature small streamlined genomes with reduced metabolic capabilities, adaptations to anaerobic fermentative metabolisms and potential ectosymbiotic lifestyles. The permafrost microbiota was also enriched with yeasts and lichenized fungi known to harbour various structural and functional adaptation mechanisms to survive under extreme sub-zero conditions. These data yield an unprecedented view on microbial life in temperate mountain permafrost, which is increasingly important for understanding the biological dynamics of permafrost in order to anticipate potential ecological trajectories in a warming world. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Spatial distribution of marine airborne bacterial communities

PubMed Central

Seifried, Jasmin S; Wichels, Antje; Gerdts, Gunnar

2015-01-01

The spatial distribution of bacterial populations in marine bioaerosol samples was investigated during a cruise from the North Sea to the Baltic Sea via Skagerrak and Kattegat. The analysis of the sampled bacterial communities with a pyrosequencing approach revealed that the most abundant phyla were represented by the Proteobacteria (49.3%), Bacteroidetes (22.9%), Actinobacteria (16.3%), and Firmicutes (8.3%). Cyanobacteria were assigned to 1.5% of all bacterial reads. A core of 37 bacterial OTUs made up more than 75% of all bacterial sequences. The most abundant OTU was Sphingomonas sp. which comprised 17% of all bacterial sequences. The most abundant bacterial genera were attributed to distinctly different areas of origin, suggesting highly heterogeneous sources for bioaerosols of marine and coastal environments. Furthermore, the bacterial community was clearly affected by two environmental parameters – temperature as a function of wind direction and the sampling location itself. However, a comparison of the wind directions during the sampling and calculated backward trajectories underlined the need for more detailed information on environmental parameters for bioaerosol investigations. The current findings support the assumption of a bacterial core community in the atmosphere. They may be emitted from strong aerosolizing sources, probably being mixed and dispersed over long distances. PMID:25800495

Minerals in soil select distinct bacterial communities in their microhabitats.

PubMed

Carson, Jennifer K; Campbell, Louise; Rooney, Deirdre; Clipson, Nicholas; Gleeson, Deirdre B

2009-03-01

We tested the hypothesis that different minerals in soil select distinct bacterial communities in their microhabitats. Mica (M), basalt (B) and rock phosphate (RP) were incubated separately in soil planted with Trifolium subterraneum, Lolium rigidum or left unplanted. After 70 days, the mineral and soil fractions were separated by sieving. Automated ribosomal intergenic spacer analysis was used to determine whether the bacterial community structure was affected by the mineral, fraction and plant treatments. Principal coordinate plots showed clustering of bacterial communities from different fraction and mineral treatments, but not from different plant treatments. Permutational multivariate anova (permanova) showed that the microhabitats of M, B and RP selected bacterial communities different from each other in unplanted and L. rigidum, and in T. subterraneum, bacterial communities from M and B differed (P<0.046). permanova also showed that each mineral fraction selected bacterial communities different from the surrounding soil fraction (P<0.05). This study shows that the structure of bacterial communities in soil is influenced by the mineral substrates in their microhabitat and that minerals in soil play a greater role in bacterial ecology than simply providing an inert matrix for bacterial growth. This study suggests that mineral heterogeneity in soil contributes to the spatial variation in bacterial communities.

Determinants of bacterial communities in Canadian agroforestry systems.

PubMed

Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

2016-06-01

Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Empowering the village communities for sustained observation of permafrost-related environmental changes, Upper Kuskokwim, Alaska

NASA Astrophysics Data System (ADS)

Panda, S. K.; Kholodov, A. L.; Hanson, T.

2016-12-01

A suite of environmental changes are underway in the North directly affecting the socio-economic state of native communities in remote Arctic villages. We cannot possibly have enough scientists and professionals on the ground to timely predict and effectively respond to the major changes. We believe the most cost-effective and possibly sustainable approach to cover more ground for monitoring and prediction of changes is by building community capacity for monitoring and research, and supporting communities to use resulting data and new findings to address emerging environmental issues and ensuing socio-economic challenges. The goal of this project is to help the communities of Upper Kuskokwim region take the lead in assessing and responding to the environmental changes that are coming with warmer climate and thawing permafrost. The permafrost related societal impacts that the communities are aware of are a) drying of lakes which affect their fishing and trapping, b) lower water level in Rivers due to bank erosion which affect their main mode of transportation in summer, c) appearance of sinkholes that pose threat to the safety of the community members and their properties, and d) eruption of a sand dune in the middle of the Telida village air strip. In August 2016 we will spend ten days in the Nikolai and Telida communities to understand the community need for monitoring through a community survey. We will offer training workshop on climate science and landscape change, and in making scientific observation and data collection. Also, we will install sensors to monitor air temperature, soil temperature, soil moisture, and snow at 12 sites spread across different ecotypes and topographic settings. Also, we will survey sites of major change to help develop a geo-hazard map for the region to facilitate safe subsistence practices and land use. As broader impact, the project will offer the traditionally-underserved native communities of the Upper Kuskokwim region an

Metamorphosis of a butterfly-associated bacterial community.

PubMed

Hammer, Tobin J; McMillan, W Owen; Fierer, Noah

2014-01-01

Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

Metamorphosis of a Butterfly-Associated Bacterial Community

PubMed Central

Hammer, Tobin J.; McMillan, W. Owen; Fierer, Noah

2014-01-01

Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies. PMID:24466308

Organic carbon biolabilty increases with depth in a yedoma permafrost profile in Interior Alaska

NASA Astrophysics Data System (ADS)

Heslop, J. K.; Walter Anthony, K. M.; Spencer, R.; Winkel, M.; Zhang, M.; Liebner, S.; Podgorski, D. C.; Zito, P.; Kholodov, A. L.

2017-12-01

Permafrost organic carbon (OC) biolability is known to be controlled by both the OC molecular composition and redox state and the microbial community structure and its response to permafrost thaw. However, due to their complexity, both these mechanisms remain poorly understood. A substantial portion ( 16%) of global permafrost OC is stored in particularly deep, ice-rich permafrost deposits known as yedoma. We anaerobically incubated sediment from four depths in a 12-m yedoma profile in Interior Alaska with three treatments: control without amendment, inoculated with sediment from an adjacent thermokarst lake, and inoculated with sterilized lake sediment. We quantified CO2 and CH4 as end products of C mineralization, used qPCR to characterize the initial methanogenic communities, and used FT-ICR-MS to characterize the molecular composition of water-extractable organic matter at the beginning and end of the 154-d incubation. Proportions of aliphatics and peptides increased with depth in the permafrost profile, which would be consistent with long-term accumulation of anaerobic fermentation end products in yedoma-type permafrost. Moreover, these compounds positively correlated with anaerobic CO2 and CH4 production and their degradation rates corresponded to high proportions (53.3 ±41.9%) of OC mineralization, suggesting increasing proportions of these compounds with depth correspond to increasing OC quality and increased C mineralization per unit OC. Methanogenic communities were below detection limits in all controls. Following exposure to modern lake sediment microbial communities with detectable methanogens, we observed increases in anaerobic CO2 (65.1% ±75.2%) and CH4 (1,197% ±914%) production. The treatments with sterilized lake sediment did not contain detectable methanogens, and had increased anaerobic CO2 (52.6% ±69.2%) production but decreased CH4 (-74.1% ±33.8%) production. These preliminary results suggest anaerobic CH4 production is limited by ancient

Temperature effects on net greenhouse gas production and bacterial communities in arctic thaw ponds.

PubMed

Negandhi, Karita; Laurion, Isabelle; Lovejoy, Connie

2016-08-01

One consequence of High Arctic permafrost thawing is the formation of small ponds, which release greenhouse gases (GHG) from stored carbon through microbial activity. Under a climate with higher summer air temperatures and longer ice-free seasons, sediments of shallow ponds are likely to become warmer, which could influence enzyme kinetics or select for less cryophilic microbes. There is little data on the direct temperature effects on GHG production and consumption or on microbial communities' composition in Arctic ponds. We investigated GHG production over 16 days at 4°C and 9°C in sediments collected from four thaw ponds. Consistent with an enzymatic response, production rates of CO2 and CH4 were significantly greater at higher temperatures, with Q10 varying from 1.2 to 2.5. The bacterial community composition from one pond was followed through the incubation by targeting the V6-V8 variable regions of the 16S rRNA gene and 16S rRNA. Several rare taxa detected from rRNA accounted for significant community compositional changes. At the higher temperature, the relative community contribution from Bacteroidetes decreased by 15% with compensating increases in Betaproteobacteria, Alphaproteobacteria, Firmicutes, Acidobacteria, Verrucomicrobia and Actinobacteria. The increase in experimental GHG production accompanied by changes in community indicates an additional factor to consider in sediment environments when evaluating future climate scenarios. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bacterial community changes in an industrial algae production system.

PubMed

Fulbright, Scott P; Robbins-Pianka, Adam; Berg-Lyons, Donna; Knight, Rob; Reardon, Kenneth F; Chisholm, Stephen T

2018-04-01

While microalgae are a promising feedstock for production of fuels and other chemicals, a challenge for the algal bioproducts industry is obtaining consistent, robust algae growth. Algal cultures include complex bacterial communities and can be difficult to manage because specific bacteria can promote or reduce algae growth. To overcome bacterial contamination, algae growers may use closed photobioreactors designed to reduce the number of contaminant organisms. Even with closed systems, bacteria are known to enter and cohabitate, but little is known about these communities. Therefore, the richness, structure, and composition of bacterial communities were characterized in closed photobioreactor cultivations of Nannochloropsis salina in F/2 medium at different scales, across nine months spanning late summer-early spring, and during a sequence of serially inoculated cultivations. Using 16S rRNA sequence data from 275 samples, bacterial communities in small, medium, and large cultures were shown to be significantly different. Larger systems contained richer bacterial communities compared to smaller systems. Relationships between bacterial communities and algae growth were complex. On one hand, blooms of a specific bacterial type were observed in three abnormal, poorly performing replicate cultivations, while on the other, notable changes in the bacterial community structures were observed in a series of serial large-scale batch cultivations that had similar growth rates. Bacteria common to the majority of samples were identified, including a single OTU within the class Saprospirae that was found in all samples. This study contributes important information for crop protection in algae systems, and demonstrates the complex ecosystems that need to be understood for consistent, successful industrial algae cultivation. This is the first study to profile bacterial communities during the scale-up process of industrial algae systems.

Archaeal communities of Arctic methane-containing permafrost.

PubMed

Shcherbakova, Victoria; Yoshimura, Yoshitaka; Ryzhmanova, Yana; Taguchi, Yukihiro; Segawa, Takahiro; Oshurkova, Victoria; Rivkina, Elizaveta

2016-10-01

In the present study, we used culture-independent methods to investigate the diversity of methanogenic archaea and their distribution in five permafrost samples collected from a borehole in the Kolyma River Lowland (north-east of Russia). Total DNA was extracted from methane-containing permafrost samples of different age and amplified by PCR. The resulting DNA fragments were cloned. Phylogenetic analysis of the sequences showed the presence of archaea in all studied samples; 60%-95% of sequences belonged to the Euryarchaeota. Methanogenic archaea were novel representatives of Methanosarcinales, Methanomicrobiales, Methanobacteriales and Methanocellales orders. Bathyarchaeota (Miscellaneous Crenarchaeota Group) representatives were found among nonmethanogenic archaea in all the samples studied. The Thaumarchaeota representatives were not found in the upper sample, whereas Woesearchaeota (formerly DHVEG-6) were found in the three deepest samples. Unexpectedly, the greatest diversity of archaea was observed at a depth of 22.3 m, probably due to the availability of the labile organic carbon and/or due to the migration of the microbial cells during the freezing front towards the bottom. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial Insights into Shifting Methane Production Potential in Thawing Permafrost

NASA Astrophysics Data System (ADS)

Crossen, K.; Wilson, R.; Raab, N.; Neumann, R.; Chanton, J.; Saleska, S. R.; Rich, V. I.

2017-12-01

Permafrost, which stores 50% of global soil carbon, is thawing rapidly due to climate change, and resident microbes are contributing to changing carbon gas emissions. Predictions of the fate of carbon in these regions is poorly constrained; however, improved, careful mapping of microbial community members influencing CO2 and CH4 emissions will help clarify the system response to continued change. In order to more fully understand connections between the microbial communities, major geochemical transformations, and CO2 and CH4 emissions, peat cores were collected from the active layers of three permafrost habitats spanning a thaw gradient (collapsed palsa, bog, and fen) at Stordalen Mire, Abisko, Sweden. Anaerobic incubations of shallow and deep subsamples from these sites were performed, with time-course characterization of the changes in microbial communities, peat geochemistry, and carbon gas production. The latter were profiled with 16S rRNA amplicon sequencing, and targeted metagenomes. The communities within each habitat and depth were statistically distinct, and changed significantly over the course of the incubations. Acidobacteria was consistently the dominant bacterial phylum in all three habitat types. With increased thaw, the relative abundance of Actinobacteria tended to decrease, while Chloroflexi and Bacteroidetes increased with thaw. The relative abundance of methanogens increased with thaw and with depth within each habitat. Over time in the incubations, the richness of the communities tended to decrease. Homoacetogenesis (CO2 + H2 -> CH3COOH) has been documented in other peatlands, and homoacetogens can influence CH4 production by interacting with methanogens, competing with hydrogenotrophs while providing substrate for acetoclasts. Modelling of microbial reaction networks suggests potential for highest homoacetogenesis rates in the collapsed palsa, which also contains the highest relative abundances of lineages taxonomically affiliated with known

Microbial survival strategies in ancient permafrost: insights from metagenomics

USGS Publications Warehouse

Mackelprang, Rachel; Burkert, Alexander; Haw, Monica; Mahendrarajah, Tara; Conaway, Christopher H.; Douglas, Thomas A.; Waldrop, Mark P.

2017-01-01

In permafrost (perennially frozen ground) microbes survive oligotrophic conditions, sub-zero temperatures, low water availability and high salinity over millennia. Viable life exists in permafrost tens of thousands of years old but we know little about the metabolic and physiological adaptations to the challenges presented by life in frozen ground over geologic time. In this study we asked whether increasing age and the associated stressors drive adaptive changes in community composition and function. We conducted deep metagenomic and 16 S rRNA gene sequencing across a Pleistocene permafrost chronosequence from 19 000 to 33 000 years before present (kyr). We found that age markedly affected community composition and reduced diversity. Reconstruction of paleovegetation from metagenomic sequence suggests vegetation differences in the paleo record are not responsible for shifts in community composition and function. Rather, we observed shifts consistent with long-term survival strategies in extreme cryogenic environments. These include increased reliance on scavenging detrital biomass, horizontal gene transfer, chemotaxis, dormancy, environmental sensing and stress response. Our results identify traits that may enable survival in ancient cryoenvironments with no influx of energy or new materials.

Microbial survival strategies in ancient permafrost: insights from metagenomics.

PubMed

Mackelprang, Rachel; Burkert, Alexander; Haw, Monica; Mahendrarajah, Tara; Conaway, Christopher H; Douglas, Thomas A; Waldrop, Mark P

2017-10-01

In permafrost (perennially frozen ground) microbes survive oligotrophic conditions, sub-zero temperatures, low water availability and high salinity over millennia. Viable life exists in permafrost tens of thousands of years old but we know little about the metabolic and physiological adaptations to the challenges presented by life in frozen ground over geologic time. In this study we asked whether increasing age and the associated stressors drive adaptive changes in community composition and function. We conducted deep metagenomic and 16 S rRNA gene sequencing across a Pleistocene permafrost chronosequence from 19 000 to 33 000 years before present (kyr). We found that age markedly affected community composition and reduced diversity. Reconstruction of paleovegetation from metagenomic sequence suggests vegetation differences in the paleo record are not responsible for shifts in community composition and function. Rather, we observed shifts consistent with long-term survival strategies in extreme cryogenic environments. These include increased reliance on scavenging detrital biomass, horizontal gene transfer, chemotaxis, dormancy, environmental sensing and stress response. Our results identify traits that may enable survival in ancient cryoenvironments with no influx of energy or new materials.

Microbial survival strategies in ancient permafrost: insights from metagenomics

PubMed Central

Mackelprang, Rachel; Burkert, Alexander; Haw, Monica; Mahendrarajah, Tara; Conaway, Christopher H; Douglas, Thomas A; Waldrop, Mark P

2017-01-01

In permafrost (perennially frozen ground) microbes survive oligotrophic conditions, sub-zero temperatures, low water availability and high salinity over millennia. Viable life exists in permafrost tens of thousands of years old but we know little about the metabolic and physiological adaptations to the challenges presented by life in frozen ground over geologic time. In this study we asked whether increasing age and the associated stressors drive adaptive changes in community composition and function. We conducted deep metagenomic and 16 S rRNA gene sequencing across a Pleistocene permafrost chronosequence from 19 000 to 33 000 years before present (kyr). We found that age markedly affected community composition and reduced diversity. Reconstruction of paleovegetation from metagenomic sequence suggests vegetation differences in the paleo record are not responsible for shifts in community composition and function. Rather, we observed shifts consistent with long-term survival strategies in extreme cryogenic environments. These include increased reliance on scavenging detrital biomass, horizontal gene transfer, chemotaxis, dormancy, environmental sensing and stress response. Our results identify traits that may enable survival in ancient cryoenvironments with no influx of energy or new materials. PMID:28696425

Terrestrial Permafrost Models of Martian Habitats and Inhabitants

NASA Astrophysics Data System (ADS)

Gilichinsky, D.

2011-12-01

Martian permafrost is still 100 times older. Only one terrestrial environment is close to Mars in age - volcanoes in permafrost areas. The age of volcanic deposits frozen after eruption is much younger than the age of surrounding permafrost. Culture- and culture-independent methods show the presence of viable thermophiles and their genes within pyroclastic frozen material on Deception Island, Antarctica and Kamchatka peninsula. These bacteria and archeae have not been found in permafrost outside the volcanic areas. The only way for thermophiles to get into frozen soil is through deposition during eruption, i.e. the catastrophic geological events transport microbes from the depths to the surface and they survive at subzero temperatures. The past activity of Martian volcanoes periodically burned through the frozen strata and products of eruptions rose from the depths to the surface and froze. Images taken by the Stereo Camera on board the Mars Express discovered volcanoes 2-15Myr old that date back to ages close to permafrost on Earth. Terrestrial communities might serve as a model of inhabitants for these young volcanoes. 3. The only opportunity for free water on Mars is the overcooled water brines, and halo/psychrophilc community of Arctic cryopegs, sandwiched within permafrost, represents a plausible prototype for Martian microbial life.

Temporal variability of bacterial communities in cryoconite on an alpine glacier.

PubMed

Franzetti, Andrea; Navarra, Federico; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Minora, Umberto; Azzoni, Roberto Sergio; Diolaiuti, Guglielmina; Smiraglia, Claudio; Ambrosini, Roberto

2017-04-01

Cryoconite holes, that is, small ponds that form on glacier surface, are considered the most biologically active environments on glaciers. Bacterial communities in these environments have been extensively studied, but often through snapshot studies based on the assumption of a general stability of community structure. In this study, the temporal variation of bacterial communities in cryoconite holes on the Forni Glacier (Italian Alps) was investigated by high throughput DNA sequencing. A temporal change of bacterial communities was observed with autotrophic Cyanobacteria populations dominating communities after snowmelt, and heterotrophic Sphingobacteriales populations increasing in abundance later in the season. Bacterial communities also varied according to hole depth and area, amount of organic matter in the cryoconite and oxygen concentration. However, variation in environmental features explained a lower fraction of the variation in bacterial communities than temporal variation. Temporal change along ablation season seems therefore more important than local environmental conditions in shaping bacterial communities of cryoconite of the Forni Glacier. These findings challenge the assumption that bacterial communities of cryoconite holes are stable. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Long-term preservation of microbial ecosystems in permafrost

NASA Astrophysics Data System (ADS)

Gilichinsky, D. A.; Vorobyova, E. A.; Erokhina, L. G.; Fyordorov-Dayvdov, D. G.; Chaikovskaya, N. R.

It has been established that significant numbers (up to 10 million cells per gram of sample) of living microorganisms of various ecological and morphological groups have been preserved under permafrost conditions, at temperatures ranging from -9 to -13°C and depths of up to 100 m, for thousands and sometimes millions of years. Preserved since the formation of permafrost in sand-clay sediments of the Pliocene-Quaternary period and in paleosols and peats buried among them, these cells are the only living organisms that have survived for a geologically significant period of time. The complexity of the microbial community preserved varies with the age of the permafrost. Eukaryotes are found only in Holocene sediments; while prokaryotes are found to greater ages, i.e., Pliocene and Pleistocene. The diversity of microorganisms decreases with increasing age of sediments, and as a result cocci and corynebacteria are predominant. Enzyme activity (catalase and hydrolytic enzymes) and photosynthetic pigments (chlorophyll and pheophytin have also been detected in permafrost sediments. These results permit us to outline some approaches to the search for traces of life in the permafrost of Martian sediments by borehole core sampling. It is in the deep horizons (and not on the planet surface), isolated by permafrost from the external conditions, that results similar to those obtained on Earth can be expected.

Soil bacterial community shifts associated with sugarcane straw removal

NASA Astrophysics Data System (ADS)

Pimentel, Laisa; Gumiere, Thiago; Andreote, Fernando; Cerri, Carlos

2017-04-01

In Brazil, the adoption of the mechanical unburned sugarcane harvest potentially increase the quantity of residue left in the field after harvesting. Economically, this material has a high potential for second generation ethanol (2G) production. However, crop residues have an essential role in diverse properties and processes in the soil. The greater part of the uncertainties about straw removal for 2G ethanol production is based on its effects in soil microbial community. In this sense, it is important to identify the main impacts of sugarcane straw removal on soil microbial community. Therefore, we conducted a field study, during one year, in Valparaíso (São Paulo state - Brazil) to evaluate the effects of straw decomposition on soil bacterial community. Specifically, we wanted: i) to compare the rates of straw removal and ii) to evaluate the effects of straw decomposition on soil bacterial groups over one year. The experiment was in a randomized block design with treatments arranged in strip plot. The treatments are different rates of sugarcane straw removal, namely: no removal, 50, 75 and 100% of straw removal. Soil sampling was carried out at 0, 4, 8 and 12 months after the sugarcane harvest (August 2015). Total DNA was extracted from soil using the PowersoilTM DNA Isolation kit. And the abundance of bacterial in each soil sample was estimated via quantification of 16S rRNA gene. The composition of the bacterial communities was estimated via terminal restriction fragment length polymorphism (T-RFLP) analysis, and the T-RF sizes were performed on a 3500 Genetic Analyzer. Finally, the results were examined with GeneMapper 4.1 software. There was bacterial community shifts through the time and among the rates of sugarcane straw removal. Bacterial community was firstly determined by the time scale, which explained 29.16% of total variation. Rates of straw removal explained 11.55% of shifts on bacterial community. Distribution through the time is an important

Impacts of Permafrost on Infrastructure and Ecosystem Services

NASA Astrophysics Data System (ADS)

Trochim, E.; Schuur, E.; Schaedel, C.; Kelly, B. P.

2017-12-01

The Study of Environmental Arctic Change (SEARCH) program developed knowledge pyramids as a tool for advancing scientific understanding and making this information accessible for decision makers. Knowledge pyramids are being used to synthesize, curate and disseminate knowledge of changing land ice, sea ice, and permafrost in the Arctic. Each pyramid consists of a one-two page summary brief in broadly accessible language and literature organized by levels of detail including synthesizes and scientific building blocks. Three knowledge pyramids have been produced related to permafrost on carbon, infrastructure, and ecosystem services. Each brief answers key questions with high societal relevance framed in policy-relevant terms. The knowledge pyramids concerning infrastructure and ecosystem services were developed in collaboration with researchers specializing in the specific topic areas in order to identify the most pertinent issues and accurately communicate information for integration into policy and planning. For infrastructure, the main issue was the need to build consensus in the engineering and science communities for developing improved methods for incorporating data applicable to building infrastructure on permafrost. In ecosystem services, permafrost provides critical landscape properties which affect basic human needs including fuel and drinking water availability, access to hunting and harvest, and fish and wildlife habitat. Translating these broad and complex topics necessitated a systematic and iterative approach to identifying key issues and relating them succinctly to the best state of the art research. The development of the knowledge pyramids provoked collaboration and synthesis across distinct research and engineering communities. The knowledge pyramids also provide a solid basis for policy development and the format allows the content to be regularly updated as the research community advances.

Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

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

Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.

2010-03-01

Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomicmore » units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.« less

Characterization of Coastal Urban Watershed Bacterial Communities Leads to Alternative Community-Based Indicators

PubMed Central

Wu, Cindy H.; Sercu, Bram; Van De Werfhorst, Laurie C.; Wong, Jakk; DeSantis, Todd Z.; Brodie, Eoin L.; Hazen, Terry C.; Holden, Patricia A.; Andersen, Gary L.

2010-01-01

Background Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Methodology/Principal Findings Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and α-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC∶A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. Conclusions/Significance This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health. PMID:20585654

Decomposition and organic matter quality in continental peatlands: The ghost of permafrost past

USGS Publications Warehouse

Turetsky, M.R.

2004-01-01

Permafrost patterning in boreal peatlands contributes to landscape heterogeneity, as peat plateaus, palsas, and localized permafrost mounds are interspersed among unfrozen bogs and fens. The degradation of localized permafrost in peatlands alters local topography, hydrology, thermal regimes, and plant communities, and creates unique peatland features called "internal lawns." I used laboratory incubations to quantify carbon dioxide (CO 2) production in peat formed under different permafrost regimes (with permafrost, without permafrost, melted permafrost), and explored the relationships among proximate organic matter fractions, nutrient concentrations, and decomposition. Peat within each feature (internal lawn, bog, permafrost mound) is more chemically similar than peat collected within the same province (Alberta, Saskatchewan) or within depth intervals (surface, deep). Internal lawn peat produces more CO2 than the other peatland types. Across peatland features, acid-insoluble material (AIM) and AIM/nitrogen are significant predictors of decomposition. However, within each peatland feature, soluble proximate fractions are better predictors of CO2 production. Permafrost stability in peatlands influences plant and soil environments, which control litter inputs, organic matter quality, and decomposition rates. Spatial patterns of permafrost, as well as ecosystem processes within various permafrost features, should be considered when assessing the fate of soil carbon in northern ecosystems. ?? 2004 Springer Science+Business Media, Inc.

Permafrost Thaw, Soil Moisture and Plant Community Change Alter Organic Matter Decomposition in Alaskan Tundra

NASA Astrophysics Data System (ADS)

Natali, S.; Mauritz, M.; Pegoraro, E.; Schuur, E.

2015-12-01

Climate warming in arctic tundra has been associated with increased plant productivity and a shift in plant community composition, specifically an increase in shrub cover, which can impact soil organic matter through changes in the size and composition of the leaf litter pool. Shifts in litter quantity and quality will in turn interact with changes in the soil environment as the climate continues to warm. We examined the effects of permafrost thaw, soil moisture changes, and plant community composition on leaf litter decomposition in an upland tundra ecosystem in Interior Alaska. We present warming and drying effects on decomposition rates of graminoid-dominated and shrub-dominated leaf litter mixtures over three years (2 cm depth), and annual decomposition of a common cellulose substrate (0-10 cm and 10-20 cm) over five years at a permafrost thaw and soil drying experiment. We expected that warming and drying would increase decomposition, and that decomposition would be greater in the shrub litter than in the graminoid litter mix. Decomposition of Betula nana, the dominant shrub, was 50% greater in the shrub-dominated litter mix compared to the graminoid-dominated litter. Surprisingly, there was no significant difference in total litter mass loss between graminoid and shrub litter mixtures, despite significant differences in decomposition rates of the dominant plant species when decomposed alone and in community mixtures. Drying decreased decomposition of B. nana and of the shrub community litter overall, but after two years there was no detected warming effect on shrub-community decomposition. In contrast to leaf litter decomposition, both warming and drying increased decomposition of the common substrate. Warming caused an almost twofold increase in cellulose decomposition in surface soil (0-10cm), and drying caused a twofold increase in cellulose decomposition from deeper organic layer soils (10-20cm). These results demonstrate the importance of interactions

ADAPT: building conceptual models of the physical and biological processes across permafrost landscapes

NASA Astrophysics Data System (ADS)

Allard, M.; Vincent, W. F.; Lemay, M.

2012-12-01

Fundamental and applied permafrost research is called upon in Canada in support of environmental protection, economic development and for contributing to the international efforts in understanding climatic and ecological feedbacks of permafrost thawing under a warming climate. The five year "Arctic Development and Adaptation to Permafrost in Transition" program (ADAPT) funded by NSERC brings together 14 scientists from 10 Canadian universities and involves numerous collaborators from academia, territorial and provincial governments, Inuit communities and industry. The geographical coverage of the program encompasses all of the permafrost regions of Canada. Field research at a series of sites across the country is being coordinated. A common protocol for measuring ground thermal and moisture regime, characterizing terrain conditions (vegetation, topography, surface water regime and soil organic matter contents) is being applied in order to provide inputs for designing a general model to provide an understanding of transfers of energy and matter in permafrost terrain, and the implications for biological and human systems. The ADAPT mission is to produce an 'Integrated Permafrost Systems Science' framework that will be used to help generate sustainable development and adaptation strategies for the North in the context of rapid socio-economic and climate change. ADAPT has three major objectives: to examine how changing precipitation and warming temperatures affect permafrost geosystems and ecosystems, specifically by testing hypotheses concerning the influence of the snowpack, the effects of water as a conveyor of heat, sediments, and carbon in warming permafrost terrain and the processes of permafrost decay; to interact directly with Inuit communities, the public sector and the private sector for development and adaptation to changes in permafrost environments; and to train the new generation of experts and scientists in this critical domain of research in Canada

Controls on ecosystem and root respiration across a permafrost and wetland gradient in interior Alaska

USGS Publications Warehouse

McConnell, Nicole A.; Turetsky, Merritt R.; McGuire, A. David; Kane, Evan S.; Waldrop, Mark P.; Harden, Jennifer W.

2013-01-01

Permafrost is common to many northern wetlands given the insulation of thick organic soil layers, although soil saturation in wetlands can lead to warmer soils and increased thaw depth. We analyzed five years of soil CO2 fluxes along a wetland gradient that varied in permafrost and soil moisture conditions. We predicted that communities with permafrost would have reduced ecosystem respiration (ER) but greater temperature sensitivity than communities without permafrost. These predictions were partially supported. The colder communities underlain by shallow permafrost had lower ecosystem respiration (ER) than communities with greater active layer thickness. However, the apparent Q10 of monthly averaged ER was similar in most of the vegetation communities except the rich fen, which had smaller Q10 values. Across the gradient there was a negative relationship between water table position and apparent Q10, showing that ER was more temperature sensitive under drier soil conditions. We explored whether root respiration could account for differences in ER between two adjacent communities (sedge marsh and rich fen), which corresponded to the highest and lowest ER, respectively. Despite differences in root respiration rates, roots contributed equally (~40%) to ER in both communities. Also, despite similar plant biomass, ER in the rich fen was positively related to root biomass, while ER in the sedge marsh appeared to be related more to vascular green area. Our results suggest that ER across this wetland gradient was temperature-limited, until conditions became so wet that respiration became oxygen-limited and influenced less by temperature. But even in sites with similar hydrology and thaw depth, ER varied significantly likely based on factors such as soil redox status and vegetation composition.

Discovery of a novel methanogen prevalent in thawing permafrost.

PubMed

Mondav, Rhiannon; Woodcroft, Ben J; Kim, Eun-Hae; McCalley, Carmody K; Hodgkins, Suzanne B; Crill, Patrick M; Chanton, Jeffrey; Hurst, Gregory B; VerBerkmoes, Nathan C; Saleska, Scott R; Hugenholtz, Philip; Rich, Virginia I; Tyson, Gene W

2014-01-01

Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.

Experimental sulfate amendment alters peatland bacterial community structure.

PubMed

Strickman, R J S; Fulthorpe, R R; Coleman Wasik, J K; Engstrom, D R; Mitchell, C P J

2016-10-01

As part of a long-term, peatland-scale sulfate addition experiment, the impact of varying sulfate deposition on bacterial community responses was assessed using 16S tag encoded pyrosequencing. In three separate areas of the peatland, sulfate manipulations included an eight year quadrupling of atmospheric sulfate deposition (experimental), a 3-year recovery to background deposition following 5years of elevated deposition (recovery), and a control area. Peat concentrations of methylmercury (MeHg), a bioaccumulative neurotoxin, were measured, the production of which is attributable to a growing list of microorganisms, including many sulfate-reducing Deltaproteobacteria. The total bacterial and Deltaproteobacterial community structures in the experimental treatment differed significantly from those in the control and recovery treatments that were either indistinguishable or very similar to one another. Notably, the relatively rapid return (within three years) of bacterial community structure in the recovery treatment to a state similar to the control, demonstrates significant resilience of the peatland bacterial community to changes in atmospheric sulfate deposition. Changes in MeHg accumulation between sulfate treatments correlated with changes in the Deltaproteobacterial community, suggesting that sulfate may affect MeHg production through changes in the community structure of this group. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbial Populations in Antarctic Permafrost: Biodiversity, State, Age, and Implication for Astrobiology

NASA Astrophysics Data System (ADS)

Gilichinsky, D. A.; Wilson, G. S.; Friedmann, E. I.; McKay, C. P.; Sletten, R. S.; Rivkina, E. M.; Vishnivetskaya, T. A.; Erokhina, L. G.; Ivanushkina, N. E.; Kochkina, G. A.; Shcherbakova, V. A.; Soina, V. S.; Spirina, E. V.; Vorobyova, E. A.; Fyodorov-Davydov, D. G.; Hallet, B.; Ozerskaya, S. M.; Sorokovikov, V. A.; Laurinavichyus, K. S.; Shatilovich, A. V.; Chanton, J. P.; Ostroumov, V. E.; Tiedje, J. M.

2007-05-01

Antarctic permafrost soils have not received as much geocryological and biological study as has been devoted to the ice sheet, though the permafrost is more stable and older and inhabited by more microbes. This makes these soils potentially more informative and a more significant microbial repository than ice sheets. Due to the stability of the subsurface physicochemical regime, Antarctic permafrost is not an extreme environment but a balanced natural one. Up to 104 viable cells/g, whose age presumably corresponds to the longevity of the permanently frozen state of the sediments, have been isolated from Antarctic permafrost. Along with the microbes, metabolic by-products are preserved. This presumed natural cryopreservation makes it possible to observe what may be the oldest microbial communities on Earth. Here, we describe the Antarctic permafrost habitat and biodiversity and provide a model for martian ecosystems.

Bacterial community diversity of the deep-sea octocoral Paramuricea placomus.

PubMed

Kellogg, Christina A; Ross, Steve W; Brooke, Sandra D

2016-01-01

Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus . Samples from five colonies of P. placomus were collected from Baltimore Canyon (379-382 m depth) in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each) and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomus colonies was identified, comprising 68-90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomus does not appear to include the genus Endozoicomonas , which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.

Bacterial community diversity of the deep-sea octocoral Paramuricea placomus

USGS Publications Warehouse

Kellogg, Christina A.; Ross, Steve W.; Brooke, Sandra D.

2016-01-01

Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus. Samples from five colonies of P. placomus were collected from Baltimore Canyon (379–382 m depth) in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each) and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomuscolonies was identified, comprising 68–90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomusdoes not appear to include the genus Endozoicomonas, which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.

Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure.

PubMed

Ma, Xiao; Vikram, Amit; Casson, Leonard; Bibby, Kyle

2017-07-05

Drinking water microbial communities impact opportunistic pathogen colonization and corrosion of water distribution systems, and centralized drinking water treatment represents a potential control for microbial community structure in finished drinking water. In this article, we examine bacterial and fungal abundance and diversity, as well as the microbial community taxonomic structure following each unit operation in a conventional surface water treatment plant. Treatment operations drove the microbial composition more strongly than sampling time. Both bacterial and fungal abundance and diversity decreased following sedimentation and filtration; however, only bacterial abundance and diversity was significantly impacted by free chlorine disinfection. Similarly, each treatment step was found to shift bacterial and fungal community beta-diversity, with the exception of disinfection on the fungal community structure. We observed the enrichment of bacterial and fungal taxa commonly found in drinking water distribution systems through the treatment process, for example, Sphingomonas following filtration and Leptospirillium and Penicillium following disinfection. Study results suggest that centralized drinking water treatment processes shape the final drinking water microbial community via selection of community members and that the bacterial community is primarily driven by disinfection while the eukaryotic community is primarily controlled by physical treatment processes.

Community-acquired bacterial meningitis.

PubMed

Costerus, Joost M; Brouwer, Matthijs C; Bijlsma, Merijn W; van de Beek, Diederik

2017-02-01

Bacterial meningitis is a medical emergency and is associated with a high disease burden. We reviewed recent progress in the management of patients with community-acquired bacterial meningitis. The worldwide burden of disease of bacterial meningitis remains high, despite the decreasing incidence following introduction of routine vaccination campaigns. Delay in diagnosis and treatment remain major concerns in the management of acute bacterial meningitis. European Society of Clinical Microbiology and Infectious Diseases guidelines strive for a door-to-antibiotic-time less than 1 h. Polymerase chain reaction (PCR) has emerged as an important diagnostic tool to identify the causative organism. Point-of-care tests using fast multiplex PCR have been developed, but additional value has not been proven. Although anecdotal observations advocate pressure-based management, a randomized controlled trial will need to be performed first to determine efficacy and safety of such an aggressive treatment approach. Adjunctive dexamethasone remains the only adjunctive therapy with proven efficacy. The incidence of bacterial meningitis has been decreasing after the implementation of effective vaccines. Treatment should be administered as soon as possible and time to treatment should not exceed 1 h.

Successional trajectories of rhizosphere bacterial communities over consecutive seasons

DOE PAGES

Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; ...

2015-08-04

It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative tomore » background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable

Successional trajectories of rhizosphere bacterial communities over consecutive seasons

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

Shi, Shengjing; Nuccio, Erin; Herman, Donald J.

It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative tomore » background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable

Different bacterial communities in ectomycorrhizae and surrounding soil

PubMed Central

Vik, Unni; Logares, Ramiro; Blaalid, Rakel; Halvorsen, Rune; Carlsen, Tor; Bakke, Ingrid; Kolstø, Anne-Brit; Økstad, Ole Andreas; Kauserud, Håvard

2013-01-01

Several eukaryotic symbioses have shown to host a rich diversity of prokaryotes that interact with their hosts. Here, we study bacterial communities associated with ectomycorrhizal root systems of Bistorta vivipara compared to bacterial communities in bulk soil using pyrosequencing of 16S rRNA amplicons. A high richness of Operational Taxonomic Units (OTUs) was found in plant roots (3,571 OTUs) and surrounding soil (3,476 OTUs). The community composition differed markedly between these two environments. Actinobacteria, Armatimonadetes, Chloroflexi and OTUs unclassified at phylum level were significantly more abundant in plant roots than in soil. A large proportion of the OTUs, especially those in plant roots, presented low similarity to Sanger 16S rRNA reference sequences, suggesting novel bacterial diversity in ectomycorrhizae. Furthermore, the bacterial communities of the plant roots were spatially structured up to a distance of 60 cm, which may be explained by bacteria using fungal hyphae as a transport vector. The analyzed ectomycorrhizae presents a distinct microbiome, which likely influence the functioning of the plant-fungus symbiosis. PMID:24326907

Metagenomic insights into zooplankton‐associated bacterial communities

PubMed Central

Srivastava, Abhishek; Koski, Marja; Garcia, Juan Antonio L.; Takaki, Yoshihiro; Yokokawa, Taichi; Nunoura, Takuro; Elisabeth, Nathalie H.; Sintes, Eva; Herndl, Gerhard J.

2017-01-01

Summary Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton‐associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton‐associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton‐associated microbiome suggests that this zooplankton‐associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters. PMID:28967193

A central database for the Global Terrestrial Network for Permafrost (GTN-P)

NASA Astrophysics Data System (ADS)

Elger, Kirsten; Lanckman, Jean-Pierre; Lantuit, Hugues; Karlsson, Ævar Karl; Johannsson, Halldór

2013-04-01

The Global Terrestrial Network for Permafrost (GTN-P) is the primary international observing network for permafrost sponsored by the Global Climate Observing System (GCOS) and the Global Terrestrial Observing System (GTOS), and managed by the International Permafrost Association (IPA). It monitors the Essential Climate Variable (ECV) permafrost that consists of permafrost temperature and active-layer thickness, with the long-term goal of obtaining a comprehensive view of the spatial structure, trends, and variability of changes in the active layer and permafrost. The network's two international monitoring components are (1) CALM (Circumpolar Active Layer Monitoring) and the (2) Thermal State of Permafrost (TSP), which is made of an extensive borehole-network covering all permafrost regions. Both programs have been thoroughly overhauled during the International Polar Year 2007-2008 and extended their coverage to provide a true circumpolar network stretching over both Hemispheres. GTN-P has gained considerable visibility in the science community in providing the baseline against which models are globally validated and incorporated in climate assessments. Yet it was until now operated on a voluntary basis, and is now being redesigned to meet the increasing expectations from the science community. To update the network's objectives and deliver the best possible products to the community, the IPA organized a workshop to define the user's needs and requirements for the production, archival, storage and dissemination of the permafrost data products it manages. From the beginning on, GNT-P data was "outfitted" with an open data policy with free data access via the World Wide Web. The existing data, however, is far from being homogeneous: is not yet optimized for databases, there is no framework for data reporting or archival and data documentation is incomplete. As a result, and despite the utmost relevance of permafrost in the Earth's climate system, the data has not been

Vulnerability of Permafrost Soil Carbon to Climate Warming: Evaluating Controls on Microbial Community Composition

USDA-ARS?s Scientific Manuscript database

Abstract: Despite the fact that permafrost soils contain up to half of the carbon (C) in terrestrial pools, we have a poor understanding of the controls on decomposition in thawed permafrost. Global climate models assume that decomposition increases linearly with temperature, yet decomposition in th...

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments.

PubMed

Yang, Sizhong; Wen, Xi; Shi, Yulan; Liebner, Susanne; Jin, Huijun; Perfumo, Amedea

2016-11-25

Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments

PubMed Central

Yang, Sizhong; Wen, Xi; Shi, Yulan; Liebner, Susanne; Jin, Huijun; Perfumo, Amedea

2016-01-01

Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies. PMID:27886221

Insight into the effects of different cropping systems on soil bacterial community and tobacco bacterial wilt rate.

PubMed

Niu, Jiaojiao; Chao, Jin; Xiao, Yunhua; Chen, Wu; Zhang, Chao; Liu, Xueduan; Rang, Zhongwen; Yin, Huaqun; Dai, Linjian

2017-01-01

Rotation is an effective strategy to control crop disease and improve plant health. However, the effects of crop rotation on soil bacterial community composition and structure, and crop health remain unclear. In this study, using 16S rRNA gene sequencing, we explored the soil bacterial communities under four different cropping systems, continuous tobacco cropping (control group), tobacco-maize rotation, tobacco-lily rotation, and tobacco-turnip rotation. Results of detrended correspondence analysis and dissimilarity tests showed that soil bacterial community composition and structure changed significantly among the four groups, such that Acidobacteria and Actinobacteria were more abundant in the maize rotation group (16.6 and 11.5%, respectively) than in the control (8.5 and 7.1%, respectively). Compared with the control group (57.78%), maize and lily were effective rotation crops in controlling tobacco bacterial wilt (about 23.54 and 48.67%). On the other hand, tobacco bacterial wilt rate was increased in the turnip rotation (59.62%) relative to the control. Further study revealed that the abundances of several bacterial populations were directly correlated with tobacco bacterial wilt. For example, Acidobacteria and Actinobacteria were significantly negatively correlated to the tobacco bacterial wilt rate, so they may be probiotic bacteria. Canonical correspondence analysis showed that soil pH and calcium content were key factors in determining soil bacterial communities. In conclusion, our study revealed the composition and structure of bacterial communities under four different cropping systems and may unveil molecular mechanisms for the interactions between soil microorganisms and crop health. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Jellyfish modulate bacterial dynamic and community structure.

PubMed

Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

2012-01-01

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in

Design of synthetic bacterial communities for predictable plant phenotypes

PubMed Central

Herrera Paredes, Sur; Gao, Tianxiang; Law, Theresa F.; Finkel, Omri M.; Mucyn, Tatiana; Teixeira, Paulo José Pereira Lima; Salas González, Isaí; Feltcher, Meghan E.; Powers, Matthew J.; Shank, Elizabeth A.; Jones, Corbin D.; Jojic, Vladimir; Dangl, Jeffery L.; Castrillo, Gabriel

2018-01-01

Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant–bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation–responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities. PMID:29462153

Achieving the NOAA Arctic Action Plan: The Missing Permafrost Element - Permafrost Forecasting Listening Session Results

NASA Astrophysics Data System (ADS)

Buxbaum, T. M.; Thoman, R.; Romanovsky, V. E.

2015-12-01

Permafrost is ground at or below freezing for at least two consecutive years. It currently occupies 80% of Alaska. Permafrost temperature and active layer thickness (ALT) are key climatic variables for monitoring permafrost conditions. Active layer thickness is the depth that the top layer of ground above the permafrost thaws each summer season and permafrost temperature is the temperature of the frozen permafrost under this active layer. Knowing permafrost conditions is key for those individuals working and living in Alaska and the Arctic. The results of climate models predict vast changes and potential permafrost degradation across Alaska and the Arctic. NOAA is working to implement its 2014 Arctic Action Plan and permafrost forecasting is a missing piece of this plan. The Alaska Center for Climate Assessment and Policy (ACCAP), using our webinar software and our diverse network of statewide stakeholder contacts, hosted a listening session to bring together a select group of key stakeholders. During this listening session the National Weather Service (NWS) and key permafrost researchers explained what is possible in the realm of permafrost forecasting and participants had the opportunity to discuss and share with the group (NWS, researchers, other stakeholders) what is needed for usable permafrost forecasting. This listening session aimed to answer the questions: Is permafrost forecasting needed? If so, what spatial scale is needed by stakeholders? What temporal scales do stakeholders need/want? Are there key times (winter, fall freeze-up, etc.) or locations (North Slope, key oil development areas, etc.) where forecasting would be most applicable and useful? Are there other considerations or priority needs we haven't thought of regarding permafrost forecasting? This presentation will present the results of that listening session.

Potential microbial contamination during sampling of permafrost soil assessed by tracers

NASA Astrophysics Data System (ADS)

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

2017-02-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

Potential microbial contamination during sampling of permafrost soil assessed by tracers.

PubMed

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S

2017-02-23

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

NASA Astrophysics Data System (ADS)

Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel; David, Maude M.; McFarland, Jack; Blazewicz, Steven J.; Harden, Jennifer; Turetsky, Merritt R.; McGuire, A. David; Shah, Manesh B.; Verberkmoes, Nathan C.; Lee, Lang Ho; Mavrommatis, Kostas; Jansson, Janet K.

2015-05-01

Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular `omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.

PubMed

Hultman, Jenni; Waldrop, Mark P; Mackelprang, Rachel; David, Maude M; McFarland, Jack; Blazewicz, Steven J; Harden, Jennifer; Turetsky, Merritt R; McGuire, A David; Shah, Manesh B; VerBerkmoes, Nathan C; Lee, Lang Ho; Mavrommatis, Kostas; Jansson, Janet K

2015-05-14

Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular 'omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

Potential microbial contamination during sampling of permafrost soil assessed by tracers

PubMed Central

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

2017-01-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores. PMID:28230151

Urban greenness influences airborne bacterial community composition.

PubMed

Mhuireach, Gwynne; Johnson, Bart R; Altrichter, Adam E; Ladau, Joshua; Meadow, James F; Pollard, Katherine S; Green, Jessica L

2016-11-15

Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing

Do honeybees shape the bacterial community composition in floral nectar?

PubMed

Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

2013-01-01

Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers' nectar, but not from those in the uncovered flowers' nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves.

Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

PubMed Central

Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

2013-01-01

Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers’ nectar, but not from those in the uncovered flowers’ nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves. PMID:23844027

An active bacterial community linked to high chl-a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community.

PubMed

Eronen-Rasimus, Eeva; Luhtanen, Anne-Mari; Rintala, Janne-Markus; Delille, Bruno; Dieckmann, Gerhard; Karkman, Antti; Tison, Jean-Louis

2017-10-01

Antarctic sea-ice bacterial community composition and dynamics in various developmental stages were investigated during the austral winter in 2013. Thick snow cover likely insulated the ice, leading to high (<4 μg l -1 ) chlorophyll-a (chl-a) concentrations and consequent bacterial production. Typical sea-ice bacterial genera, for example, Octadecabacter, Polaribacter and Glaciecola, often abundant in spring and summer during the sea-ice algal bloom, predominated in the communities. The variability in bacterial community composition in the different ice types was mainly explained by the chl-a concentrations, suggesting that as in spring and summer sea ice, the sea-ice bacteria and algae may also be coupled during the Antarctic winter. Coupling between the bacterial community and sea-ice algae was further supported by significant correlations between bacterial abundance and production with chl-a. In addition, sulphate-reducing bacteria (for example, Desulforhopalus) together with odour of H 2 S were observed in thick, apparently anoxic ice, suggesting that the development of the anaerobic bacterial community may occur in sea ice under suitable conditions. In all, the results show that bacterial community in Antarctic sea ice can stay active throughout the winter period and thus possible future warming of sea ice and consequent increase in bacterial production may lead to changes in bacteria-mediated processes in the Antarctic sea-ice zone.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments.

PubMed

Rocha, Lidianne L; Colares, Geórgia B; Nogueira, Vanessa L R; Paes, Fernanda A; Melo, Vânia M M

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

PubMed Central

Rocha, Lidianne L.; Colares, Geórgia B.; Nogueira, Vanessa L. R.; Paes, Fernanda A.; Melo, Vânia M. M.

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

Permafrost and organic layer interactions over a climate gradient in a discontinuous permafrost zone

Treesearch

Kristofer D. Johnson; Jennifer W. Harden; A. David McGuire; Mark Clark; Fengming Yuan; Andrew O. Finley

2013-01-01

Permafrost is tightly coupled to the organic soil layer, an interaction that mediates permafrost degradation in response to regional warming. We analyzed changes in permafrost occurrence and organic layer thickness (OLT) using more than 3000 soil pedons across a mean annual temperature (MAT) gradient. Cause and effect relationships between permafrost probability (PF),...

Electron acceptor-based regulation of microbial greenhouse gas production from thawing permafrost

NASA Astrophysics Data System (ADS)

Bak, Ebbe; Jones, Eleanor; Yde, Jacob; Hodson, Andy; Mallon, Gunnar; Fisnter, Kai

2017-04-01

Permafrost contains about 35% of the global soil organic carbon (0-3 m depth). As a consequence of global warming, the active layer thickness is steadily increasing and its organic carbon is becoming available for degradation, causing a concomitant release of CO2 and CH4. The climate forcing feedbacks of permafrost thaw are determined by the rate of organic carbon degradation and to which degree it is released as CO2 or CH4. Methane is produced under anoxic conditions, but the factors that regulate its production are poorly constrained. In this study, we investigate how CH4 production is influenced by the presence of competing anaerobic processes with focus on the role of iron and sulfate reduction. We have collected permafrost cores to 2.2 meters depth from three different lowland sites in Adventdalen on Svalbard. From these cores, we have prepared anoxic batch incubation for each 25 cm depth interval and followed the production of CO2 and CH4 as well as the iron and sulfate reduction. This approach allows us to monitor the rate of the CO2 and CH4 production as well as to investigate the correlation between CH4 production and competing anaerobic respiration processes in the active layer as well in the permafrost. These investigations are accompanied by characterization of the carbon, iron and sulfate content in the soil and will be followed by characterization of the microbial community structure. The aim of this study is to get a better understanding of how the availability of sulfate and iron and the microbial community structure regulate the production of CO2 and CH4 in thawing permafrost, and to elucidate how the rate of the organic carbon degradation changes with depth in permafrost-affected soils. This study improves our understanding of climate feedback mechanisms operating during permafrost thaw.

Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures

PubMed Central

Wang, Hui; Wang, Bin; Dong, Wenwen; Hu, Xiaoke

2016-01-01

Crude oil is a complex mixture of hydrocarbons with different structures; its components vary in bioavailability and toxicity. It is important to understand how bacterial communities response to different hydrocarbons and their co-acclimation in the process of degradation. In this study, microcosms with the addition of structurally different hydrocarbons were setup to investigate the successions of bacterial communities and the interactions between different bacterial taxa. Hydrocarbons were effectively degraded in all microcosms after 40 days. High-throughput sequencing offered a great quantity of data for analyzing successions of bacterial communities. The results indicated that the bacterial communities responded dramatically different to various hydrocarbons. KEGG database and PICRUSt were applied to predict functions of individual bacterial taxa and networks were constructed to analyze co-acclimations between functional bacterial groups. Almost all functional genes catalyzing degradation of different hydrocarbons were predicted in bacterial communities. Most of bacterial taxa were believed to conduct biodegradation processes via interactions with each other. This study addressed a few investigated area of bacterial community responses to structurally different organic pollutants and their co-acclimation and interactions in the process of biodegradation. The study could provide useful information to guide the bioremediation of crude oil pollution. PMID:27698451

Scaling isotopic emissions and microbes across a permafrost thaw landscape

NASA Astrophysics Data System (ADS)

Varner, R. K.; Palace, M. W.; Saleska, S. R.; Bolduc, B.; Braswell, B. H., Jr.; Crill, P. M.; Chanton, J.; DelGreco, J.; Deng, J.; Frolking, S. E.; Herrick, C.; Hines, M. E.; Li, C.; McArthur, K. J.; McCalley, C. K.; Persson, A.; Roulet, N. T.; Torbick, N.; Tyson, G. W.; Rich, V. I.

2017-12-01

High latitude peatlands are a significant source of atmospheric methane. This source is spatially and temporally heterogeneous, resulting in a wide range of emission estimates for the atmospheric budget. Increasing atmospheric temperatures are causing degradation of underlying permafrost, creating changes in surface soil moisture, the surface and sub-surface hydrological patterns, vegetation and microbial communities, but the consequences to rates and magnitudes of methane production and emissions are poorly accounted for in global budgets. We combined field observations, multi-source remote sensing data and biogeochemical modeling to predict methane dynamics, including the fraction derived from hydrogenotrophic versus acetoclastic microbial methanogenesis across Stordalen mire, a heterogeneous discontinuous permafrost wetland located in northernmost Sweden. Using the field measurement validated Wetland-DNDC biogeochemical model, we estimated mire-wide CH4 and del13CH4 production and emissions for 2014 with input from field and unmanned aerial system (UAS) image derived vegetation maps, local climatology and water table from insitu and remotely sensed data. Model simulated methanogenic pathways correlate with sequence-based observations of methanogen community composition in samples collected from across the permafrost thaw landscape. This approach enables us to link below ground microbial community composition with emissions and indicates a potential for scaling across broad areas of the Arctic region.

Impact of disinfection on drinking water biofilm bacterial community.

PubMed

Mi, Zilong; Dai, Yu; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-11-01

Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination. Copyright © 2015. Published by Elsevier B.V.

Mapping permafrost change hot-spots with Landsat time-series

NASA Astrophysics Data System (ADS)

Grosse, G.; Nitze, I.

2016-12-01

Recent and projected future climate warming strongly affects permafrost stability over large parts of the terrestrial Arctic with local, regional and global scale consequences. The monitoring and quantification of permafrost and associated land surface changes in these areas is crucial for the analysis of hydrological and biogeochemical cycles as well as vegetation and ecosystem dynamics. However, detailed knowledge of the spatial distribution and the temporal dynamics of these processes is scarce and likely key locations of permafrost landscape dynamics may remain unnoticed. As part of the ERC funded PETA-CARB and ESA GlobPermafrost projects, we developed an automated processing chain based on data from the entire Landsat archive (excluding MSS) for the detection of permafrost change related processes and hotspots. The automated method enables us to analyze thousands of Landsat scenes, which allows for a multi-scaled spatio-temporal analysis at 30 meter spatial resolution. All necessary processing steps are carried out automatically with minimal user interaction, including data extraction, masking, reprojection, subsetting, data stacking, and calculation of multi-spectral indices. These indices, e.g. Landsat Tasseled Cap and NDVI among others, are used as proxies for land surface conditions, such as vegetation status, moisture or albedo. Finally, a robust trend analysis is applied to each multi-spectral index and each pixel over the entire observation period of up to 30 years from 1985 to 2015, depending on data availability. Large transects of around 2 million km² across different permafrost types in Siberia and North America have been processed. Permafrost related or influencing landscape dynamics were detected within the trend analysis, including thermokarst lake dynamics, fires, thaw slumps, and coastal dynamics. The produced datasets will be distributed to the community as part of the ERC PETA-CARB and ESA GlobPermafrost projects. Users are encouraged to

Effects of permafrost thaw on nitrogen availability and plant nitrogen acquisition in Interior Alaska

NASA Astrophysics Data System (ADS)

Finger, R.; Euskirchen, E. S.; Turetsky, M.

2013-12-01

The degradation of ice-rich permafrost, which covers a large portion of Interior Alaska, typically leads to thermokarst and increases in soil saturation. As a result, conifer peat plateaus degrade and are often replaced by wet collapse scar bogs. This state change results in profound changes in regional hydrology, biogeochemical cycling, and plant community composition. Preliminary data suggest that permafrost thaw can increase surface soil inorganic nitrogen (IN) concentrations but it is still unknown whether these changes in nutrient availability are short-lived (pulse releases) and whether or not they impact collapse scar vegetation composition or productivity, particularly as collapse scars undergo succession with time-after-thaw. Therefore we are currently examining changes in plant community composition, N availability and plant N acquisition along three thermokarst gradients in Interior Alaska. Each gradient is comprised of a forested permafrost peat plateau, adjacent ecotones experiencing active permafrost degradation (including a collapsing forest canopy and a saturated moat), and a collapse scar bog where permafrost has completely degraded. We predicted that IN concentrations would be highest along the active thaw margin, and lowest in the peat plateau. We also predicted that IN concentrations would be positively related to shifts in vegetation community composition, nutrient use efficiency (NUE) and tissue 15N concentrations. Preliminary results have shown that IN concentrations increase in newer collapse scar features as well as with thaw depth. Our data also show a shift from feather moss and ericaceous shrub-dominate understories in the permafrost plateau to Sphagnum and sedge dominated thaw ecotone and bog communities. Further successional development of the collapse scar bog results in the reintroduction of small evergreen and deciduous shrubs as the peat mat develops. Over time, collapse scar succession and peat accumulation appears to lead to

Permafrost soils and carbon cycling

DOE PAGES

Ping, C. L.; Jastrow, J. D.; Jorgenson, M. T.; ...

2015-02-05

Knowledge of soils in the permafrost region has advanced immensely in recent decades, despite the remoteness and inaccessibility of most of the region and the sampling limitations posed by the severe environment. These efforts significantly increased estimates of the amount of organic carbon stored in permafrost-region soils and improved understanding of how pedogenic processes unique to permafrost environments built enormous organic carbon stocks during the Quaternary. This knowledge has also called attention to the importance of permafrost-affected soils to the global carbon cycle and the potential vulnerability of the region's soil organic carbon (SOC) stocks to changing climatic conditions. Inmore » this review, we briefly introduce the permafrost characteristics, ice structures, and cryopedogenic processes that shape the development of permafrost-affected soils, and discuss their effects on soil structures and on organic matter distributions within the soil profile. We then examine the quantity of organic carbon stored in permafrost-region soils, as well as the characteristics, intrinsic decomposability, and potential vulnerability of this organic carbon to permafrost thaw under a warming climate. Overall, frozen conditions and cryopedogenic processes, such as cryoturbation, have slowed decomposition and enhanced the sequestration of organic carbon in permafrost-affected soils over millennial timescales. Due to the low temperatures, the organic matter in permafrost soils is often less humified than in more temperate soils, making some portion of this stored organic carbon relatively vulnerable to mineralization upon thawing of permafrost.« less

Cryofacial Analysis of Permafrost Soils

NASA Astrophysics Data System (ADS)

Shur, Y.; Kanevskiy, M.; Jorgenson, M. T.; Fortier, D.

2008-12-01

Cryogenic structure of soils, specifically the patterns formed by ice inclusions and massive ice in permafrost, depends on the genesis of soils and the way they are transformed into a perennially frozen state. Katasonov (1963) recognized that the analysis of relationship between the patterns of cryogenic structure and the processes of permafrost formation (he termed 'cryofacial analysis') is a powerful tool for understanding of genesis of permafrost in relation to different sediment types. He applied cryofacial analysis to Late Pleistocene syngenetic permafrost (yedoma) and to permafrost formed during freezing of thaw bulbs under drained lakes in the continuous permafrost zone. Our long-term studies of cryogenic structure in Alaska and Russia found that cryofacial analysis can be applied to all types of permafrost soil. We described the evolution of cryogenic structure associated with alluvial chronosequences on arctic floodplains in Russia and Alaska and found the differing cryofacies are highly related to patterns of ecosystem development. Cryogenic structure of glacial-lacustrine deposits in several parts of Alaska is similar to cryogenic structure of these deposits in differing permafrost areas in Russia. Cryofacial analysis is extremely useful in recognition of later modifications of permafrost when compared soils are identical in composition. For example, we differentiated original syngenetic permafrost from permafrost modified by thermokarst and thermal erosion in the CRREL permafrost tunnel at Fox, Alaska on the basis of differences in cryogenic structure. We identified unique cryogenic structures associated with the transient zone of the upper permafrost and with the formation of thermokarst-cave ice. Cryofacial analysis showed that parts of permafrost which were previously thawed after fire can be easily distinguished from parts unaffected by thawing. Cryofacial analysis helped in recognizing areas in central and northern Alaska unaffected by the last

Bacterial Communities in the Groundwater of Xikuangshan Antimony Mine, China

NASA Astrophysics Data System (ADS)

Wu, M.; Wang, H.; Wang, N.; Wang, M.

2017-12-01

Xikuangshan (XKS) is the biggest antimony (Sb) mine around the word, which causes serious environmental contamination due to the mining actives. To fully understand the bacterial compositions in the groundwater around the mining area in XKS and their correlation with environmental factors, groundwater samples were collected and subject to 16S rDNA high throughput sequencing. Results indicated that Proteobacteria (especially Gamma-Proteobacteria) dominated bacterial communities in high-Sb groundwater samples, whereas Bacteroidetes predominated in low-Sb groundwater. Furthermore, antimony concentration was found to be the most significant factor shaping bacterial communities (P=0.002) with an explanation of 9.16% of the variation. Other factors such as pH, contents of Mg, Ca and orthophosphate were also observed to significantly correlate with bacterial communities. This was the first report to show the important impact of Sb concentration on bacterial community structure in the groundwater in the mining area. Our results will enhance the understanding of subsurface biogeochemical processes mediated by microbes.

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert.

PubMed

Goordial, Jacqueline; Davila, Alfonso; Greer, Charles W; Cannam, Rebecca; DiRuggiero, Jocelyne; McKay, Christopher P; Whyte, Lyle G

2017-02-01

Permafrost in the high elevation McMurdo Dry Valleys of Antarctica ranks among the driest and coldest on Earth. Permafrost soils appear to be largely inhospitable to active microbial life, but sandstone lithic microhabitats contain a trophically simple but functional cryptoendolithic community. We used metagenomic sequencing and activity assays to examine the functional capacity of permafrost soils and cryptoendolithic communities in University Valley, one of the most extreme regions in the Dry Valleys. We found metagenomic evidence that cryptoendolithic microorganisms are adapted to the harsh environment and capable of metabolic activity at in situ temperatures, possessing a suite of stress response and nutrient cycling genes to fix carbon under the fluctuating conditions that the sandstone rock would experience during the summer months. We additionally identified genes involved in microbial competition and cooperation within the cryptoendolithic habitat. In contrast, permafrost soils have a lower richness of stress response genes, and instead the metagenome is enriched in genes involved with dormancy and sporulation. The permafrost soils also have a large presence of phage genes and genes involved in the recycling of cellular material. Our results underlie two different habitability conditions under extreme cold and dryness: the permafrost soil which is enriched in traits which emphasize survival and dormancy, rather than growth and activity; and the cryptoendolithic environment that selects for organisms capable of growth under extremely oligotrophic, arid and cold conditions. This study represents the first metagenomic interrogation of Antarctic permafrost and polar cryptoendolithic microbial communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Nutrient Controls on Methane Emissions in a Permafrost Thaw Subarctic Peatland

NASA Astrophysics Data System (ADS)

Kashi, N. N.; Perryman, C. R.; Malhotra, A.; Marek, E. A.; Giesler, R.; Varner, R. K.

2015-12-01

Permafrost peatlands in northern latitudes are large reservoirs of sequestered carbon that are vulnerable to climate change. While peatlands account for a small fraction of total global land surfaces, their potential to release sequestered carbon in response to higher temperatures is of concern. Of particular relevance is the conversion of these carbon stores into methane (CH4), a strong greenhouse gas with a global warming potential 20 times greater than that of CO2 over a 100-year time frame. Here, we explore how key nutrients impact the consumption of CH4 at the Stordalen Mire in Abisko, Sweden, a discontinuous permafrost peatland with expanding thaw over the last century. Peatland CH4 emissions are highly spatially variable due to multiple emission pathways and strong dependence on several environmental factors. Among controls on CH4 emissions, such as temperature and water table depth, primary production of wetland vegetation is also a strong factor in the variability of CH4 emissions. Plant community shifts among permafrost thaw stages subsequently change nutrient cycling and availability, which in turn impacts primary production. Early stages of permafrost thaw are mosaicked with a variety of vascular plants and mosses. We analyzed potential enzymatic activities of chitinase, glucosidase, and phosphatase as proxies for organic nitrogen, carbon, and phosphorus cycling, respectively, in tandem with potential CH4 oxidation rates. In addition, stoichiometric ratios of carbon, nitrogen, and phosphorus concentrations are used to illustrate nutrient limitation controls on CH4 oxidation rates. While CH4 emissions are low throughout initial thaw stages, < 7 CH4 mg m-2 day-1, we found they had the highest rates of potential CH4 oxidation. These permafrost thaw-induced CH4 oxidation rates are 5 and 11 times higher, in the surface and depth of the peat profile respectively, than subsequent aerobic permafrost thaw stages. As CH4 emissions are low in intact permafrost

The paleoecology, peat chemistry and carbon storage of a discontinuous permafrost peatland

NASA Astrophysics Data System (ADS)

Talbot, Julie; Pelletier, Nicolas; Olefeldt, David; Turetsky, Merritt; Blodau, Christian; Sonnentag, Oliver; Quinton, William

2017-04-01

Permafrost in peatlands strongly influences ecosystem biogeochemical functioning, vegetation composition and hydrological functions. Permafrost peatlands of northwestern Canada store large amounts of carbon but the peatlands located at the southern margin of the permafrost zone are thawing rapidly. This thaw triggers changes in vegetation, hydrology and peat characteristics, and may affect carbon stocks. We present data from a permafrost plateau to thermokarst bog chronosequence located in the southern portion of the Scotty Creek watershed near Fort Simpson, Northwest Territories, Canada. We assessed changes in plant communities, hydrology, biogeochemistry and permafrost status over 9000 years of peatland development using plant macrofossil, testate amoeba and peat chemical characteristics. Peat accumulation started after the infilling of a lake 8500 cal. yr BP. Minerotrophic peat prevailed at the site until permafrost formed around 5000 cal. yr BP. Permafrost apparently formed three times, although there is spatial variability in the permafrost aggradation - degradation cycles. Permafrost thawed 550 cal. yr BP in the center of the thermokarst bog. Ombrotrophic peat is a fairly recent feature of the peat profiles, only appearing after the most recent permafrost thaw event. Both allogenic (temperature/precipitation/snow cover changes and wildfire) and autogenic (peat accumulation, Sphagnum growth) processes likely influenced permafrost aggradation and thaw. While apparent carbon accumulation rates were lower during present and past permafrost periods than during non-permafrost periods, long term carbon accumulation remained similar between cores with different permafrost period lengths. Deep peat was more decomposed in the thermokarst bog peat profile than in the permafrost plateau profile, highlighting the importance of considering potential deep peat carbon losses to project the fate of thawing permafrost peat carbon stores. Average long-term carbon accumulation

Rapid recovery of soil bacterial communities after wildfire in a Chinese boreal forest

PubMed Central

Xiang, Xingjia; Shi, Yu; Yang, Jian; Kong, Jianjian; Lin, Xiangui; Zhang, Huayong; Zeng, Jun; Chu, Haiyan

2014-01-01

Fires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20–100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4+ content and carbon/nitrogen ratio (P < 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties. PMID:24452061

Effects of permafrost microorganisms on skin wound reparation.

PubMed

Kalenova, L F; Novikova, M A; Subbotin, A M

2015-02-01

Local application of ointment with Bacillus spp. strain MG8 (15,000-20,000 living bacterial cells), isolated from permafrost specimens, on the skin wound of about 60 mm(2) stimulated the reparation processes in experimental mice. A possible mechanism stimulating the regeneration of the damaged tissues under the effect of MG8 could be modulation of the immune system reactivity with more rapid switchover to humoral immunity anti-inflammatory mechanisms aimed at de novo synthesis of protein.

The bacterial community of entomophilic nematodes and host beetles.

PubMed

Koneru, Sneha L; Salinas, Heilly; Flores, Gilberto E; Hong, Ray L

2016-05-01

Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment. © 2016 John Wiley & Sons Ltd.

Strategies for managing rival bacterial communities: Lessons from burying beetles.

PubMed

Duarte, Ana; Welch, Martin; Swannack, Chris; Wagner, Josef; Kilner, Rebecca M

2018-03-01

The role of bacteria in animal development, ecology and evolution is increasingly well understood, yet little is known of how animal behaviour affects bacterial communities. Animals that benefit from defending a key resource from microbial competitors are likely to evolve behaviours to control or manipulate the animal's associated external microbiota. We describe four possible mechanisms by which animals could gain a competitive edge by disrupting a rival bacterial community: "weeding," "seeding," "replanting" and "preserving." By combining detailed behavioural observations with molecular and bioinformatic analyses, we then test which of these mechanisms best explains how burying beetles, Nicrophorus vespilloides, manipulate the bacterial communities on their carcass breeding resource. Burying beetles are a suitable species to study how animals manage external microbiota because reproduction revolves around a small vertebrate carcass. Parents shave a carcass and apply antimicrobial exudates on its surface, shaping it into an edible nest for their offspring. We compared bacterial communities in mice carcasses that were either fresh, prepared by beetles or unprepared but buried underground for the same length of time. We also analysed bacterial communities in the burying beetle's gut, during and after breeding, to understand whether beetles could be "seeding" the carcass with particular microbes. We show that burying beetles do not "preserve" the carcass by reducing bacterial load, as is commonly supposed. Instead, our results suggest they "seed" the carcass with bacterial groups which are part of the Nicrophorus core microbiome. They may also "replant" other bacteria from the carcass gut onto the surface of their carrion nest. Both these processes may lead to the observed increase in bacterial load on the carcass surface in the presence of beetles. Beetles may also "weed" the bacterial community by eliminating some groups of bacteria on the carcass, perhaps through

Changes in soil bacterial community structure with increasing disturbance frequency.

PubMed

Kim, Mincheol; Heo, Eunjung; Kang, Hojeong; Adams, Jonathan

2013-07-01

Little is known of the responsiveness of soil bacterial community structure to disturbance. In this study, we subjected a soil microcosm to physical disturbance, sterilizing 90 % of the soil volume each time, at a range of frequencies. We analysed the bacterial community structure using 454 pyrosequencing of the 16S rRNA gene. Bacterial diversity was found to decline with the increasing disturbance frequencies. Total bacterial abundance was, however, higher at intermediate and high disturbance frequencies, compared to low and no-disturbance treatments. Changing disturbance frequency also led to changes in community composition, with changes in overall species composition and some groups becoming abundant at the expense of others. Some phylogenetic groups were found to be relatively more disturbance-sensitive or tolerant than others. With increasing disturbance frequency, phylogenetic species variability (an index of community composition) itself became more variable from one sample to another, suggesting a greater role of chance in community composition. Compared to the tightly clustered community of the original undisturbed soil, in all the aged disturbed soils the lists of most abundant operational taxonomic units (OTUs) in each replicate were very different, suggesting a possible role of stochasticity in resource colonization and exploitation in the aged and disturbed soils. For example, colonization may be affected by whichever localized concentrations of bacterial populations happen to survive the last disturbance and be reincorporated in abundance into each pot. Overall, it appears that the soil bacterial community is very sensitive to physical disturbance, losing diversity, and that certain groups have identifiable 'high disturbance' vs. 'low disturbance' niches.

Composition and development of oral bacterial communities.

PubMed

Palmer, Robert J

2014-02-01

The oral bacterial microbiome encompasses approximately 700 commonly occurring phylotypes, approximately half of which can be present at any time in any individual. These bacteria are largely indigenous to the oral cavity; this limited habitat range suggests that interactions between the various phylotypes, and between the phylotypes and their environment, are crucial for their existence. Molecular cataloging has confirmed many basic observations on the composition of the oral microbiome that were formulated well before ribosomal RNA-based systematics, but the power and the scope of molecular taxonomy have resulted in the discovery of new phylotypes and, more importantly, have made possible a level of bacterial community analysis that was unachievable with classical methods. Bacterial community structure varies with location within the mouth, and changes in community structure are related to disease initiation and disease progression. Factors that influence the formation and the evolution of communities include selective adherence to epithelial or tooth surfaces, specific cell-to-cell binding as a driver of early community composition, and interorganismal interaction leading to alteration of the local environment, which represents the first step on the road to oral disease. A comprehensive understanding of how these factors interact to drive changes in the composition of the oral microbial community can lead to new strategies for the inhibition of periodontal diseases and dental caries. Published 2013. This article is a US Government work and is in the public domain in the USA.

Natural bacterial communities serve as quantitative geochemical biosensors.

PubMed

Smith, Mark B; Rocha, Andrea M; Smillie, Chris S; Olesen, Scott W; Paradis, Charles; Wu, Liyou; Campbell, James H; Fortney, Julian L; Mehlhorn, Tonia L; Lowe, Kenneth A; Earles, Jennifer E; Phillips, Jana; Techtmann, Steve M; Joyner, Dominique C; Elias, Dwayne A; Bailey, Kathryn L; Hurt, Richard A; Preheim, Sarah P; Sanders, Matthew C; Yang, Joy; Mueller, Marcella A; Brooks, Scott; Watson, David B; Zhang, Ping; He, Zhili; Dubinsky, Eric A; Adams, Paul D; Arkin, Adam P; Fields, Matthew W; Zhou, Jizhong; Alm, Eric J; Hazen, Terry C

2015-05-12

Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts. Copyright © 2015 Smith et al.

Natural bacterial communities serve as quantitative geochemical biosensors

DOE PAGES

Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; ...

2015-05-12

Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination,more » even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.« less

Dynamics of bacterial and fungal communities associated with eggshells during incubation

PubMed Central

Grizard, Stéphanie; Dini-Andreote, Francisco; Tieleman, B Irene; Salles, Joana F

2014-01-01

Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture-based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16S rRNA gene and internal transcribed spacer (ITS) region, we, respectively, described bacterial and fungal communities on eggshells of the homing pigeon Columba livia. We explored their structure, abundance, and composition. Firstly, we showed that sampling technique affected the outcome of the results. While broadly used, the egg swabbing procedure led to a lower DNA extraction efficiency and provided different profiles of bacterial communities than those based on crushed eggshell pieces. Secondly, we observed shifts in bacterial and fungal communities during incubation. At late incubation, bacterial communities showed a reduction in diversity, while their abundance increased, possibly due to the competitive advantage of some species. When compared to their bacterial counterparts, fungal communities also decreased in diversity at late incubation. In that case, however, the decline was associated with a diminution of their overall abundance. Conclusively, our results showed that although incubation might inhibit microbial growth when compared to unincubated eggs, we observed the selective growth of specific bacterial species during incubation. Moreover, we showed that fungi are a substantial component of the microbial communities associated with eggshells and require further investigations in avian ecology. Identifying the functional roles of these microorganisms is likely to provide news insights into the evolutionary strategies that control embryo survival. We aimed to describe the dynamics of bacterial and fungal communities on homing pigeon eggshell surfaces. We investigated these communities at early and late incubation stages. PMID:24772289

Permafrost soils and carbon cycling

DOE PAGES

Ping, C. L.; Jastrow, J. D.; Jorgenson, M. T.; ...

2014-10-30

Knowledge of soils in the permafrost region has advanced immensely in recent decades, despite the remoteness and inaccessibility of most of the region and the sampling limitations posed by the severe environment. These efforts significantly increased estimates of the amount of organic carbon (OC) stored in permafrost-region soils and improved understanding of how pedogenic processes unique to permafrost environments built enormous OC stocks during the Quaternary. This knowledge has also called attention to the importance of permafrost-affected soils to the global C cycle and the potential vulnerability of the region's soil OC stocks to changing climatic conditions. In this review,more » we briefly introduce the permafrost characteristics, ice structures, and cryopedogenic processes that shape the development of permafrost-affected soils and discuss their effects on soil structures and on organic matter distributions within the soil profile. We then examine the quantity of OC stored in permafrost-region soils, as well as the characteristics, intrinsic decomposability, and potential vulnerability of this OC to permafrost thaw under a warming climate.« less

Architectural Design Drives the Biogeography of Indoor Bacterial Communities

PubMed Central

O’Connor, Timothy K.; Mhuireach, Gwynne; Northcutt, Dale; Kline, Jeff; Moriyama, Maxwell; Brown, G. Z.; Bohannan, Brendan J. M.; Green, Jessica L.

2014-01-01

Background Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Results Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Conclusions Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our

Modeling long-term permafrost degradation

NASA Astrophysics Data System (ADS)

Nicolsky, D.; Romanovsky, V. E.

2017-12-01

Permafrost, as an important part of the Cryosphere, has been also strongly affected by climate warming and a wide spread of the permafrost responses to the warming is currently observed. In particular, at some locations rather slow rates of the permafrost degradations are noticed. We related this behavior to the presence of unfrozen water in frozen fine-grained earth material. In this research, we examine not-very-commonly-discussed heat flux from the ground surface into the permafrost and consequently discuss implications of the unfrozen liquid water content on the long-term thawing of permafrost. We conduct a series of numerical experiments and demonstrate that the presence of fine-grained material with substantial unfrozen liquid water content at below 0C temperature can significantly slow down the thawing rate and hence can increase resilience of permafrost to the warming events. This effect is highly nonlinear and a difference between the rates of thawing in fine- and coarse-grained materials is more drastic for lower values of the incoming into permafrost heat flux. For the high heat flux, the difference between these rates almost disappears. As near-surface permafrost temperature increases towards 0C and the changes in the ground temperature become less evident, the future observation networks should try to incorporate measurements of the unfrozen liquid water content in the near-surface permafrost and heat flux into permafrost in addition to the existing temperature observations.

Geophysical mapping of palsa peatland permafrost

NASA Astrophysics Data System (ADS)

Sjöberg, Y.; Marklund, P.; Pettersson, R.; Lyon, S. W.

2014-10-01

Permafrost peatlands are hydrological and biogeochemical hotspots in the discontinuous permafrost zone. Non-intrusive geophysical methods offer possibility to map current permafrost spatial distributions in these environments. In this study, we estimate the depths to the permafrost table surface and base across a peatland in northern Sweden, using ground penetrating radar and electrical resistivity tomography. Seasonal thaw frost tables (at ~0.5 m depth), taliks (2.1-6.7 m deep), and the permafrost base (at ~16 m depth) could be detected. Higher occurrences of taliks were discovered at locations with a lower relative height of permafrost landforms indicative of lower ground ice content at these locations. These results highlight the added value of combining geophysical techniques for assessing spatial distribution of permafrost within the rapidly changing sporadic permafrost zone. For example, based on a simple thought experiment for the site considered here, we estimated that the thickest permafrost could thaw out completely within the next two centuries. There is a clear need, thus, to benchmark current permafrost distributions and characteristics particularly in under studied regions of the pan-arctic.

Geophysical mapping of palsa peatland permafrost

NASA Astrophysics Data System (ADS)

Sjöberg, Y.; Marklund, P.; Pettersson, R.; Lyon, S. W.

2015-03-01

Permafrost peatlands are hydrological and biogeochemical hotspots in the discontinuous permafrost zone. Non-intrusive geophysical methods offer a possibility to map current permafrost spatial distributions in these environments. In this study, we estimate the depths to the permafrost table and base across a peatland in northern Sweden, using ground penetrating radar and electrical resistivity tomography. Seasonal thaw frost tables (at ~0.5 m depth), taliks (2.1-6.7 m deep), and the permafrost base (at ~16 m depth) could be detected. Higher occurrences of taliks were discovered at locations with a lower relative height of permafrost landforms, which is indicative of lower ground ice content at these locations. These results highlight the added value of combining geophysical techniques for assessing spatial distributions of permafrost within the rapidly changing sporadic permafrost zone. For example, based on a back-of-the-envelope calculation for the site considered here, we estimated that the permafrost could thaw completely within the next 3 centuries. Thus there is a clear need to benchmark current permafrost distributions and characteristics, particularly in under studied regions of the pan-Arctic.

Responses of Baltic Sea Ice and Open-Water Natural Bacterial Communities to Salinity Change

PubMed Central

Kaartokallio, Hermanni; Laamanen, Maria; Sivonen, Kaarina

2005-01-01

To investigate the responses of Baltic Sea wintertime bacterial communities to changing salinity (5 to 26 practical salinity units), an experimental study was conducted. Bacterial communities of Baltic seawater and sea ice from a coastal site in southwest Finland were used in two batch culture experiments run for 17 or 18 days at 0°C. Bacterial abundance, cell volume, and leucine and thymidine incorporation were measured during the experiments. The bacterial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes with sequencing of DGGE bands from initial communities and communities of day 10 or 13 of the experiment. The sea ice-derived bacterial community was metabolically more active than the open-water community at the start of the experiment. Ice-derived bacterial communities were able to adapt to salinity change with smaller effects on physiology and community structure, whereas in the open-water bacterial communities, the bacterial cell volume evolution, bacterial abundance, and community structure responses indicated the presence of salinity stress. The closest relatives for all eight partial 16S rRNA gene sequences obtained were either organisms found in polar sea ice and other cold habitats or those found in summertime Baltic seawater. All sequences except one were associated with the α- and γ-proteobacteria or the Cytophaga-Flavobacterium-Bacteroides group. The overall physiological and community structure responses were parallel in ice-derived and open-water bacterial assemblages, which points to a linkage between community structure and physiology. These results support previous assumptions of the role of salinity fluctuation as a major selective factor shaping the sea ice bacterial community structure. PMID:16085826

Methane production as key to the greenhouse gas budget of thawing permafrost

NASA Astrophysics Data System (ADS)

Knoblauch, Christian; Beer, Christian; Liebner, Susanne; Grigoriev, Mikhail N.; Pfeiffer, Eva-Maria

2018-04-01

Permafrost thaw liberates frozen organic carbon, which is decomposed into carbon dioxide (CO2) and methane (CH4). The release of these greenhouse gases (GHGs) forms a positive feedback to atmospheric CO2 and CH4 concentrations and accelerates climate change1,2. Current studies report a minor importance of CH4 production in water-saturated (anoxic) permafrost soils3-6 and a stronger permafrost carbon-climate feedback from drained (oxic) soils1,7. Here we show through seven-year laboratory incubations that equal amounts of CO2 and CH4 are formed in thawing permafrost under anoxic conditions after stable CH4-producing microbial communities have established. Less permafrost carbon was mineralized under anoxic conditions but more CO2-carbon equivalents (CO2-Ce) were formed than under oxic conditions when the higher global warming potential (GWP) of CH4 is taken into account8. A model of organic carbon decomposition, calibrated with the observed decomposition data, predicts a higher loss of permafrost carbon under oxic conditions (113 ± 58 g CO2-C kgC-1 (kgC, kilograms of carbon)) by 2100, but a twice as high production of CO2-Ce (241 ± 138 g CO2-Ce kgC-1) under anoxic conditions. These findings challenge the view of a stronger permafrost carbon-climate feedback from drained soils1,7 and emphasize the importance of CH4 production in thawing permafrost on climate-relevant timescales.

Landscape effects of wildfire on permafrost distribution in interior Alaska derived from remote sensing

USGS Publications Warehouse

Brown, Dana R. N.; Jorgenson, M. Torre; Kielland, Knut; Verbyla, David L.; Prakash, Anupma; Koch, Joshua C.

2016-01-01

Climate change coupled with an intensifying wildfire regime is becoming an important driver of permafrost loss and ecosystem change in the northern boreal forest. There is a growing need to understand the effects of fire on the spatial distribution of permafrost and its associated ecological consequences. We focus on the effects of fire a decade after disturbance in a rocky upland landscape in the interior Alaskan boreal forest. Our main objectives were to (1) map near-surface permafrost distribution and drainage classes and (2) analyze the controls over landscape-scale patterns of post-fire permafrost degradation. Relationships among remote sensing variables and field-based data on soil properties (temperature, moisture, organic layer thickness) and vegetation (plant community composition) were analyzed using correlation, regression, and ordination analyses. The remote sensing data we considered included spectral indices from optical datasets (Landsat 7 Enhanced Thematic Mapper Plus (ETM+) and Landsat 8 Operational Land Imager (OLI)), the principal components of a time series of radar backscatter (Advanced Land Observing Satellite—Phased Array type L-band Synthetic Aperture Radar (ALOS-PALSAR)), and topographic variables from a Light Detection and Ranging (LiDAR)-derived digital elevation model (DEM). We found strong empirical relationships between the normalized difference infrared index (NDII) and post-fire vegetation, soil moisture, and soil temperature, enabling us to indirectly map permafrost status and drainage class using regression-based models. The thickness of the insulating surface organic layer after fire, a measure of burn severity, was an important control over the extent of permafrost degradation. According to our classifications, 90% of the area considered to have experienced high severity burn (using the difference normalized burn ratio (dNBR)) lacked permafrost after fire. Permafrost thaw, in turn, likely increased drainage and resulted in

New member of the hormone-sensitive lipase family from the permafrost microbial community.

PubMed

Petrovskaya, Lada E; Novototskaya-Vlasova, Ksenia A; Gapizov, Sultan Sh; Spirina, Elena V; Durdenko, Ekaterina V; Rivkina, Elizaveta M

2017-07-04

Siberian permafrost is a unique environment inhabited with diverse groups of microorganisms. Among them, there are numerous producers of biotechnologically relevant enzymes including lipases and esterases. Recently, we have constructed a metagenomic library from a permafrost sample and identified in it several genes coding for potential lipolytic enzymes. In the current work, properties of the recombinant esterases obtained from this library are compared with the previously characterized lipase from Psychrobacter cryohalolentis and other representatives of the hormone-sensitive lipase family.

Characterization of Bioaerosol Bacterial Communities During Hazy and Foggy Weather in Qingdao, China

NASA Astrophysics Data System (ADS)

Qi, Jianhua; Li, Mengzhe; Zhen, Yu; Wu, Lijing

2018-06-01

This study was conducted to evaluate the impact of hazy and foggy weather on the bacterial communities in bioaerosols, for which samples were collected from the Qingdao coastal region on sunny, foggy, and hazy days in January and March 2013. Bacterial community compositions were determined using polymerase chain reaction denaturing gradient gel electrophoresis (PCRDGGE). The bacterial community diversity was found to be high on foggy and hazy days, and the dominant species differed during hazy weather. The Shannon-Wiener index revealed that the bacterial community diversity of coarse particles was higher than that of fine particles in the bioaerosols. The bacterial community diversity of fine particles significantly correlated with relative humidity (RH; r 2 = 0.986). The cluster analysis results indicated that the bacterial communities on sunny days differed from those on hazy and foggy days. Compared with sunny days, the bacterial communities in the fine particles during hazy weather exhibited greater changes than those in the coarse particles. Most of the sequenced bacteria were found to be closely affiliated with uncultured bacteria. During hazy weather, members of the classes Bacilli and Gammaproteobacteria ( Pseudomonas and Acinetobacter) were dominant. The DGGE analysis revealed that Proteobacteria and Firmicutes were the predominant phyla, and their relative percentages to all the measured species changed significantly on hazy days, particularly in the fine particles. Haze and fog had a significant impact on the bacterial communities in bioaerosols, and the bacterial community diversity varied on different hazy days.

Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

PubMed

Ibarbalz, Federico M; Figuerola, Eva L M; Erijman, Leonardo

2013-07-01

Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks. Copyright © 2013 Elsevier Ltd. All rights reserved.

Utilization of ancient permafrost carbon in headwaters of Arctic fluvial networks.

PubMed

Mann, Paul J; Eglinton, Timothy I; McIntyre, Cameron P; Zimov, Nikita; Davydova, Anna; Vonk, Jorien E; Holmes, Robert M; Spencer, Robert G M

2015-07-24

Northern high-latitude rivers are major conduits of carbon from land to coastal seas and the Arctic Ocean. Arctic warming is promoting terrestrial permafrost thaw and shifting hydrologic flowpaths, leading to fluvial mobilization of ancient carbon stores. Here we describe (14)C and (13)C characteristics of dissolved organic carbon from fluvial networks across the Kolyma River Basin (Siberia), and isotopic changes during bioincubation experiments. Microbial communities utilized ancient carbon (11,300 to >50,000 (14)C years) in permafrost thaw waters and millennial-aged carbon (up to 10,000 (14)C years) across headwater streams. Microbial demand was supported by progressively younger ((14)C-enriched) carbon downstream through the network, with predominantly modern carbon pools subsidizing microorganisms in large rivers and main-stem waters. Permafrost acts as a significant and preferentially degradable source of bioavailable carbon in Arctic freshwaters, which is likely to increase as permafrost thaw intensifies causing positive climate feedbacks in response to on-going climate change.

Panamanian frog species host unique skin bacterial communities

PubMed Central

Belden, Lisa K.; Hughey, Myra C.; Rebollar, Eria A.; Umile, Thomas P.; Loftus, Stephen C.; Burzynski, Elizabeth A.; Minbiole, Kevin P. C.; House, Leanna L.; Jensen, Roderick V.; Becker, Matthew H.; Walke, Jenifer B.; Medina, Daniel; Ibáñez, Roberto; Harris, Reid N.

2015-01-01

Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd), that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species) community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26%) were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in these skin symbiont

ESA GlobPermafrost - mapping the extent and thermal state of permafrost with satellite data

NASA Astrophysics Data System (ADS)

Westermann, Sebastian; Obu, Jaroslav; Aalstad, Kristoffer; Bartsch, Annett; Kääb, Andreas

2017-04-01

The ESA GlobPermafrost initiative (2016-2019) aims at developing, validating and implementing information products based on remote sensing data to support permafrost research. Mapping of permafrost extent and ground temperatures is conducted at 1 km scale using remotely sensed land surface temperatures (MODIS), snow water equivalent (ESA GlobSnow) and land cover (ESA CCI landcover) in conjunction with a simple ground thermal model (CryoGrid 1). The spatial variability of the ground thermal regime at scales smaller than the model resolution is explicitly taken into account by considering an ensemble of realizations with different model properties. The approach has been tested for the unglacierized land areas in the North Atlantic region, an area of more than 5 million km2. The results have been compared to in-situ temperature measurements in more than 100 boreholes, indicating an accuracy of approximately 2.5°C. Within GlobPermafrost, the scheme will be extended to cover the entire the circum-polar permafrost area. Here, we provide an evaluation of the first prototype covering "lowland" permafrost areas north of 40° latitude (available on www.globpermafrost.info in early 2017). We give a feasibility assessment for extending the scheme to global scale, including both mountain and Antarctic permafrost. Finally, we discuss the potential and limitations for estimating changes of permafrost extent on decadal timescales.

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

PubMed Central

Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

2015-01-01

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

PubMed Central

Kembel, Steven W.; O’Connor, Timothy K.; Arnold, Holly K.; Hubbell, Stephen P.; Wright, S. Joseph; Green, Jessica L.

2014-01-01

The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function. PMID:25225376

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

PubMed Central

Wright, Justin; Kirchner, Veronica; Bernard, William; Ulrich, Nikea; McLimans, Christopher; Campa, Maria F.; Hazen, Terry; Macbeth, Tamzen; Marabello, David; McDermott, Jacob; Mackelprang, Rachel; Roth, Kimberly; Lamendella, Regina

2017-01-01

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

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

Wright, Justin; Kirchner, Veronica; Bernard, William

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. Here, we investigate the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L.more » Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. And across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

DOE PAGES

Wright, Justin; Kirchner, Veronica; Bernard, William; ...

2017-11-22

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. Here, we investigate the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L.more » Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. And across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges

Bacterial communities in Arctic first-year drift ice during the winter/spring transition.

PubMed

Eronen-Rasimus, Eeva; Piiparinen, Jonna; Karkman, Antti; Lyra, Christina; Gerland, Sebastian; Kaartokallio, Hermanni

2016-08-01

Horizontal and vertical variability of first-year drift-ice bacterial communities was investigated along a North-South transect in the Fram Strait during the winter/spring transition. Two different developmental stages were captured along the transect based on the prevailing environmental conditions and the differences in bacterial community composition. The differences in the bacterial communities were likely driven by the changes in sea-ice algal biomass (2.6-5.6 fold differences in chl-a concentrations). Copiotrophic genera common in late spring/summer sea ice, such as Polaribacter, Octadecabacter and Glaciecola, dominated the bacterial communities, supporting the conclusion that the increase in the sea-ice algal biomass was possibly reflected in the sea-ice bacterial communities. Of the dominating bacterial genera, Polaribacter seemed to benefit the most from the increase in algal biomass, since they covered approximately 39% of the total community at the southernmost stations with higher (>6 μg l(-1) ) chl-a concentrations and only 9% at the northernmost station with lower chl-a concentrations (<6 μg l(-1) ). The sea-ice bacterial communities also varied between the ice horizons at all three stations and thus we recommend that for future studies multiple ice horizons be sampled to cover the variability in sea-ice bacterial communities in spring. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas

NASA Astrophysics Data System (ADS)

Vences, Miguel; Lyra, Mariana L.; Kueneman, Jordan G.; Bletz, Molly C.; Archer, Holly M.; Canitz, Julia; Handreck, Svenja; Randrianiaina, Roger-Daniel; Struck, Ulrich; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; McKenzie, Valerie J.; Tebbe, Christoph C.; Haddad, Célio F. B.; Glos, Julian

2016-04-01

Animal-associated microbial communities can play major roles in the physiology, development, ecology, and evolution of their hosts, but the study of their diversity has yet focused on a limited number of host species. In this study, we used high-throughput sequencing of partial sequences of the bacterial 16S rRNA gene to assess the diversity of the gut-inhabiting bacterial communities of 212 specimens of tropical anuran amphibians from Brazil and Madagascar. The core gut-associated bacterial communities among tadpoles from two different continents strongly overlapped, with eight highly represented operational taxonomic units (OTUs) in common. In contrast, the core communities of adults and tadpoles from Brazil were less similar with only one shared OTU. This suggests a community turnover at metamorphosis. Bacterial diversity was higher in tadpoles compared to adults. Distinct differences in composition and diversity occurred among gut bacterial communities of conspecific tadpoles from different water bodies and after experimental fasting for 8 days, demonstrating the influence of both environmental factors and food on the community structure. Communities from syntopic tadpoles clustered by host species both in Madagascar and Brazil, and the Malagasy tadpoles also had species-specific isotope signatures. We recommend future studies to analyze the turnover of anuran gut bacterial communities at metamorphosis, compare the tadpole core communities with those of other aquatic organisms, and assess the possible function of the gut microbiota as a reservoir for protective bacteria on the amphibian skin.

Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems.

PubMed

Reverter, Miriam; Sasal, Pierre; Tapissier-Bontemps, N; Lecchini, D; Suzuki, M

2017-06-01

While recent studies have suggested that fish mucus microbiota play an important role in homeostasis and prevention of infections, very few studies have investigated the bacterial communities of gill mucus. We characterised the gill mucus bacterial communities of four butterflyfish species and although the bacterial diversity of gill mucus varied significantly between species, Shannon diversities were high (H = 3.7-5.7) in all species. Microbiota composition differed between butterflyfishes, with Chaetodon lunulatus and C. ornatissimus having the most similar bacterial communities, which differed significantly from C. vagabundus and C. reticulatus. The core bacterial community of all species consisted of mainly Proteobacteria followed by Actinobacteria and Firmicutes. Chaetodonlunulatus and C. ornatissimus bacterial communities were mostly dominated by Gammaproteobacteria with Vibrio as the most abundant genus. Chaetodonvagabundus and C. reticulatus presented similar abundances of Gammaproteobacteria and Alphaproteobacteria, which were well represented by Acinetobacter and Paracoccus, respectively. In conclusion, our results indicate that different fish species present specific bacterial assemblages. Finally, as mucus layers are nutrient hotspots for heterotrophic bacteria living in oligotrophic environments, such as coral reef waters, the high bacterial diversity found in butterflyfish gill mucus might indicate external fish mucus surfaces act as a reservoir of coral reef bacterial diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Diversity of Bacterial Communities in Container Habitats of Mosquitoes

PubMed Central

Ponnusamy, Loganathan; Xu, Ning; Stav, Gil; Wesson, Dawn M.; Schal, Coby

2010-01-01

We investigated the bacterial diversity of microbial communities in water-filled, human-made and natural container habitats of the mosquitoes Aedes aegypti and Aedes albopictus in suburban landscapes of New Orleans, Louisiana in 2003. We collected water samples from three classes of containers, including tires (n=12), cemetery urns (n=23), and miscellaneous containers that included two tree holes (n=19). Total genomic DNA was extracted from water samples, and 16S ribosomal DNA fragments (operational taxonomic units, OTUs) were amplified by PCR and separated by denaturing gradient gel electrophoresis (DGGE). The bacterial communities in containers represented diverse DGGE-DNA banding patterns that were not related to the class of container or to the local spatial distribution of containers. Mean richness and evenness of OTUs were highest in water samples from tires. Bacterial phylotypes were identified by comparative sequence analysis of 90 16S rDNA DGGE band amplicons. The majority of sequences were placed in five major taxa: Alpha-, Beta- and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and an unclassified group; Proteobacteria and Bacteroidetes were the predominant heterotrophic bacteria in containers. The bacterial communities in human-made containers consisted mainly of undescribed species, and a phylogenetic analysis based on 16S rRNA sequences suggested that species composition was independent of both container type and the spatial distribution of containers. Comparative PCR-based, cultivation-independent rRNA surveys of microbial communities associated with mosquito habitats can provide significant insight into community organization and dynamics of bacterial species. PMID:18373113

Controls on ecosystem and root respiration across a permafrost and wetland gradient in interior Alaska

Treesearch

N.A McConnell; M.R. Turetsky; A.D. McGuire; E.S. Kane; M.P. Waldrop; J.W. Harden

2013-01-01

Permafrost is common to many northern wetlands given the insulation of thick organic soil layers, although soil saturation in wetlands can lead to warmer soils and increased thaw depth. We analyzed five years of soil CO2 fluxes along a wetland gradient that varied in permafrost and soil moisture conditions. We predicted that communities with...

Characterisation of the bacterial community structures in the intestine of Lampetra morii.

PubMed

Li, Yingying; Xie, Wenfang; Li, Qingwei

2016-07-01

The metagenomic analysis and 16S rDNA sequencing method were used to investigate the bacterial community in the intestines of Lampetra morii. The bacterial community structure in L. morii intestine was relatively simple. Eight different operational taxonomic units were observed. Chitinophagaceae_unclassified (26.5 %) and Aeromonas spp. (69.6 %) were detected as dominant members at the genus level. The non-dominant genera were as follows: Acinetobacter spp. (1.4 %), Candidatus Bacilloplasma (2.5 %), Enterobacteria spp. (1.5 %), Shewanella spp. (0.04 %), Vibrio spp. (0.09 %), and Yersinia spp. (1.8 %). The Shannon-Wiener (H) and Simpson (1-D) indexes were 0.782339 and 0.5546, respectively. The rarefaction curve representing the bacterial community richness and Shannon-Wiener curve representing the bacterial community diversity reached asymptote, which indicated that the sequence depth were sufficient to represent the majority of species richness and bacterial community diversity. The number of Aeromonas in lamprey intestine was two times higher after stimulation by lipopolysaccharide than PBS. This study provides data for understanding the bacterial community harboured in lamprey intestines and exploring potential key intestinal symbiotic bacteria essential for the L. morii immune response.

Comparison of bacterial communities of conventional and A-stage activated sludge systems

PubMed Central

Gonzalez-Martinez, Alejandro; Rodriguez-Sanchez, Alejandro; Lotti, Tommaso; Garcia-Ruiz, Maria-Jesus; Osorio, Francisco; Gonzalez-Lopez, Jesus; van Loosdrecht, Mark C. M.

2016-01-01

The bacterial community structure of 10 different wastewater treatment systems and their influents has been investigated through pyrosequencing, yielding a total of 283486 reads. These bioreactors had different technological configurations: conventional activated sludge (CAS) systems and very highly loaded A-stage systems. A-stage processes are proposed as the first step in an energy producing municipal wastewater treatment process. Pyrosequencing analysis indicated that bacterial community structure of all influents was similar. Also the bacterial community of all CAS bioreactors was similar. Bacterial community structure of A-stage bioreactors showed a more case-specific pattern. A core of genera was consistently found for all influents, all CAS bioreactors and all A-stage bioreactors, respectively, showing that different geographical locations in The Netherlands and Spain did not affect the functional bacterial communities in these technologies. The ecological roles of these bacteria were discussed. Influents and A-stage bioreactors shared several core genera, while none of these were shared with CAS bioreactors communities. This difference is thought to reside in the different operational conditions of the two technologies. This study shows that bacterial community structure of CAS and A-stage bioreactors are mostly driven by solids retention time (SRT) and hydraulic retention time (HRT), as suggested by multivariate redundancy analysis. PMID:26728449

Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition.

PubMed

Poosakkannu, Anbu; Nissinen, Riitta; Kytöviita, Minna-Maarit

2017-11-01

The effects of arbuscular mycorrhizal (AM) fungi on plant-associated microbes are poorly known. We tested the hypothesis that colonization by an AM fungus affects microbial species richness and microbial community composition of host plant tissues. We grew the grass, Deschampsia flexuosa in a greenhouse with or without the native AM fungus, Claroideoglomus etunicatum. We divided clonally produced tillers into two parts: one inoculated with AM fungus spores and one without AM fungus inoculation (non-mycorrhizal, NM). We characterized bacterial (16S rRNA gene) and fungal communities (internal transcribed spacer region) in surface-sterilized leaf and root plant compartments. AM fungus inoculation did not affect microbial species richness or diversity indices in leaves or roots, but the AM fungus inoculation significantly affected bacterial community composition in leaves. A total of three OTUs in leaves belonging to the phylum Firmicutes positively responded to the presence of the AM fungus in roots. Another six OTUs belonging to the Proteobacteria (Alpha, Beta, and Gamma) and Bacteroidetes were significantly more abundant in NM plants when compared to AM fungus-inoculated plants. Further, there was a significant correlation between plant dry weight and leaf microbial community compositional shift. Also, there was a significant correlation between leaf bacterial community compositional shift and foliar nitrogen content changes due to AM fungus inoculation. The results suggest that AM fungus colonization in roots has a profound effect on plant physiology that is reflected in leaf bacterial community composition.

Observations and Impacts of Permafrost Thaw in the Lower Yukon River Basin and Yukon Delta Region: the Importance of Local Knowledge

NASA Astrophysics Data System (ADS)

Herman-Mercer, N. M.; Elder, K.; Toohey, R.; Mutter, E. A.

2015-12-01

In regions of the arctic and subarctic baseline measurements of permafrost dynamics are lacking and scientific research can be especially expensive when remote sensing techniques are utilized. This research demonstrated the importance of local observations, a powerful tool for understanding landscape change, such as permafrost dynamics. Fifty-five interviews were recently conducted with community members in four villages of the lower Yukon River Basin and Yukon Delta to understand local environmental and landscape changes and the impacts these changes may be having on the lives and livelihoods of these communities. The interviews were semi-structured and focused on many climate and landscape change factors including knowledge of permafrost in their community or the surrounding landscape. All positive respondents stated that they believe the permafrost is thawing. The research revealed that residents of the arctic and subarctic interact with permafrost in a variety of ways. Some people utilize permafrost to store food resources and have found that they have to dig deeper presently than in their youth in order to find ground cold enough. Others are involved in digging graves and report encountering easier excavation in recent years. Subsistence hunters and gatherers travel long distances by snowmobile and boat, and have noticed slumping ground, eroding river banks and coast lines, as well as land that seems to be rising. Finally, all residents of the arctic and subarctic interact with permafrost in terms of the stability of their homes and other infrastructure. Many interview participants complained of their houses leaning and needing more frequent adjustment than in the past. Indigenous residents of the arctic and subarctic have intimate relationships with their landscape owing to their subsistence lifestyle and are also connected to the landscape of the past through the teachings of their elders. Further, arctic and subarctic communities will sustain the majority

Arctic cities and climate change: climate-induced changes in stability of Russian urban infrastructure built on permafrost

NASA Astrophysics Data System (ADS)

Shiklomanov, Nikolay; Streletskiy, Dmitry; Swales, Timothy

2014-05-01

Planned socio-economic development during the Soviet period promoted migration into the Arctic and work force consolidation in urbanized settlements to support mineral resources extraction and transportation industries. These policies have resulted in very high level of urbanization in the Soviet Arctic. Despite the mass migration from the northern regions during the 1990s following the collapse of the Soviet Union and the diminishing government support, the Russian Arctic population remains predominantly urban. In five Russian Administrative regions underlined by permafrost and bordering the Arctic Ocean 66 to 82% (depending on region) of the total population is living in Soviet-era urban communities. The political, economic and demographic changes in the Russian Arctic over the last 20 years are further complicated by climate change which is greatly amplified in the Arctic region. One of the most significant impacts of climate change on arctic urban landscapes is the warming and degradation of permafrost which negatively affects the structural integrity of infrastructure. The majority of structures in the Russian Arctic are built according to the passive principle, which promotes equilibrium between the permafrost thermal regime and infrastructure foundations. This presentation is focused on quantitative assessment of potential changes in stability of Russian urban infrastructure built on permafrost in response to ongoing and future climatic changes using permafrost - geotechnical model forced by GCM-projected climate. To address the uncertainties in GCM projections we have utilized results from 6 models participated in most recent IPCC model inter-comparison project. The analysis was conducted for entire extent of Russian permafrost-affected area and on several representative urban communities. Our results demonstrate that significant observed reduction in urban infrastructure stability throughout the Russian Arctic can be attributed to climatic changes and that

Bacterial community structure in the drinking water microbiome is governed by filtration processes.

PubMed

Pinto, Ameet J; Xi, Chuanwu; Raskin, Lutgarde

2012-08-21

The bacterial community structure of a drinking water microbiome was characterized over three seasons using 16S rRNA gene based pyrosequencing of samples obtained from source water (a mix of a groundwater and a surface water), different points in a drinking water plant operated to treat this source water, and in the associated drinking water distribution system. Even though the source water was shown to seed the drinking water microbiome, treatment process operations limit the source water's influence on the distribution system bacterial community. Rather, in this plant, filtration by dual media rapid sand filters played a primary role in shaping the distribution system bacterial community over seasonal time scales as the filters harbored a stable bacterial community that seeded the water treatment processes past filtration. Bacterial taxa that colonized the filter and sloughed off in the filter effluent were able to persist in the distribution system despite disinfection of finished water by chloramination and filter backwashing with chloraminated backwash water. Thus, filter colonization presents a possible ecological survival strategy for bacterial communities in drinking water systems, which presents an opportunity to control the drinking water microbiome by manipulating the filter microbial community. Grouping bacterial taxa based on their association with the filter helped to elucidate relationships between the abundance of bacterial groups and water quality parameters and showed that pH was the strongest regulator of the bacterial community in the sampled drinking water system.

Plants of the fynbos biome harbour host species-specific bacterial communities.

PubMed

Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

2016-08-01

The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The effect of permafrost thaw on short- and long-term carbon accumulation in permafrost mires

NASA Astrophysics Data System (ADS)

Olid, Carolina; Klaminder, Jonatan; Monteux, Sylvain; Johansson, Margareta; Dorrepaal, Ellen

2017-04-01

Permafrost stores twice as much carbon (C) as is currently present in the atmosphere. During recent years, warmer temperatures in the Arctic has caused rapid thawing of permafrost, which have dramatically altered permafrost C storage by increasing both microbial decomposition and plant productivity. Although current research focuses on the effects of climate change on these two processes, there are still no scientific consensus about the magnitude or even the direction of future C feedbacks from permafrost ecosystems. Field manipulation experiments have been widely used during the last decade to improve our knowledge about the net effects of permafrost thaw in the permafrost C storage. However, due to the slow response (decades) of permafrost ecosystems to environmental changes and the short-time nature of these experiments (usually shorter than 5-9 years), there are still concerns when attempting to extrapolate the results to predict long term effects. In addition, measurements are mostly taken exclusively during the summer season, without taking into account inter-annual variability in C fluxes and underestimating microbial activity throughout the cold season. The need to develop a comprehensive understanding of C fluxes over the entire year and at long temporal scales sets the basis of this study. This study aims to quantify the effects of permafrost thawing in permafrost C fluxes using a 12 years permafrost thaw experiment in northern Sweden. Our aims were to quantify the effect of permafrost thaw in both decomposition and primary production in active layer and newly thawed permafrost, and its implications for the C balance. Based on previous observations, we hypothesized that 1) soil decomposition rates were higher in manipulated thaw plots. However, 2) the observed increase in nutrients availability and the higher presence of vascular plants after thawing stimulate primary production, which compensates to some extent the increased C losses by respiration. To

Parental material and cultivation determine soil bacterial community structure and fertility.

PubMed

Sun, Li; Gao, Jusheng; Huang, Ting; Kendall, Joshua R A; Shen, Qirong; Zhang, Ruifu

2015-01-01

Microbes are the key components of the soil environment, playing important roles during soil development. Soil parent material provides the foundation elements that comprise the basic nutritional environment for the development of microbial community. After 30 years artificial maturation of cultivation, the soil developments of three different parental materials were evaluated and bacterial community compositions were investigated using the high-throughput sequencing approach. Thirty years of cultivation increased the soil fertility and soil microbial biomass, richness and diversity, greatly changed the soil bacterial communities, the proportion of phylum Actinobacteria decreased significantly, while the relative abundances of the phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Armatimonadetes and Nitrospira were significantly increased. Soil bacterial communities of parental materials were separated with the cultivated ones, and comparisons of different soil types, granite soil and quaternary red clay soil were similar and different with purple sandy shale soil in both parental materials and cultivated treatments. Bacterial community variations in the three soil types were affected by different factors, and their alteration patterns in the soil development also varied with soil type. Soil properties (except total potassium) had a significant effect on the soil bacterial communities in all three soil types and a close relationship with abundant bacterial phyla. The amounts of nitrogen-fixing bacteria as well as the abundances of the nifH gene in all cultivated soils were higher than those in the parental materials; Burkholderia and Rhizobacte were enriched significantly with long-term cultivation. The results suggested that crop system would not deplete the nutrients of soil parental materials in early stage of soil maturation, instead it increased soil fertility and changed bacterial community, specially enriched the nitrogen-fixing bacteria to accumulate

Airborne electromagnetic imaging of discontinuous permafrost

USGS Publications Warehouse

Minsley, B.J.; Abraham, J.D.; Smith, B.D.; Cannia, J.C.; Voss, C.I.; Jorgenson, M.T.; Walvoord, Michelle Ann; Wylie, B.K.; Anderson, L.; Ball, L.B.; Deszcz-Pan, M.; Wellman, T.P.; Ager, T.A.

2012-01-01

The evolution of permafrost in cold regions is inextricably connected to hydrogeologic processes, climate, and ecosystems. Permafrost thawing has been linked to changes in wetland and lake areas, alteration of the groundwater contribution to streamflow, carbon release, and increased fire frequency. But detailed knowledge about the dynamic state of permafrost in relation to surface and groundwater systems remains an enigma. Here, we present the results of a pioneering ∼1,800 line-kilometer airborne electromagnetic survey that shows sediments deposited over the past ∼4 million years and the configuration of permafrost to depths of ∼100 meters in the Yukon Flats area near Fort Yukon, Alaska. The Yukon Flats is near the boundary between continuous permafrost to the north and discontinuous permafrost to the south, making it an important location for examining permafrost dynamics. Our results not only provide a detailed snapshot of the present-day configuration of permafrost, but they also expose previously unseen details about potential surface – groundwater connections and the thermal legacy of surface water features that has been recorded in the permafrost over the past ∼1,000 years. This work will be a critical baseline for future permafrost studies aimed at exploring the connections between hydrogeologic, climatic, and ecological processes, and has significant implications for the stewardship of Arctic environments.

Complexity of Bacterial Communities in a River-Floodplain System (Danube, Austria)

PubMed Central

Besemer, Katharina; Moeseneder, Markus M.; Arrieta, Jesus M.; Herndl, Gerhard J.; Peduzzi, Peter

2005-01-01

Natural floodplains play an essential role in the processing and decomposition of organic matter and in the self-purification ability of rivers, largely due to the activity of bacteria. Knowledge about the composition of bacterial communities and its impact on organic-matter cycling is crucial for the understanding of ecological processes in river-floodplain systems. Particle-associated and free-living bacterial assemblages from the Danube River and various floodplain pools with different hydrological characteristics were investigated using terminal restriction fragment length polymorphism analysis. The particle-associated bacterial community exhibited a higher number of operational taxonomic units (OTUs) and was more heterogeneous in time and space than the free-living community. The temporal dynamics of the community structure were generally higher in isolated floodplain pools. The community structures of the river and the various floodplain pools, as well as those of the particle-associated and free-living bacteria, differed significantly. The compositional dynamics of the planktonic bacterial communities were related to changes in the algal biomass, temperature, and concentrations of organic and inorganic nutrients. The OTU richness of the free-living community was correlated with the concentration and origin of organic matter and the concentration of inorganic nutrients, while no correlation with the OTU richness of the particle-associated assemblage was found. Our results demonstrate the importance of the river-floodplain interactions and the influence of damming and regulation on the bacterial-community composition. PMID:15691909

Bacterial Community Composition Associated with Chironomid Egg Masses

PubMed Central

Senderovich, Yigal; Halpern, Malka

2012-01-01

Chironomids (Diptera: Chironomidae) are the most widely distributed and often the most abundant insect in freshwater. They undergo a complete metamorphosis of four life stages, of which the egg, larva, and pupae are aquatic and the adult is terrestrial. Chironomid egg masses were found to be natural reservoirs of Vibrio cholerae and Aeromonas species. To expand the knowledge of the endogenous bacterial community associated with chironomid egg masses, denaturing gradient gel electrophoresis and clone analysis of 16S rRNA gene libraries were used in this study. Bacterial community composition associated with chironomid egg masses was found to be stable among different sampling periods. Cloned libraries of egg masses revealed that about 40% of the clones were related to bacteria known to degrade various toxicants. These findings were further supported when bacterial species that showed resistance to different toxic metals were isolated from egg masses and larval samples. Chironomids are found under a wide range of water conditions and are able to survive pollutants. However, little is known about their protective mechanisms under these conditions. Chironomid egg masses are inhabited by a stable endogenous bacterial community, which may potentially play a role in protecting chironomids from toxicants in polluted environments. Further study is needed to support this hypothesis. PMID:23461272

Data Integration Tool: Permafrost Data Debugging

NASA Astrophysics Data System (ADS)

Wilcox, H.; Schaefer, K. M.; Jafarov, E. E.; Pulsifer, P. L.; Strawhacker, C.; Yarmey, L.; Basak, R.

2017-12-01

We developed a Data Integration Tool (DIT) to significantly speed up the time of manual processing needed to translate inconsistent, scattered historical permafrost data into files ready to ingest directly into the Global Terrestrial Network-Permafrost (GTN-P). The United States National Science Foundation funded this project through the National Snow and Ice Data Center (NSIDC) with the GTN-P to improve permafrost data access and discovery. We leverage this data to support science research and policy decisions. DIT is a workflow manager that divides data preparation and analysis into a series of steps or operations called widgets (https://github.com/PermaData/DIT). Each widget does a specific operation, such as read, multiply by a constant, sort, plot, and write data. DIT allows the user to select and order the widgets as desired to meet their specific needs, incrementally interact with and evolve the widget workflows, and save those workflows for reproducibility. Taking ideas from visual programming found in the art and design domain, debugging and iterative design principles from software engineering, and the scientific data processing and analysis power of Fortran and Python it was written for interactive, iterative data manipulation, quality control, processing, and analysis of inconsistent data in an easily installable application. DIT was used to completely translate one dataset (133 sites) that was successfully added to GTN-P, nearly translate three datasets (270 sites), and is scheduled to translate 10 more datasets ( 1000 sites) from the legacy inactive site data holdings of the Frozen Ground Data Center (FGDC). Iterative development has provided the permafrost and wider scientific community with an extendable tool designed specifically for the iterative process of translating unruly data.

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica.

PubMed

Goordial, Jacqueline; Davila, Alfonso; Lacelle, Denis; Pollard, Wayne; Marinova, Margarita M; Greer, Charles W; DiRuggiero, Jocelyn; McKay, Christopher P; Whyte, Lyle G

2016-07-01

Some of the coldest and driest permafrost soils on Earth are located in the high-elevation McMurdo Dry Valleys (MDVs) of Antarctica, but little is known about the permafrost microbial communities other than that microorganisms are present in these valleys. Here, we describe the microbiology and habitable conditions of highly unique dry and ice-cemented permafrost in University Valley, one of the coldest and driest regions in the MDVs (1700 m above sea level; mean temperature -23 °C; no degree days above freezing), where the ice in permafrost originates from vapour deposition rather than liquid water. We found that culturable and total microbial biomass in University Valley was extremely low, and microbial activity under ambient conditions was undetectable. Our results contrast with reports from the lower-elevation Dry Valleys and Arctic permafrost soils where active microbial populations are found, suggesting that the combination of severe cold, aridity, oligotrophy of University Valley permafrost soils severely limit microbial activity and survival.

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica

PubMed Central

Goordial, Jacqueline; Davila, Alfonso; Lacelle, Denis; Pollard, Wayne; Marinova, Margarita M; Greer, Charles W; DiRuggiero, Jocelyn; McKay, Christopher P; Whyte, Lyle G

2016-01-01

Some of the coldest and driest permafrost soils on Earth are located in the high-elevation McMurdo Dry Valleys (MDVs) of Antarctica, but little is known about the permafrost microbial communities other than that microorganisms are present in these valleys. Here, we describe the microbiology and habitable conditions of highly unique dry and ice-cemented permafrost in University Valley, one of the coldest and driest regions in the MDVs (1700 m above sea level; mean temperature −23 °C; no degree days above freezing), where the ice in permafrost originates from vapour deposition rather than liquid water. We found that culturable and total microbial biomass in University Valley was extremely low, and microbial activity under ambient conditions was undetectable. Our results contrast with reports from the lower-elevation Dry Valleys and Arctic permafrost soils where active microbial populations are found, suggesting that the combination of severe cold, aridity, oligotrophy of University Valley permafrost soils severely limit microbial activity and survival. PMID:27323892

Diversity of bacterial communities and dissolved organic matter in a temperate estuary.

PubMed

Osterholz, Helena; Kirchman, David L; Niggemann, Jutta; Dittmar, Thorsten

2018-06-14

Relationships between bacterial community and dissolved organic matter (DOM) include microbial uptake, transformation and secretion, all of which influence DOM composition. In this study, we explore diversity and similarity metrics of dissolved organic molecules (Fourier-transform ion cyclotron resonance mass spectrometry) and bacterial communities (tag-sequencing of 16S rRNA genes) along the salinity gradient of the Delaware Estuary (USA). We found that even though mixing, discharge and seasonal changes explained most of the variation in DOM and bacterial communities, there was still a relationship, albeit weak, between the composition of DOM and bacterial communities in the estuary. Overall, many DOM molecular formulas (MFs) and bacterial operational taxonomic units (OTUs) reoccurred over years and seasons while the frequency of MF-OTU correlations varied. Diversity based on MFs and OTUs was significantly correlated, decreasing towards the open ocean. However, while the diversity of bacterial OTUs dropped markedly with low salinity, MF diversity decreased strongly only at high salinities. We hypothesize that the different turnover times of DOM and bacteria lead to different abundance distributions of OTUs and MFs. A significant portion of the detected DOM is of a more refractory nature with lifetimes largely exceeding the mixing time of the estuary, while bacterial community turnover times in the Delaware Estuary are estimated at several days.

Detecting macroecological patterns in bacterial communities across independent studies of global soils.

PubMed

Ramirez, Kelly S; Knight, Christopher G; de Hollander, Mattias; Brearley, Francis Q; Constantinides, Bede; Cotton, Anne; Creer, Si; Crowther, Thomas W; Davison, John; Delgado-Baquerizo, Manuel; Dorrepaal, Ellen; Elliott, David R; Fox, Graeme; Griffiths, Robert I; Hale, Chris; Hartman, Kyle; Houlden, Ashley; Jones, David L; Krab, Eveline J; Maestre, Fernando T; McGuire, Krista L; Monteux, Sylvain; Orr, Caroline H; van der Putten, Wim H; Roberts, Ian S; Robinson, David A; Rocca, Jennifer D; Rowntree, Jennifer; Schlaeppi, Klaus; Shepherd, Matthew; Singh, Brajesh K; Straathof, Angela L; Bhatnagar, Jennifer M; Thion, Cécile; van der Heijden, Marcel G A; de Vries, Franciska T

2018-02-01

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Modulation of post-antibiotic bacterial community reassembly and host response by Candida albicans.

PubMed

Erb Downward, John R; Falkowski, Nicole R; Mason, Katie L; Muraglia, Ryan; Huffnagle, Gary B

2013-01-01

The introduction of Candida albicans into cefoperazone-treated mice results in changes in bacterial community reassembly. Our objective was to use high-throughput sequencing to characterize at much greater depth the specific changes in the bacterial microbiome. The colonization of C. albicans significantly altered bacterial community reassembly that was evident at multiple taxonomic levels of resolution. There were marked changes in the levels of Bacteriodetes and Lactobacillaceae. Lachnospiraceae and Ruminococcaceae, the two most abundant bacterial families, did not change in relative proportions after antibiotics, but there were marked genera-level shifts within these two bacterial families. The microbiome shifts occurred in the absence of overt intestinal inflammation. Overall, these experiments demonstrate that the introduction of a single new microbe in numerically inferior numbers into the bacterial microbiome during a broad community disturbance has the potential to significantly alter the subsequent reassembly of the bacterial community as it recovers from that disturbance.

Pyrosequencing analysis of the bacterial community in drinking water wells.

PubMed

Navarro-Noya, Yendi E; Suárez-Arriaga, Mayra C; Rojas-Valdes, Aketzally; Montoya-Ciriaco, Nina M; Gómez-Acata, Selene; Fernández-Luqueño, Fabián; Dendooven, Luc

2013-07-01

Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers

PubMed Central

Jiang, Tieshan; Mandal, Rabindra K.; Wideman, Robert F.; Khatiwara, Anita; Pevzner, Igal; Min Kwon, Young

2015-01-01

Bacterial chondronecrosis with osteomyelitis (BCO) is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens). Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9%) comprised the most common phylum, followed by Firmicutes (6.1%) and Actinobacteria (2.6%), accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia), lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions), and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of lameness in

The International Permafrost Association: new structure and initiatives for cryospheric research

NASA Astrophysics Data System (ADS)

May, I.; Lewkowicz, A. G.; Christiansen, H.; Romanovsky, V. E.; Lantuit, H.; Schrott, L.; Sergeev, D.; Wei, M.

2012-12-01

The International Permafrost Association (IPA), founded in 1983, has as its objectives to foster the dissemination of knowledge concerning permafrost and to promote cooperation among persons and national or international organizations engaged in scientific investigation and engineering work on permafrost. The IPA's primary responsibilities are convening International Permafrost Conferences, undertaking special projects such as preparing databases, maps, bibliographies, and glossaries, and coordinating international field programs and networks. Membership is through adhering national or multinational organizations or as individuals in countries where no Adhering Body exists. The IPA is governed by its Executive Committee and a Council consisting of representatives from 26 Adhering Bodies having interests in some aspect of theoretical, basic and applied frozen ground research, including permafrost, seasonal frost, artificial freezing and periglacial phenomena. This presentation details recent and ongoing changes in the functioning of the IPA that will influence the way cryospheric research is conducted under its auspices. One of the most important is the development of competitively-funded Action Groups which work towards the production of well-defined products over a period of two years. Since the first call, four proposals have been accepted by the Executive Committee and the teams are currently working on high topical issues, such as the assessment of the deep permafrost organic carbon pools and the mapping of subsea permafrost, as well as fundamental questions such as the extent of permafrost during the Last Permafrost Maximum. The IPA also decided to put additional effort into facilitating the study of the significance of permafrost to the global climate systems, with human aspects playing a very important role. To achieve this goal, the IPA will encourage and assist the climate modeling community in improving the representation of perennially frozen ground

Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils

PubMed Central

Delgado-Balbuena, Laura; Bello-López, Juan M.; Navarro-Noya, Yendi E.; Rodríguez-Valentín, Analine; Luna-Guido, Marco L.; Dendooven, Luc

2016-01-01

Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the

Response of soil bacterial community to repeated applications of carbendazim.

PubMed

Wang, Xiuguo; Song, Min; Wang, Yiqi; Gao, Chunming; Zhang, Qun; Chu, Xiaoqiang; Fang, Hua; Yu, Yunlong

2012-01-01

The effect of repeated carbendazim applications on functional diversity of culturable microorganisms and bacterial community composition was studied under field conditions. The functional diversity of soil culturable microbial community (Shannon index, H') reduced significantly (P<0.05) after the first introduction of carbendazim at levels of 0.94, 1.88 and 4.70 kg active ingredient (a.i.)ha(-1) and then recovered to that in the control with subsequent applications. An evident (P<0.01) difference in the bacterial community composition was observed after the second carbendazim application by Temperature Gradient Gel Electrophoresis (TGGE) analysis of 16S rRNA genes amplified from treated and control soils, which remained after the third and fourth treatments. Our results indicated that repeated carbendazim applications have a transient harmful effect on functional diversity of soil culturable microbial community and result in an alteration in bacterial community composition largely due to one species within the γ-proteobacterium. Copyright © 2011 Elsevier Inc. All rights reserved.

Nutrient-enhanced n-alkanes biodegradation and succession of bacterial communities

NASA Astrophysics Data System (ADS)

Sun, Yanyu; Wang, Hui; Li, Junde; Wang, Bin; Qi, Cancan; Hu, Xiaoke

2017-11-01

Bioremediation, is an effective and environment-friendly method of cleaning up crude oil pollution after an oil spill. However, the in situ bioremediation of crude oil is usually inhibited by deficiency of inorganic nutrients. To understand the effects of nutrient addition on the bioremediation of crude oil and the succession of bacterial communities during process of bioremediation, microcosms containing oil-contaminated sediments were constructed and biodegradation of crude oil was assessed based on the depletion of different ingredients. We used two culture-independent methods, denaturing gradient gel electrophoresis and a 16S rRNA gene based clone library, to analyze the succession of bacterial communities. The results suggested n-alkanes were degraded after 30 days and that nutrient amendments significantly improved the efficiency of their biodegradation. Moreover, oil contamination and nutrient amendments could dramatically change bacterial community structures. Lower diversity was detected after being contaminated with oil. For instance, bacterial clones affiliated with the phylum Armatimonadetes, Firmicutes, Gemmatimonadetes, and Planctomycetes and the class Deltaproteobacteria and Epsilonproteobacteria could not be identified after 30 days of incubation with crude oil. However, "professional hydrocarbonocastic bacteria" became abundant in samples treated with oil during the bioremediation period, while these clones were almost completely absent from the control plots. Interestingly, bioinformatics analysis showed that even when dramatic differences in oil biodegradation efficiency were observed, bacterial communities in the plots with nutrient amendments were not significantly different from those in plots treated with oil alone. These findings indicated that nutrient amendments could stimulate the process of biodegradation but had less impact on bacterial communities. Overall, nutrient amendments might be able to stimulate the growth of n-alkane degrading

The Gut Bacterial Community of Mammals from Marine and Terrestrial Habitats

PubMed Central

Nelson, Tiffanie M.; Rogers, Tracey L.; Brown, Mark V.

2013-01-01

After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals) and the marine herbivore (dugong) possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores) feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness. PMID:24386245

The gut bacterial community of mammals from marine and terrestrial habitats.

PubMed

Nelson, Tiffanie M; Rogers, Tracey L; Brown, Mark V

2013-01-01

After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals) and the marine herbivore (dugong) possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores) feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness.

Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments.

PubMed

Laverock, Bonnie; Smith, Cindy J; Tait, Karen; Osborn, A Mark; Widdicombe, Steve; Gilbert, Jack A

2010-12-01

Bioturbation is a key process in coastal sediments, influencing microbially driven cycling of nutrients as well as the physical characteristics of the sediment. However, little is known about the distribution, diversity and function of the microbial communities that inhabit the burrows of infaunal macroorganisms. In this study, terminal-restriction fragment length polymorphism analysis was used to investigate variation in the structure of bacterial communities in sediment bioturbated by the burrowing shrimp Upogebia deltaura or Callianassa subterranea. Analyses of 229 sediment samples revealed significant differences between bacterial communities inhabiting shrimp burrows and those inhabiting ambient surface and subsurface sediments. Bacterial communities in burrows from both shrimp species were more similar to those in surface-ambient than subsurface-ambient sediment (R=0.258, P<0.001). The presence of shrimp was also associated with changes in bacterial community structure in surrounding surface sediment, when compared with sediments uninhabited by shrimp. Bacterial community structure varied with burrow depth, and also between individual burrows, suggesting that the shrimp's burrow construction, irrigation and maintenance behaviour affect the distribution of bacteria within shrimp burrows. Subsequent sequence analysis of bacterial 16S rRNA genes from surface sediments revealed differences in the relative abundance of bacterial taxa between shrimp-inhabited and uninhabited sediments; shrimp-inhabited sediment contained a higher proportion of proteobacterial sequences, including in particular a twofold increase in Gammaproteobacteria. Chao1 and ACE diversity estimates showed that taxon richness within surface bacterial communities in shrimp-inhabited sediment was at least threefold higher than that in uninhabited sediment. This study shows that bioturbation can result in significant structural and compositional changes in sediment bacterial communities, increasing

Permafrost Hazards and Linear Infrastructure

NASA Astrophysics Data System (ADS)

Stanilovskaya, Julia; Sergeev, Dmitry

2014-05-01

The international experience of linear infrastructure planning, construction and exploitation in permafrost zone is being directly tied to the permafrost hazard assessment. That procedure should also consider the factors of climate impact and infrastructure protection. The current global climate change hotspots are currently polar and mountain areas. Temperature rise, precipitation and land ice conditions change, early springs occur more often. The big linear infrastructure objects cross the territories with different permafrost conditions which are sensitive to the changes in air temperature, hydrology, and snow accumulation which are connected to climatic dynamics. One of the most extensive linear structures built on permafrost worldwide are Trans Alaskan Pipeline (USA), Alaska Highway (Canada), Qinghai-Xizang Railway (China) and Eastern Siberia - Pacific Ocean Oil Pipeline (Russia). Those are currently being influenced by the regional climate change and permafrost impact which may act differently from place to place. Thermokarst is deemed to be the most dangerous process for linear engineering structures. Its formation and development depend on the linear structure type: road or pipeline, elevated or buried one. Zonal climate and geocryological conditions are also of the determining importance here. All the projects are of the different age and some of them were implemented under different climatic conditions. The effects of permafrost thawing have been recorded every year since then. The exploration and transportation companies from different countries maintain the linear infrastructure from permafrost degradation in different ways. The highways in Alaska are in a good condition due to governmental expenses on annual reconstructions. The Chara-China Railroad in Russia is under non-standard condition due to intensive permafrost response. Standards for engineering and construction should be reviewed and updated to account for permafrost hazards caused by the

Changes in the bacterial community of soybean rhizospheres during growth in the field.

PubMed

Sugiyama, Akifumi; Ueda, Yoshikatsu; Zushi, Takahiro; Takase, Hisabumi; Yazaki, Kazufumi

2014-01-01

Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field.

Bacterial community shift during the startup of a full-scale oxidation ditch treating sewage.

PubMed

Chen, Yajun; Ye, Lin; Zhao, Fuzheng; Xiao, Lin; Cheng, Shupei; Zhang, Xu-Xiang

2016-10-06

Oxidation ditch (OD) is one of the most widely used processes for treating municipal wastewater. However, the microbial communities in the OD systems have not been well characterized and little information about the shift of bacterial community during the startup process of the OD systems is available. In this study, we investigated the bacterial community changes during the startup period (over 100 days) of a full-scale OD. The results showed that the bacterial community dramatically changed during the startup period. Similar to the activated sludge samples in other studies, Proteobacteria (accounting for 26.3%~48.4%) was the most dominant bacterial phylum in the OD system but its relative abundance declined nearly 40% during the startup process. It was also found that Planctomycetes proliferated greatly (from 4.79% to 13.5%) and finally replaced Bacteroidetes as the second abundant phylum in the OD system. Specifically, some bacteria affiliated with Flavobacterium genus of exhibited remarkable decreasing trends, while bacterial species belonging to OD1 candidate division and Saprospiraceae family were found to increase during the startup process. Despite of the bacterial community shift, the organic matter, nitrogen and phosphorus in the effluent were always in low concentrations, suggesting the functional redundancy of the bacterial community. Moreover, by comparing with the bacterial community in other municipal wastewater treatment bioreactors, some potentially novel bacterial species were found to be present in the OD system. Collectively, this study improved our understandings of bacterial community structure and the microbial ecology during the startup of full-scale wastewater treatment bioreactor.

Well cementing in permafrost

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

Wilson, W.N.

1979-12-04

A process for cementing a string of pipe in the permafrost region of a borehole of a well wherein aqueous drilling fluid actually used in drilling the wellbore in the permafrost region of a wellbore is employed. The drilling fluid contains or is adjusted to contain from about 2 to about 16 volume percent solids. Mixing with the drilling fluid (1) an additive selected from the group consisting of lignosulfonate, lignite, tannin, and mixtures thereof, (2) sufficient base to raise the pH of the drilling fluid into the range of from about 9 to about 12, and (3) cementitious materialmore » which will harden in from about 30 to about 40 hours at 40/sup 0/F. The resulting mixture is pumped into the permafrost region of a wellbore to be cemented and allowed to harden in the wellbore. There is also provided a process for treating an aqueous drilling fluid after it has been used in drilling the wellbore in permafrost, and a cementitious composition fro cementing in a permafrost region of a wellbore.« less

Well cementing in permafrost

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

Wilson, W.N.

1980-01-01

A process for cementing a string of pipe in the permafrost region of a borehole of a well wherein aqueous drilling fluid actually used in drilling the wellbore in the permafrost region of a wellbore is employed. The drilling fluid contains or is adjusted to contain from about 2 to about 16 volume percent solids. Mixing with the drilling fluid (1) an additive selected from the group consisting of ligno-sulfonate, lignite, tannin, and mixtures thereof, (2) sufficient base to raise the pH of the drilling fluid into the range of from about 9 to about 12, and (3) cementitious materialmore » which will harden in from about 30 to about 40 hours at 40/sup 0/F. The resulting mixture is pumped into the permafrost region of a wellbore to be cemented and allowed to harden in the wellbore. There is also provided a process for treating an aqueous drilling fluid after it has been used in drilling the wellbore in permafrost, and a cementitious composition for cementing in a permafrost region of a wellbore.« less

Invasive lionfish harbor a different external bacterial community than native Bahamian fishes

NASA Astrophysics Data System (ADS)

Stevens, J. L.; Olson, J. B.

2013-12-01

The introduction and subsequent spread of lionfish into the Atlantic Ocean and Caribbean Sea has become a worldwide conservation issue. These highly successful invaders may also be capable of introducing non-native microorganisms to the invaded regions. This study compared the bacterial communities associated with lionfish external tissue to those of native Bahamian fishes and ambient water. Terminal restriction fragment length polymorphism analyses demonstrated that lionfish bacterial communities were significantly different than those associated with three native Bahamian fishes. Additionally, all fishes harbored distinct bacterial communities from the ambient bacterioplankton. Analysis of bacterial clone libraries from invasive lionfish and native squirrelfish indicated that lionfish communities were more diverse than those associated with squirrelfish, yet did not contain known fish pathogens. Using microscopy and molecular genetic approaches, lionfish eggs were examined for the presence of bacteria to evaluate the capacity for vertical transmission. Eggs removed from the ovaries of gravid females were free of bacteria, suggesting that lionfish likely acquire bacteria from the environment. This study was the first examination of bacterial communities associated with the invasive lionfish and indicated that they support different communities of environmentally derived bacteria than Caribbean reef fishes.

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.

PubMed

Luo, Gang; Angelidaki, Irini

2014-09-01

The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. Copyright © 2014 Elsevier

Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

PubMed

Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

2013-03-01

We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Molecular characterization of soil bacterial community in a perhumid, low mountain forest.

PubMed

Lin, Yu-Te; Whitman, William B; Coleman, David C; Chih-Yu, Chiu

2011-01-01

Forest disturbance often results in changes in soil properties and microbial communities. In the present study, we characterized a soil bacterial community subjected to disturbance using 16S rRNA gene clone libraries. The community was from a disturbed broad-leaved, low mountain forest ecosystem at Huoshaoliao (HSL) located in northern Taiwan. This locality receives more than 4,000 mm annual precipitation, one of the highest precipitations in Taiwan. Based on the Shannon diversity index, Chao1 estimator, richness and rarefaction curve analysis, the bacterial community in HSL forest soils was more diverse than those previously investigated in natural and disturbed forest soils with colder or less humid weather conditions. Analysis of molecular variance also revealed that the bacterial community in disturbed soils significantly differed from natural forest soils. Most of the abundant operational taxonomic units (OTUs) in the disturbed soil community at HSL were less abundant or absent in other soils. The disturbances influenced the composition of bacterial communities in natural and disturbed forests and increased the diversity of the disturbed forest soil community. Furthermore, the warmer and humid weather conditions could also increase community diversity in HSL soils.

Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds

PubMed Central

Vincent, Warwick F.; Comte, Jérôme; Matveev, Alex; Lovejoy, Connie

2017-01-01

Lakes and ponds derived from thawing permafrost are strong emitters of carbon dioxide and methane to the atmosphere, but little is known about the methane oxidation processes in these waters. Here we investigated the distribution and potential activity of aerobic methanotrophic bacteria in thaw ponds in two types of eroding permafrost landscapes in subarctic Québec: peatlands and mineral soils. We hypothesized that methanotrophic community composition and potential activity differ regionally as a function of the landscape type and permafrost degradation stage, and locally as a function of depth-dependent oxygen conditions. Our analysis of pmoA transcripts by Illumina amplicon sequencing and quantitative PCR showed that the communities were composed of diverse and potentially active lineages. Type I methanotrophs, particularly Methylobacter, dominated all communities, however there was a clear taxonomic separation between the two landscape types, consistent with environmental control of community structure. In contrast, methanotrophic potential activity, measured by pmoA transcript concentrations, did not vary with landscape type, but correlated with conductivity, phosphorus and total suspended solids. Methanotrophic potential activity was also detected in low-oxygen bottom waters, where it was inversely correlated with methane concentrations, suggesting methane depletion by methanotrophs. Methanotrophs were present and potentially active throughout the water column regardless of oxygen concentration, and may therefore be resilient to future mixing and oxygenation regimes in the warming subarctic. PMID:29182670

Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds.

PubMed

Crevecoeur, Sophie; Vincent, Warwick F; Comte, Jérôme; Matveev, Alex; Lovejoy, Connie

2017-01-01

Lakes and ponds derived from thawing permafrost are strong emitters of carbon dioxide and methane to the atmosphere, but little is known about the methane oxidation processes in these waters. Here we investigated the distribution and potential activity of aerobic methanotrophic bacteria in thaw ponds in two types of eroding permafrost landscapes in subarctic Québec: peatlands and mineral soils. We hypothesized that methanotrophic community composition and potential activity differ regionally as a function of the landscape type and permafrost degradation stage, and locally as a function of depth-dependent oxygen conditions. Our analysis of pmoA transcripts by Illumina amplicon sequencing and quantitative PCR showed that the communities were composed of diverse and potentially active lineages. Type I methanotrophs, particularly Methylobacter, dominated all communities, however there was a clear taxonomic separation between the two landscape types, consistent with environmental control of community structure. In contrast, methanotrophic potential activity, measured by pmoA transcript concentrations, did not vary with landscape type, but correlated with conductivity, phosphorus and total suspended solids. Methanotrophic potential activity was also detected in low-oxygen bottom waters, where it was inversely correlated with methane concentrations, suggesting methane depletion by methanotrophs. Methanotrophs were present and potentially active throughout the water column regardless of oxygen concentration, and may therefore be resilient to future mixing and oxygenation regimes in the warming subarctic.

Evidence of in situ microbial activity and sulphidogenesis in perennially sub-0 °C and hypersaline sediments of a high Arctic permafrost spring.

PubMed

Lamarche-Gagnon, Guillaume; Comery, Raven; Greer, Charles W; Whyte, Lyle G

2015-01-01

The lost hammer (LH) spring perennially discharges subzero hypersaline reducing brines through thick layers of permafrost and is the only known terrestrial methane seep in frozen settings on Earth. The present study aimed to identify active microbial communities that populate the sediments of the spring outlet, and verify whether such communities vary seasonally and spatially. Microcosm experiments revealed that the biological reduction of sulfur compounds (SR) with hydrogen (e.g., sulfate reduction) was potentially carried out under combined hypersaline and subzero conditions, down to -20 °C, the coldest temperature ever recorded for SR. Pyrosequencing analyses of both 16S rRNA (i.e., cDNA) and 16S rRNA genes (i.e., DNA) of sediments retrieved in late winter and summer indicated fairly stable bacterial and archaeal communities at the phylum level. Potentially active bacterial and archaeal communities were dominated by clades related to the T78 Chloroflexi group and Halobacteria species, respectively. The present study indicated that SR, hydrogenotrophy (possibly coupled to autotrophy), and short-chain alkane degradation (other than methane), most likely represent important, previously unaccounted for, metabolic processes carried out by LH microbial communities. Overall, the obtained findings provided additional evidence that the LH system hosts active communities of anaerobic, halophilic, and cryophilic microorganisms despite the extreme conditions in situ.

Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand.

PubMed

Truu, Marika; Ostonen, Ivika; Preem, Jens-Konrad; Lõhmus, Krista; Nõlvak, Hiie; Ligi, Teele; Rosenvald, Katrin; Parts, Kaarin; Kupper, Priit; Truu, Jaak

2017-01-01

Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch ( Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes. The increased air humidity altered both bulk soil and rhizosphere bacterial community structures, and changes in the bacterial communities initiated by elevated air humidity were related to modified soil abiotic and biotic variables. Network analysis revealed that variation in soil bacterial community structural units is explained by altered abiotic conditions such as increased pH value in bulk soil, while in rhizosphere the change in absorptive root morphology had a higher effect. Among root morphological traits, the absorptive root diameter was strongest related to the bacterial community structure. The changes in bacterial community structures under elevated air humidity are associated with shifts in C, N, and P turnover as well as mineral weathering processes in soil. Increased air humidity decreased the nir and nosZ gene abundance in the rhizosphere bacterial community. The potential contribution of the denitrification to the N 2 O emission was not affected by the elevated air humidity in birch stand soil. In addition, the study revealed a strong link between the bacterial community structure, abundance of denitrification related genes, and birch absorptive root morphology in the ecosystem system adaptation to elevated air humidity.

Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand

PubMed Central

Truu, Marika; Ostonen, Ivika; Preem, Jens-Konrad; Lõhmus, Krista; Nõlvak, Hiie; Ligi, Teele; Rosenvald, Katrin; Parts, Kaarin; Kupper, Priit; Truu, Jaak

2017-01-01

Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch (Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes. The increased air humidity altered both bulk soil and rhizosphere bacterial community structures, and changes in the bacterial communities initiated by elevated air humidity were related to modified soil abiotic and biotic variables. Network analysis revealed that variation in soil bacterial community structural units is explained by altered abiotic conditions such as increased pH value in bulk soil, while in rhizosphere the change in absorptive root morphology had a higher effect. Among root morphological traits, the absorptive root diameter was strongest related to the bacterial community structure. The changes in bacterial community structures under elevated air humidity are associated with shifts in C, N, and P turnover as well as mineral weathering processes in soil. Increased air humidity decreased the nir and nosZ gene abundance in the rhizosphere bacterial community. The potential contribution of the denitrification to the N2O emission was not affected by the elevated air humidity in birch stand soil. In addition, the study revealed a strong link between the bacterial community structure, abundance of denitrification related genes, and birch absorptive root morphology in the ecosystem system adaptation to elevated air humidity. PMID:28421053

Assessing the impact of fungicide enostroburin application on bacterial community in wheat phyllosphere.

PubMed

Gu, Likun; Bai, Zhihui; Jin, Bo; Hu, Qing; Wang, Huili; Zhuang, Guoqiang; Zhang, Hongxun

2010-01-01

Fungicides have been used extensively for controlling fungal pathogens of plants. However, little is known regarding the effects that fungicides upon the indigenous bacterial communities within the plant phyllosphere. The aims of this study were to assess the impact of fungicide enostroburin upon bacterial communities in wheat phyllosphere. Culture-independent methodologies of 16S rDNA clone library and 16S rDNA directed polymerase chain reaction with denaturing gradient gel electrophoresis (PCR-DGGE) were used for monitoring the change of bacterial community. The 16S rDNA clone library and PCR-DGGE analysis both confirmed the microbial community of wheat plant phyllosphere were predominantly of the gamma-Proteobacteria phyla. Results from PCR-DGGE analysis indicated a significant change in bacterial community structure within the phyllosphere following fungicide enostroburin application. Bands sequenced within control cultures were predominantly of Pseudomonas genus, but those bands sequenced in the treated samples were predominantly strains of Pantoea genus and Pseudomonas genus. Of interest was the appearance of two DGGE bands following fungicide treatment, one of which had sequence similarities (98%) to Pantoea sp. which might be a competitor of plant pathogens. This study revealed the wheat phyllosphere bacterial community composition and a shift in the bacterial community following fungicide enostroburin application.

Distinctive bacterial communities in the rhizoplane of four tropical tree species.

PubMed

Oh, Yoon Myung; Kim, Mincheol; Lee-Cruz, Larisa; Lai-Hoe, Ang; Go, Rusea; Ainuddin, N; Rahim, Raha Abdul; Shukor, Noraini; Adams, Jonathan M

2012-11-01

It is known that the microbial community of the rhizosphere is not only influenced by factors such as root exudates, phenology, and nutrient uptake but also by the plant species. However, studies of bacterial communities associated with tropical rainforest tree root surfaces, or rhizoplane, are lacking. Here, we analyzed the bacterial community of root surfaces of four species of native trees, Agathis borneensis, Dipterocarpus kerrii, Dyera costulata, and Gnetum gnemon, and nearby bulk soils, in a rainforest arboretum in Malaysia, using 454 pyrosequencing of the 16S rRNA gene. The rhizoplane bacterial communities for each of the four tree species sampled clustered separately from one another on an ordination, suggesting that these assemblages are linked to chemical and biological characteristics of the host or possibly to the mycorrhizal fungi present. Bacterial communities of the rhizoplane had various similarities to surrounding bulk soils. Acidobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant in rhizoplane communities and in bulk soils from the same depth (0-10 cm). In contrast, the relative abundance of certain bacterial lineages on the rhizoplane was different from that in bulk soils: Bacteroidetes and Betaproteobacteria, which are known as copiotrophs, were much more abundant in the rhizoplane in comparison to bulk soil. At the genus level, Burkholderia, Acidobacterium, Dyella, and Edaphobacter were more abundant in the rhizoplane. Burkholderia, which are known as both pathogens and mutualists of plants, were especially abundant on the rhizoplane of all tree species sampled. The Burkholderia species present included known mutualists of tropical crops and also known N fixers. The host-specific character of tropical tree rhizoplane bacterial communities may have implications for understanding nutrient cycling, recruitment, and structuring of tree species diversity in tropical forests. Such understanding may prove to be useful in both

Carbendazim induces a temporary change in soil bacterial community structure.

PubMed

Wang, Xiuguo; Song, Min; Gao, Chunming; Dong, Bin; Zhang, Qun; Fang, Hua; Yu, Yunlong

2009-01-01

The effect of carbendazim applications on the diversity and structure of a soil bacterial community was studied under field conditions using temperature gradient gel electrophoresis (TGGE) and partial sequence analysis of PCR-amplified 16S rRNA gene. After four successive introductions of carbendazim at a level of 0.94 kg active ingredient (a.i.)/ha, the genetic diversity (expressed as Shannon index, H') decreased from 1.43 in the control to 1.29 in treated soil. This harmful effect seems to increase with the concentration of carbendazim. The value of H' in the soil treated with carbendazim at 4.70 kg a.i./ha was reduced to 1.05 (P < or = 0.05). The structure of soil bacterial community was also affected after four repeated applications of carbendazim at levels of 0.94, 1.88 and 4.70 kg a.i./ha, as seen in the relative intensities of the individual band. However, the bacterial community in carbendazim-treated soil recovered to that in the control 360 d after the first treatment. The results indicated that repeated applications of carbendazim could reduce soil microbial diversity and alter the bacterial community structure temporarily.

Canopy soil bacterial communities altered by severing host tree limbs

PubMed Central

Dangerfield, Cody R.; Nadkarni, Nalini M.

2017-01-01

Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities. PMID:28894646

Canopy soil bacterial communities altered by severing host tree limbs.

PubMed

Dangerfield, Cody R; Nadkarni, Nalini M; Brazelton, William J

2017-01-01

Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.

Temperature adaptation of bacterial communities in experimentally warmed forest soils.

PubMed

Rousk, Johannes; Frey, Serita D; Bååth, Erland

2012-10-01

A detailed understanding of the influence of temperature on soil microbial activity is critical to predict future atmospheric CO 2 concentrations and feedbacks to anthropogenic warming. We investigated soils exposed to 3-4 years of continuous 5 °C-warming in a field experiment in a temperate forest. We found that an index for the temperature adaptation of the microbial community, T min for bacterial growth, increased by 0.19 °C per 1 °C rise in temperature, showing a community shift towards one adapted to higher temperature with a higher temperature sensitivity (Q 10(5-15 °C) increased by 0.08 units per 1 °C). Using continuously measured temperature data from the field experiment we modelled in situ bacterial growth. Assuming that warming did not affect resource availability, bacterial growth was modelled to become 60% higher in warmed compared to the control plots, with the effect of temperature adaptation of the community only having a small effect on overall bacterial growth (<5%). However, 3 years of warming decreased bacterial growth, most likely due to substrate depletion because of the initially higher growth in warmed plots. When this was factored in, the result was similar rates of modelled in situ bacterial growth in warmed and control plots after 3 years, despite the temperature difference. We conclude that although temperature adaptation for bacterial growth to higher temperatures was detectable, its influence on annual bacterial growth was minor, and overshadowed by the direct temperature effect on growth rates. © 2012 Blackwell Publishing Ltd.

Characterizing the Bacterial Communities in Retail Stores in the United States

DTIC Science & Technology

2015-01-01

community or the factors that affect it. To our knowledge, only one study to date has investigated the indoor bacterial microbiome of retail stores...type of store affects the microbial community present, the impact of store type on the bacterial community was investigated by comparing the bacteria...genes analysis (Figure 2). Additionally, Leff and Fierer (2013) observed a high relative abundance of Enterobacteriaceae on fruits and vegetables but

Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community.

PubMed

Hortal, S; Lozano, Y M; Bastida, F; Armas, C; Moreno, J L; Garcia, C; Pugnaire, F I

2017-12-19

Competition is a key process that determines plant community structure and dynamics, often mediated by nutrients and water availability. However, the role of soil microorganisms on plant competition, and the links between above- and belowground processes, are not well understood. Here we show that the effects of interspecific plant competition on plant performance are mediated by feedbacks between plants and soil bacterial communities. Each plant species selects a singular community of soil microorganisms in its rhizosphere with a specific species composition, abundance and activity. When two plant species interact, the resulting soil bacterial community matches that of the most competitive plant species, suggesting strong competitive interactions between soil bacterial communities as well. We propose a novel mechanism by which changes in belowground bacterial communities promoted by the most competitive plant species influence plant performance and competition outcome. These findings emphasise the strong links between plant and soil communities, paving the way to a better understanding of plant community dynamics and the effects of soil bacterial communities on ecosystem functioning and services.

Hydrogeochemical characterisation of groundwater in a small watershed in a discontinuous permafrost zone.

NASA Astrophysics Data System (ADS)

Cochand, Marion; Molson, John; Barth, Johannes A. C.; van Geldern, Robert; Lemieux, Jean-Michel; Fortier, Richard; Therrien, René

2017-04-01

Impacts of climate change can already be seen in northern regions. However, the influence of increasing temperature and permafrost degradation on groundwater dynamics is still poorly understood. This study aims to improve knowledge on hydrogeological interactions in degrading permafrost environments using hydrogeochemical characterisation of groundwater. This study is being conducted in a small 2-km2 watershed, in a discontinuous permafrost zone located close to the Inuit community of Umiujaq, on the eastern shore of Hudson Bay in northern Québec, Canada. Two aquifers are being investigated, an unconfined shallow sandy aquifer located in the upper part of the watershed, and a deeper confined aquifer in sands and gravels located below the permafrost mounds. Precipitation, stream and surface water as well as ice-rich permafrost lenses were also sampled during field investigations. Various hydrogeochemical tracers including major ions, water stable isotopes (δ18OH2O and δ2HH2O), carbon phases (DIC, DOC, POC), their stable carbon isotopes (δ13C) and dating tracers (radiocarbon, tritium-helium and CFC/SF6) were analyzed. This characterisation has contributed to further understanding groundwater origin, evolution and residence time in the watershed. Preliminary results show that groundwater has a mainly Ca-HCO3 geochemical signature, typical for young and poorly evolved water. Furthermore, sample mineralisation is low, and is likely linked to limited bedrock weathering caused by short residence times, slow reaction rates as well as low levels of dissolved CO2 due to suppressed biological activity in the catchment. Inter-annual variation of major ions in the deeper aquifer is low. All groundwater samples have significant tritium concentrations, around 8.5 TU, reflecting modern recharge. Ice-rich permafrost lenses within the top four meters of permafrost have a water stable isotope signature close to modern precipitation and groundwater. This indicates that either

Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

PubMed Central

Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin

2016-01-01

ABSTRACT Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. IMPORTANCE In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study

Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

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

Jansson, Janet; Edlund, Anna; Hardeman, Fredrik

Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179 mV, -64 mV and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labeled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities weremore » most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labeled DNA and DNA from reverse transcription PCR (rt-PCR) showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.« less

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity

PubMed Central

Messier, Christian; Kembel, Steven W.

2017-01-01

ABSTRACT Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria. Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity.

PubMed

Laforest-Lapointe, Isabelle; Messier, Christian; Kembel, Steven W

2017-01-01

Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria . Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed.

PubMed

Song, Liyan; Li, Lei

2016-08-01

Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a

Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.

PubMed

Andrus, J Malia; Porter, Matthew D; Rodríguez, Luis F; Kuehlhorn, Timothy; Cooke, Richard A C; Zhang, Yuanhui; Kent, Angela D; Zilles, Julie L

2014-02-01

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

DOE PAGES

Linz, Alexandra M.; Crary, Benjamin C.; Shade, Ashley; ...

2017-06-28

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likelymore » reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “CandidatusOmnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

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

Linz, Alexandra M.; Crary, Benjamin C.; Shade, Ashley

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likelymore » reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “CandidatusOmnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community

Bacterial communities in soil samples from the Mingyong Glacier of southwestern China.

PubMed

Li, Haoyu; Taj, Muhammad Kamran; Ji, Xiuling; Zhang, Qi; Lin, Liangbing; Zhou, Zhimei; Wei, Yunlin

2017-05-01

The present study was an effort to determine the bacterial diversity of soils in Mingyong Glacier located at the Meili Snow Mountains of southwestern China. Mingyong Glacier has different climatic zones within a very narrow area, and bacterial community diversity in this low temperature area remains largely unknown. In this study, soil samples were collected from four different climatic zones: M11A (dry warm valley), M14 (forest), M15 (grass land), and M16 (glacier zones). Phylogenetic analysis based on 16S rRNA gene V6 hypervariable region showed high bacterial abundance in the glacier. The number of Operational Taxonomic Units ranged from 2.24×10 3 to 5.56×10 3 in soil samples. Statistical analysis of 16S rRNA gene clone libraries results showed that bacterial diversity in zones M11A，M14 and M16 are higher than in zone M15. The bacterial community structures are clearly distinguishable, and phylogenetic analysis showed that the predominant phyla were Proteobacteria, Deinococcus-Thermus, Firmicutes, Actinobacteria, and Nitrospirae in Mingyong Glacier. Seventy-nine different orders from four zones have been isolated. Bacterial diversity and distribution of bacterial communities related to the anthropogenic perturbations in zone (M15) were confirmed by diversity index analysis, and the diversity index of other three zones was satisfactory through this analysis software. The results suggest that bacterial diversity and distribution analyses using bacterial 16S rRNA gene V6 hypervariable region were successful, and bacterial communities in this area not only had the same bacterial phyla compared to other glaciers but also had their own rare species.

Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea)

PubMed Central

Pop Ristova, Petra; Wenzhöfer, Frank; Ramette, Alban; Felden, Janine; Boetius, Antje

2015-01-01

Cold seeps are highly productive, fragmented marine ecosystems that form at the seafloor around hydrocarbon emission pathways. The products of microbial utilization of methane and other hydrocarbons fuel rich chemosynthetic communities at these sites, with much higher respiration rates compared with the surrounding deep-sea floor. Yet little is known as to the richness, composition and spatial scaling of bacterial communities of cold seeps compared with non-seep communities. Here we assessed the bacterial diversity across nine different cold seeps in the Eastern Mediterranean deep-sea and surrounding seafloor areas. Community similarity analyses were carried out based on automated ribosomal intergenic spacer analysis (ARISA) fingerprinting and high-throughput 454 tag sequencing and were combined with in situ and ex situ geochemical analyses across spatial scales of a few tens of meters to hundreds of kilometers. Seep communities were dominated by Deltaproteobacteria, Epsilonproteobacteria and Gammaproteobacteria and shared, on average, 36% of bacterial types (ARISA OTUs (operational taxonomic units)) with communities from nearby non-seep deep-sea sediments. Bacterial communities of seeps were significantly different from those of non-seep sediments. Within cold seep regions on spatial scales of only tens to hundreds of meters, the bacterial communities differed considerably, sharing <50% of types at the ARISA OTU level. Their variations reflected differences in porewater sulfide concentrations from anaerobic degradation of hydrocarbons. This study shows that cold seep ecosystems contribute substantially to the microbial diversity of the deep-sea. PMID:25500510

Ericoid Roots and Mycospheres Govern Plant-Specific Bacterial Communities in Boreal Forest Humus.

PubMed

Timonen, Sari; Sinkko, Hanna; Sun, Hui; Sietiö, Outi-Maaria; Rinta-Kanto, Johanna M; Kiheri, Heikki; Heinonsalo, Jussi

2017-05-01

In this study, the bacterial populations of roots and mycospheres of the boreal pine forest ericoid plants, heather (Calluna vulgaris), bilberry (Vaccinium myrtillus), and lingonberry (Vaccinium vitis-idaea), were studied by qPCR and next-generation sequencing (NGS). All bacterial communities of mycosphere soils differed from soils uncolonized by mycorrhizal mycelia. Colonization by mycorrhizal hyphae increased the total number of bacterial 16S ribosomal DNA (rDNA) gene copies in the humus but decreased the number of different bacterial operational taxonomic units (OTUs). Nevertheless, ericoid roots and mycospheres supported numerous OTUs not present in uncolonized humus. Bacterial communities in bilberry mycospheres were surprisingly similar to those in pine mycospheres but not to bacterial communities in heather and lingonberry mycospheres. In contrast, bacterial communities of ericoid roots were more similar to each other than to those of pine roots. In all sample types, the relative abundances of bacterial sequences belonging to Alphaproteobacteria and Acidobacteria were higher than the sequences belonging to other classes. Soil samples contained more Actinobacteria, Deltaproteobacteria, Opitutae, and Planctomycetia, whereas Armatimonadia, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia were more common to roots. All mycosphere soils and roots harbored bacteria unique to that particular habitat. Our study suggests that the habitation by ericoid plants increases the overall bacterial diversity of boreal forest soils.

Permafrost slowly exhales methane

NASA Astrophysics Data System (ADS)

Herndon, Elizabeth M.

2018-04-01

Permafrost soils store vast quantities of organic matter that are vulnerable to decomposition under a warming climate. Recent research finds that methane release from thawing permafrost may outpace carbon dioxide as a major contributor to global warming over the next century.

Bacterial and fungal communities and contribution of physicochemical factors during cattle farm waste composting.

PubMed

Huhe; Jiang, Chao; Wu, Yanpei; Cheng, Yunxiang

2017-12-01

During composting, the composition of microbial communities is subject to constant change owing to interactions with fluctuating physicochemical parameters. This study explored the changes in bacterial and fungal communities during cattle farm waste composting and aimed to identify and prioritize the contributing physicochemical factors. Microbial community compositions were determined by high-throughput sequencing. While the predominant phyla in the bacterial and fungal communities were largely consistent during the composting, differences in relative abundances were observed. Bacterial and fungal community diversity and relative abundance varied significantly, and inversely, over time. Relationships between physicochemical factors and microbial community compositions were evaluated by redundancy analysis. The variation in bacterial community composition was significantly related to water-soluble organic carbon (WSOC), and pile temperature and moisture (p < .05), while the largest portions of variation in fungal community composition were explained by pile temperature, WSOC, and C/N (p < .05). These findings indicated that those parameters are the most likely ones to influence, or be influenced by the bacterial and fungal communities. Variation partitioning analyses indicated that WSOC and pile temperature had predominant effects on bacterial and fungal community composition, respectively. Our findings will be useful for improving the quality of cattle farm waste composts. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

The GTN-P Data Management System: A central database for permafrost monitoring parameters of the Global Terrestrial Network for Permafrost (GTN-P) and beyond

NASA Astrophysics Data System (ADS)

Lanckman, Jean-Pierre; Elger, Kirsten; Karlsson, Ævar Karl; Johannsson, Halldór; Lantuit, Hugues

2013-04-01

Permafrost is a direct indicator of climate change and has been identified as Essential Climate Variable (ECV) by the global observing community. The monitoring of permafrost temperatures, active-layer thicknesses and other parameters has been performed for several decades already, but it was brought together within the Global Terrestrial Network for Permafrost (GTN-P) in the 1990's only, including the development of measurement protocols to provide standardized data. GTN-P is the primary international observing network for permafrost sponsored by the Global Climate Observing System (GCOS) and the Global Terrestrial Observing System (GTOS), and managed by the International Permafrost Association (IPA). All GTN-P data was outfitted with an "open data policy" with free data access via the World Wide Web. The existing data, however, is far from being homogeneous: it is not yet optimized for databases, there is no framework for data reporting or archival and data documentation is incomplete. As a result, and despite the utmost relevance of permafrost in the Earth's climate system, the data has not been used by as many researchers as intended by the initiators of the programs. While the monitoring of many other ECVs has been tackled by organized international networks (e.g. FLUXNET), there is still no central database for all permafrost-related parameters. The European Union project PAGE21 created opportunities to develop this central database for permafrost monitoring parameters of GTN-P during the duration of the project and beyond. The database aims to be the one location where the researcher can find data, metadata, and information of all relevant parameters for a specific site. Each component of the Data Management System (DMS), including parameters, data levels and metadata formats were developed in cooperation with the GTN-P and the IPA. The general framework of the GTN-P DMS is based on an object oriented model (OOM), open for as many parameters as possible, and

Meteorological factors had more impact on airborne bacterial communities than air pollutants.

PubMed

Zhen, Quan; Deng, Ye; Wang, Yaqing; Wang, Xiaoke; Zhang, Hongxing; Sun, Xu; Ouyang, Zhiyun

2017-12-01

Airborne bacteria have gained increasing attention because they affect ecological balance and pose potential risks on human health. Recently, some studies have focused on the abundance and composition of airborne bacteria under heavy, hazy polluted weather in China, but they reached different conclusions about the comparisons with non-polluted days. In this study, we tested the hypothesis that meteorological factors could have a higher impact on shaping airborne bacterial communities than air pollutants by systematically monitoring the communities for 1year. Total suspended particles in Beijing were sampled for 20 consecutive days in each season of 2015. Bacterial abundance varied from 8.71×10 3 to 2.14×10 7 ribosomal operons per cubic meter according to the quantitative PCR analysis. There were relatively higher bacterial counts in spring and in autumn than in winter and summer. Airborne bacterial communities displayed a strong seasonality, according to the hierarchical cluster analysis. Only two exceptions overtook the seasonal trend, and both occurred in or after violent meteorological changes (sandstorm or rain). Aggregated boosted tree analysis performed on bacterial abundance showed that the dominant factors shaping bacterial communities were meteorological. They were air pressure in winter, air temperature and relative humidity in spring, RH in summer, and vapor pressure in autumn. Variation partition analysis on community structure showed that meteorological factors explained more variations than air pollutants. Therefore, both of the two models verified our hypothesis that the differences in airborne bacterial communities in polluted days or non-polluted days were mainly driven by the discrepancies of meteorological factors rather than by the presence of air pollutants. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterizing the bacterial communities in retail stores in the United States.

PubMed

Hoisington, A; Maestre, J P; Kinney, K A; Siegel, J A

2016-12-01

The microorganisms present in retail environments have not been studied in detail despite the fact that these environments represent a potentially important location for exposure. In this study, HVAC filter dust samples in 13 US retail stores were collected and analyzed via pyrosequencing to characterize the indoor bacterial communities and to explore potential relationships between these communities and building and environmental parameters. Although retail stores contained a diverse bacterial community of 788 unique genera, over half of the nearly 118K sequences were attributed to the Proteobacteria phylum. Streptophyta, Bacillus, Corynebacterium, Pseudomonas, and Acinetobacter were the most prevalent genera detected. The recovered indoor airborne microbial community was statistically associated with both human oral and skin microbiota, indicating occupants are important contributors, despite a relatively low occupant density per unit volume in retail stores. Bacteria generally associated with outdoor environments were present in the indoor communities with no obvious association with air exchange rate, even when considering relative abundance. No significant association was observed between the indoor bacterial community recovered and store location, store type, or season. However, predictive functional gene profiling showed significant associations between the indoor community and season. The microbiome recovered from multiple samples collected months apart from the same building varied significantly indicating that caution is warranted when trying to characterize the bacterial community with a single sampling event. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments

PubMed Central

Bowers, Robert M; McLetchie, Shawna; Knight, Rob; Fierer, Noah

2011-01-01

Although bacteria are ubiquitous in the near-surface atmosphere and they can have important effects on human health, airborne bacteria have received relatively little attention and their spatial dynamics remain poorly understood. Owing to differences in meteorological conditions and the potential sources of airborne bacteria, we would expect the atmosphere over different land-use types to harbor distinct bacterial communities. To test this hypothesis, we sampled the near-surface atmosphere above three distinct land-use types (agricultural fields, suburban areas and forests) across northern Colorado, USA, sampling five sites per land-use type. Microbial abundances were stable across land-use types, with ∼105–106 bacterial cells per m3 of air, but the concentrations of biological ice nuclei, determined using a droplet freezing assay, were on average two and eight times higher in samples from agricultural areas than in the other two land-use types. Likewise, the composition of the airborne bacterial communities, assessed via bar-coded pyrosequencing, was significantly related to land-use type and these differences were likely driven by shifts in the sources of bacteria to the atmosphere across the land-uses, not local meteorological conditions. A meta-analysis of previously published data shows that atmospheric bacterial communities differ from those in potential source environments (leaf surfaces and soils), and we demonstrate that we may be able to use this information to determine the relative inputs of bacteria from these source environments to the atmosphere. This work furthers our understanding of bacterial diversity in the atmosphere, the terrestrial controls on this diversity and potential approaches for source tracking of airborne bacteria. PMID:21048802

Changes to the Carbon and Energy fluxes in a Northern Peatland with Thawing Permafrost

NASA Astrophysics Data System (ADS)

Harder, S. R.; Roulet, N. T.; Crill, P. M.; Strachan, I. B.

2017-12-01

The maintenance of thaw of high carbon density landscapes in the permafrost region ultimately depends of how the energy balance is partitioned as temperatures and precipitation change, yet there are comparatively few energy balance studies, especially in peatlands that contain permafrost. While permafrost peatlands are currently net sinks of carbon, as Arctic temperatures rise and permafrost thaws, the future of these ecosystems and their capacity for carbon uptake is in question. Since 2012 we have been measuring the spatially integrated CO2, energy and water vapour fluxes from the Stordalen peatland (68°22'N, 19°03'E) using eddy covariance (EC). The Stordalen peatland is a heterogeneous peatland in the discontinuous permafrost zone where permafrost thaw is actively occurring, resulting in large changes to the landscape from year to year. Areas where permafrost is present are elevated by up to 1.5 m compared to the areas where permafrost has thawed causing differences in water table depth, peat temperatures, snow distribution, vegetation community and therefore in the carbon and energy fluxes. Our EC tower is located on the edge of a permafrost peat plateau (or palsa) where one fetch measures fluxes from an area underlain by permafrost and the other fetch sees the portion of the peatland where the permafrost has thawed. Within each sector, we have an array of soil temperature and water content sensors to determine the physical characteristics of each fetch. Extensive vegetation surveys (based on plant functional types or PFTs) have also been conducted to run a footprint analysis on the flux data to complete a comparative analysis of the magnitude and variability of the carbon and energy exchanges from PFT. The footprint analysis allows us to explain the difference in energy and carbon fluxes by examining the ecological, biogeochemical and physical characteristics within each footprint. We see distinctly different energy partitioning between the fetches

Large-scale modelling permafrost distribution in Ötztal, Pitztal and Kaunertal (Tyrol)

NASA Astrophysics Data System (ADS)

Hoinkes, S.; Sailer, R.; Lehning, M.; Steinkogler, W.

2012-04-01

Permafrost is an important element of the global cryosphere, which is seriously affected by climate change. Due to the fact that permafrost is a mostly invisible phenomenon, the area-wide distribution is not properly known. Point measurements are conducted to get information, whether permafrost is present at certain places or not. For an area wide distribution mapping, models have to be built and applied. Different kinds of permafrost distribution models already exist, which are based on different approaches and complexities. Differences in model approaches are mainly due to scaling issues, availability of input data and type of output parameters. In the presented work, we want to map and model the distribution of permafrost in the most elevated parts of the Ötztal, Pitztal and Kaunertal, which are situated in the Eastern European Alps and cover an area of approximately 750 km2. As air temperature is believed to be the best and simplest proxy for energy balance in mountainous regions, we took only the mean annual air temperature from the interpolated ÖKLIM dataset of the Central Institute of Meteorology and Geodynamics to calculate areas with possible presence of permafrost. In a second approach we took a high resolution digital elevation model (DEM) derived by air-borne laser scanning and calculated possible areas with permafrost based on elevation and aspect only which is an established approach among the permafrost community since years. These two simple approaches are compared with each other and in order to validate the model we will compare the outputs with point measurements such as temperature recorded at the snow-soil interface (BTS), continuous temperature data, rock glacier inventories, geophysical measurements. We show that the model based on the mean annual air temperature (≤ -2°C) only, would predict less permafrost in the northerly exposed slopes and in lower elevation than the model based on elevation and aspect. In the southern aspects, more

Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing

NASA Technical Reports Server (NTRS)

Shi, T.; Reeves, R. H.; Gilichinsky, D. A.; Friedmann, E. I.

1997-01-01

Viable bacteria were found in permafrost core samples from the Kolyma-Indigirka lowland of northeast Siberia. The samples were obtained at different depths; the deepest was about 3 million years old. The average temperature of the permafrost is -10 degrees C. Twenty-nine bacterial isolates were characterized by 16S rDNA sequencing and phylogenetic analysis, cell morphology, Gram staining, endospore formation, and growth at 30 degrees C. The majority of the bacterial isolates were rod shaped and grew well at 30 degrees C; but two of them did not grow at or above 28 degrees C, and had optimum growth temperatures around 20 degrees C. Thirty percent of the isolates could form endospores. Phylogenetic analysis revealed that the isolates fell into four categories: high-GC Gram-positive bacteria, beta-proteobacteria, gamma-proteobacteria, and low-GC Gram-positive bacteria. Most high-GC Gram-positive bacteria and beta-proteobacteria, and all gamma-proteobacteria, came from samples with an estimated age of 1.8-3.0 million years (Olyor suite). Most low-GC Gram-positive bacteria came from samples with an estimated age of 5,000-8,000 years (Alas suite).

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

PubMed Central

Pereira e Silva, Michele C.; Dias, Armando Cavalcante Franco; van Elsas, Jan Dirk; Salles, Joana Falcão

2012-01-01

Background Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. Conclusions Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities. PMID:23284712

Bacterial communities associated with four ctenophore genera from the German Bight (North Sea).

PubMed

Hao, Wenjin; Gerdts, Gunnar; Peplies, Jörg; Wichels, Antje

2015-01-01

Intense research has been conducted on jellyfish and ctenophores in recent years. They are increasingly recognized as key elements in the marine ecosystem that serve as critical indicators and drivers of ecosystem performance and change. However, the bacterial community associated with ctenophores is still poorly investigated. Based on automated ribosomal intergenic spacer analysis (ARISA) and 16S ribosomal RNA gene amplicon pyrosequencing, we investigated bacterial communities associated with the frequently occurring ctenophore species Mnemiopsis leidyi, Beroe sp., Bolinopsis infundibulum and Pleurobrachia pileus at Helgoland Roads in the German Bight (North Sea). We observed significant differences between the associated bacterial communities of the different ctenophore species based on ARISA patterns. With respect to bacterial taxa, all ctenophore species were dominated by Proteobacteria as revealed by pyrosequencing. Mnemiopsis leidyi and P. pileus mainly harboured Gammaproteobacteria, with Marinomonas as the dominant phylotype of M. leidyi. By contrast, Pseudoalteromonas and Psychrobacter were the most abundant Gammaproteobacteria in P. pileus. Beroe sp. was mainly dominated by Alphaproteobacteria, particularly by the genus Thalassospira. For B. infundibulum, the bacterial community was composed of Alphaproteobacteria and Gammaproteobacteria in equal parts, which consisted of the genera Thalassospira and Marinomonas. In addition, the bacterial communities associated with M. leidyi display a clear variation over time that needs further investigation. Our results indicate that the bacterial communities associated with ctenophores are highly species- specific. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Soil phosphorus depletion and shifts in plant communities change bacterial community structure in a long-term grassland management trial.

PubMed

Adair, Karen L; Wratten, Steve; Lear, Gavin

2013-06-01

Agricultural systems rely on healthy soils and their sustainability requires understanding the long-term impacts of agricultural practices on soils, including microbial communities. We examined the impact of 17 years of land management on soil bacterial communities in a New Zealand randomized-block pasture trial. Significant variation in bacterial community structure related to mowing and plant biomass removal, while nitrogen fertilizer had no effect. Changes in soil chemistry and legume abundance described 52% of the observed variation in the bacterial community structure. Legumes (Trifolium species) were absent in unmanaged plots but increased in abundance with management intensity; 11% of the variation in soil bacterial community structure was attributed to this shift in the plant community. Olsen P explained 10% of the observed heterogeneity, which is likely due to persistent biomass removal resulting in P limitation; Olsen P was significantly lower in plots with biomass removed (14 mg kg(-1) ± 1.3SE) compared with plots that were not mown, or where biomass was left after mowing (32 mg kg(-1) ± 1.6SE). Our results suggest that removal of plant biomass and associated phosphorus, as well as shifts in the plant community, have greater long-term impacts on soil bacterial community structure than application of nitrogen fertilizers. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Two decades of warming increases diversity of a potentially lignolytic bacterial community

PubMed Central

Pold, Grace; Melillo, Jerry M.; DeAngelis, Kristen M.

2015-01-01

As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming. PMID:26042112

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function.

PubMed

Flues, Sebastian; Bass, David; Bonkowski, Michael

2017-08-01

Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Effects of remediation on the bacterial community of an acid mine drainage impacted stream.

PubMed

Ghosh, Suchismita; Moitra, Moumita; Woolverton, Christopher J; Leff, Laura G

2012-11-01

Acid mine drainage (AMD) represents a global threat to water resources, and as such, remediation of AMD-impacted streams is a common practice. During this study, we examined bacterial community structure and environmental conditions in a low-order AMD-impacted stream before, during, and after remediation. Bacterial community structure was examined via polymerase chain reaction amplification of 16S rRNA genes followed by denaturing gradient gel electrophoresis. Also, bacterial abundance and physicochemical data (including metal concentrations) were collected and relationships to bacterial community structure were determined using BIO-ENV analysis. Remediation of the study stream altered environmental conditions, including pH and concentrations of some metals, and consequently, the bacterial community changed. However, remediation did not necessarily restore the stream to conditions found in the unimpacted reference stream; for example, bacterial abundances and concentrations of some elements, such as sulfur, magnesium, and manganese, were different in the remediated stream than in the reference stream. BIO-ENV analysis revealed that changes in pH and iron concentration, associated with remediation, primarily explained temporal alterations in bacterial community structure. Although the sites sampled in the remediated stream were in relatively close proximity to each other, spatial variation in community composition suggests that differences in local environmental conditions may have large impacts on the microbial assemblage.

Bacterial communities in the fruit bodies of ground basidiomycetes

NASA Astrophysics Data System (ADS)

Zagryadskaya, Yu. A.; Lysak, L. V.; Chernov, I. Yu.

2015-06-01

Fruit bodies of basidiomycetes at different stages of decomposition serve as specific habitats in forest biocenoses for bacteria and differ significantly with respect to the total bacterial population and abundance of particular bacterial genera. A significant increase in the total bacterial population estimated by the direct microscopic method with acridine orange staining and in the population of saprotrophic bacteria (inoculation of glucose peptone yeast agar) in fruit bodies of basidiomycetes Armillaria mellea and Coprinus comatus was recorded at the final stage of their decomposition in comparison with the initial stage. Gramnegative bacteria predominated in the tissues of fruit bodies at all the stages of decomposition and were represented at the final stage by the Aeromonas, Vibrio, and Pseudomonas genera (for fruit bodies of A. mellea) the Pseudomonas genus (for fruit bodies of C. comatus). The potential influence of bacterial communities in the fruit bodies of soil basidiomycetes on the formation of bacterial communities in the upper soil horizons in forest biocenoses is discussed. The loci connected with the development and decomposition of fruit bodies of basidiomycetes on the soil surface are promising for targeted search of Gram-negative bacteria, the important objects of biotechnology.

The 50th Anniversary of the First International Conference on Permafrost

NASA Astrophysics Data System (ADS)

Brown, J.

2013-12-01

), one more in Russia (Salekhard 2012). Throughout the 50-year history of the International Conferences on Permafrost, publication of Proceedings has been the major legacy of each conference. Over the course of the 50 years more than 2000 papers in English were published in the ICOP Proceedings with the assistance of many hundreds of international reviewers. Starting in 2003 (8th ICOP), a second form of publication was initiated that involved Extended Abstracts. Following the formation of the International Permafrost Association (IPA) at the 1983 ICOP, subsequent conferences were under the auspices of the IPA. Starting with the 2008 conference, the Permafrost Young Researchers Network (PYRN) participated in conference activities. The IPA remains the lead organization that represents collectively both the international permafrost science and engineering communities. This first Conference, 50 years ago, provided the foundation for the development of an international community of scientists and engineers committed to the advancement of permafrost research and related cold regions design and performance.

Comparison of benthic bacterial community composition in nine streams

Treesearch

Xueqing Gao; Ola A. Olapade; Laura G. Leff

2005-01-01

In this study, the abundance of major bacterial taxa (based on fluorescent in situ hybridization, FISH) and the structure of the bacterial community (based on denaturing gradient gel electrophoresis, DGGE) were determined in the benthos of 9 streams in the southeastern and midwestern United States and related to differences in environmental...

Host plant species determines symbiotic bacterial community mediating suppression of plant defenses.

PubMed

Chung, Seung Ho; Scully, Erin D; Peiffer, Michelle; Geib, Scott M; Rosa, Cristina; Hoover, Kelli; Felton, Gary W

2017-01-03

Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We previously showed that symbiotic gut bacteria from CPB larvae suppressed jasmonate (JA)-induced defenses in tomato. However, little is known about how changes in the bacterial community may be involved in the manipulation of induced defenses in wild and cultivated Solanum plants of CPB. Here, we examined suppression of JA-mediated defense in wild and cultivated hosts of CPB by chemical elicitors and their symbiotic bacteria. Furthermore, we investigated associations between the gut bacterial community and suppression of plant defenses using 16 S rRNA amplicon sequencing. Symbiotic bacteria decreased plant defenses in all Solanum hosts and there were different gut bacterial communities in CPB fed on different host plants. When larvae were reared on different hosts, defense suppression differed among host plants. These results demonstrate that host plants influence herbivore gut bacterial communities and consequently affect the herbivore's ability to manipulate JA-mediated plant defenses. Thus, the presence of symbiotic bacteria that suppress plant defenses might help CPB adapt to host plants.

Host plant species determines symbiotic bacterial community mediating suppression of plant defenses

PubMed Central

Chung, Seung Ho; Scully, Erin D.; Peiffer, Michelle; Geib, Scott M.; Rosa, Cristina; Hoover, Kelli; Felton, Gary W.

2017-01-01

Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We previously showed that symbiotic gut bacteria from CPB larvae suppressed jasmonate (JA)-induced defenses in tomato. However, little is known about how changes in the bacterial community may be involved in the manipulation of induced defenses in wild and cultivated Solanum plants of CPB. Here, we examined suppression of JA-mediated defense in wild and cultivated hosts of CPB by chemical elicitors and their symbiotic bacteria. Furthermore, we investigated associations between the gut bacterial community and suppression of plant defenses using 16 S rRNA amplicon sequencing. Symbiotic bacteria decreased plant defenses in all Solanum hosts and there were different gut bacterial communities in CPB fed on different host plants. When larvae were reared on different hosts, defense suppression differed among host plants. These results demonstrate that host plants influence herbivore gut bacterial communities and consequently affect the herbivore’s ability to manipulate JA-mediated plant defenses. Thus, the presence of symbiotic bacteria that suppress plant defenses might help CPB adapt to host plants. PMID:28045052

Storm-scale dynamics of bacterial community composition in throughfall and stemflow

NASA Astrophysics Data System (ADS)

Van Stan, J. T., II; Teachey, M. E.; Pound, P.; Ottesen, E. A.

2017-12-01

Transport of bacteria between ecosystem spheres can significantly affect microbially-mediated biogeochemical processes. During rainfall, there is a large, temporally-concentrated exchange of bacteria between the forest phyllosphere and the pedosphere by rain dripping from canopy surfaces, as throughfall (TF), and draining to the stem, as stemflow (SF). Many phyllosphere bacteria possibly transported by TF and SF have been linked to important litter and soil processes (like cyanobacteria and actinobacteria). Despite this, no work has applied high throughput DNA sequencing to assess the community composition of bacteria transported by TF and SF. We characterized bacterial community composition for TF and SF from an epiphyte-laden (Tillandsia usneoides L., Spanish moss) southern live oak (Quercus virginiana) forest in southeastern Georgia (USA) to address two hypotheses: that bacterial community composition will differ between (1) TF and SF, and (2) TF sampled beneath bare and epiphyte-laden canopy. Variability in family-level bacterial abundance, Bray-Curtis dissimilarity, and Shannon diversity index was greater between storms than between net rainfall fluxes. In fact, TF and SF bacterial communities were relatively similar for individual storms and may be driven by pre-storm atmospheric deposition rather than the communities affixed to leaves, bark, and epiphyte surfaces.

Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time.

PubMed

Torres, Sheila; Clayton, Jonathan B; Danzeisen, Jessica L; Ward, Tonya; Huang, Hu; Knights, Dan; Johnson, Timothy J

2017-01-01

It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter). Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs' microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs) identified across all dogs sampled. Taxonomic classification revealed Propionibacterium acnes and Haemophilus sp. as key members of the dog skin bacterial community, along with Corynebacterium sp. and Staphylococcus epidermidis . This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation.

Bacterial Community Assembly and Turnover within the Intestines of Developing Zebrafish

PubMed Central

Yan, Qingyun; van der Gast, Christopher J.; Yu, Yuhe

2012-01-01

Background The majority of animal associated microorganisms are present in digestive tract communities. These intestinal communities arise from selective pressures of the gut habitats as well as host's genotype are regarded as an extra ‘organ’ regulate functions that have not evolved wholly on the host. They are functionally essential in providing nourishment, regulating epithelial development, and influencing immunity in the vertebrate host. As vertebrates are born free of microorganisms, what is poorly understood is how intestinal bacterial communities assemble and develop in conjunction with the development of the host. Methodology/Principal Findings Set within an ecological framework, we investigated the bacterial community assembly and turnover within the intestinal habitats of developing zebrafish (from larvae to adult animals). Spatial and temporal species-richness relationships and Mantel and partial Mantel tests revealed that turnover was low and that richness and composition was best predicted by time and not intestinal volume (habitat size) or changes in food diet. We also observed that bacterial communities within the zebrafish intestines were deterministically assembled (reflected by the observed low turnover) switching to stochastic assembly in the later stages of zebrafish development. Conclusions/Significance This study is of importance as it provides a novel insight into how intestinal bacterial communities assemble in tandem with the host's development (from early to adult stages). It is our hope that by studying intestinal microbiota of this vertebrate model with such or some more refined approaches in the future could well provide ecological insights for clinical benefit. In addition, this study also adds to our still fledgling knowledge of how spatial and temporal species-richness relationships are shaped and provides further mounting evidence that bacterial community assembly and dynamics are shaped by both deterministic and stochastic

Comparative Activity and Functional Ecology of Permafrost Soils and Lithic Niches in a Hyper-Arid Polar Desert

NASA Technical Reports Server (NTRS)

Goordial, J.; Davila, A.; Greer, C. W.; Cannam, R.; DiRuggiero, J.; McKay, C. P.; Whyte, L. G.

2016-01-01

This study represents the first metagenomic interrogation of Antarctic permafrost and polar cryptoendolithic microbial communities. The results underlie two different habitability conditions in the same location under extreme cold and dryness: the permafrost habitat where viable microbial life and activity is questionable, and the cryptoendolithic habitat which contains organisms capable of growth under the extreme conditions of the Antarctic Dry Valleys.

Structure of the Bacterial Community in Different Stages of Early Childhood Caries.

PubMed

Ximenes, Marcos; Armas, Rafael Dutra de; Triches, Thaisa Cezária; Cardoso, Mariane; Vieira, Ricardo de Souza

2018-01-15

To characterise in vivo the structure of bacterial communities in decayed and sound primary teeth. Samples of biofilms were collected from three groups of patients with complete and exclusively primary dentition (n = 45): G1: sound teeth (n = 15); G2: enamel lesion (n = 15); G3: dentin lesion (n = 15). DNA was extracted (CTAB 2%) from the biofilm, the partial 16S rRNA gene was amplified with Bacteria Universal Primers (BA338fGC - UN518r) and subjected to DGGE (denaturing gradient gel electrophoresis). Multidimensional scaling and ANOSIM (analysis of similarity) were employed to determine the structure of the bacterial communities. The amplicon richness was determined by averaging amplicons, with the differences between treatments determined with ANOVA, while means were compared using Tukey's test (p < 0.05). Compared to sound teeth, a greater variety of bacterial communities was found in decayed teeth. Despite the differences between the bacterial communities of sound teeth and decayed teeth, the Venn diagram showed that the samples had 38 amplicons in common. Greater amplicon richness was observed in samples of decayed teeth (enamel: 20.5 ± 2.7; dentin: 20.1 ± 2.8) compared with the sound samples (12.0 ± 4.3) (p <0.05), indicating enhanced growth for specific groups of bacteria on decayed teeth. Although there is less bacterial diversity on sound than ECC-decayed teeth, the bacterial communities are very similar.

Groundwater Resources Evolution in Degrading Permafrost Environments: A Small Catchment-Scale Study in Northern Quebec, Canada

NASA Astrophysics Data System (ADS)

Molson, John; Lemieux, Jean-Michel; Fortier, Richard; Therrien, Rene; Ouellet, Michel; Barth, Johannes; van Geldern, Robert; Cochand, Marion; Sottas, Jonathan; Murray, Renaud; Banville, David

2015-04-01

A two square kilometre catchment in a discontinuous permafrost zone near the Inuit community of Umiujaq on the eastern shore of Hudson Bay in Northern Quebec, Canada, is being investigated to determine the impact of permafrost degradation on groundwater resources. The catchment, which became deglaciated about 7500 years ago, lies in a valley which includes about 30-40 m of glacial-fluvial and marine Quaternary sediments. Permafrost mounds at the site extend from a few meters below ground surface to depths of about 10-30 m. Instrumentation has been installed to measure groundwater levels and temperature, as well as groundwater and surface water geochemistry, isotope signatures (including δ18O and 3H) and stream flow. Preliminary groundwater isotope data reflect depleted δ18O signals that differ from expected values for local groundwater, possibly representing permafrost thaw. In addition, stable water isotopes indicate evaporation from shallow thermokarst lakes. Meteorological conditions including air temperatures, precipitation and snowpack are also being monitored. Near-surface geophysical surveys using electrical resistivity tomography (ERT), induced polarization tomography (IPT), georadar and seismic refraction tomography have been carried out to characterize the catchment and to build a 3D geological site model. A numerical model of coupled groundwater flow and heat transport, including thermal advection, conduction, freeze-thaw and latent heat, is being developed for the site to help develop the conceptual model and to assess future impacts of permafrost degradation due to climate warming. The model (Heatflow/3D) includes nonlinear functions for the temperature-dependent unfrozen moisture content and relative permeability, and has been tested against analytical solutions and using benchmarks developed by the INTERFROST modelling consortium. A conceptual 2D vertical-plane model including several permafrost mounds along a 1 km section shows dynamic seasonal

Characteristics of aquatic bacterial community and the influencing factors in an urban river.

PubMed

Wang, Peng; Chen, Bo; Yuan, Ruiqiang; Li, Chuangqiong; Li, Yan

2016-11-01

Bacteria play a critical role in environmental and ecological processes in river ecosystems. We studied the bacterial community in the Ganjiang River, a major tributary of the Yangtze River, as it flowed through Nanchang, the largest city in the Ganjiang River basin. Water was sampled at five sites monthly during the wet season, and the bacterial community was characterized using Illumina high-throughput sequencing. A total of 811 operational taxonomic units (OTUs) were observed for all samples, ranging from 321 to 519 for each sample. The bacterial communities were maintained by a core of OTUs that persisted longitudinally and monthly. Actinobacteria (41.17% of total sequences) and Proteobacteria (31.80%) were the dominant phyla, while Firmicutes (mostly genus Lactococcus) became most abundant during flooding. Temperature and flow rate, rather than water chemistry, were the main factors influencing the bacterial community in river water. Temperature was the best individual parameter explaining the variations in OTU abundance, while flow rate was the best individual parameter explaining the variations in phylum abundance. Except for Proteobacteria, the relative abundance of bacterial phyla did not differ significantly between sites, and the degrees of influence of urban landscape on the bacterial community were estimated to be 17%-34%. Copyright © 2016 Elsevier B.V. All rights reserved.

Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton

PubMed Central

Bagatini, Inessa Lacativa; Eiler, Alexander; Bertilsson, Stefan; Klaveness, Dag; Tessarolli, Letícia Piton; Vieira, Armando Augusto Henriques

2014-01-01

Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways. PMID:24465807

Bacterial community analysis of drinking water biofilms in southern Sweden.

PubMed

Lührig, Katharina; Canbäck, Björn; Paul, Catherine J; Johansson, Tomas; Persson, Kenneth M; Rådström, Peter

2015-01-01

Next-generation sequencing of the V1-V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82-87%), with 22-40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. The biofilm communities in pipes were distinct from those in water meters, and contained sequences that were identified as Mycobacterium, Nocardia, Desulfovibrio, and Sulfuricurvum. The approach employed in the present study resolved the bacterial diversity present in these biofilm communities as well as the differences that occurred in biofilms within a single distribution system, and suggests that next-generation sequencing of 16S rRNA amplicons can show changes in bacterial biofilm communities associated with different water qualities.

Future permafrost degradation positively enhances Arctic ecohydrological processes

NASA Astrophysics Data System (ADS)

Park, Hotaek; Walsh, John

2013-04-01

Permafrost is considered vulnerable to increasing temperatures. Air temperatures over the Arctic have indeed increased considerably over the last century. Most climate models project that the warming will continue, enhancing permafrost degradation. The degradation of permafrost has the potential to initiate numerous feedbacks, predominantly positive, in the Arctic climatic, hydrological, and biogeochemical processes. For instance, the Arctic terrestrial evapotranspiration during summer season tends to overpass precipitation of the period. The unbalance of water budget seems to be offset by permafrost contribution. A considerable amount of soil carbon cumulating within the permafrost is also released with permafrost degradation. However, it is still uncertain on how much amount of soil carbon will be released. Furthermore, the largest uncertainty is on the magnitude of permafrost degradation under the future climate change. Therefore, the major purpose of this study is to reduce the uncertainties relating to permafrost degradation and then is to assess influences of permafrost dynamics on ecohydrological processes. A land surface model CHANGE, including hydrological and biogeochemical processes, was applied to the pan-Arctic terrestrial region over the period 1901-2100. For exploring the influence of permafrost dynamics on ecohydrological processes in the future, outputs from four scenarios (RCP 4.5, 6.0, and 8.5) of three GCMs (MIROC, CCSM4, and HadGCM2) were used for the simulation of CHANGE. Permafrost positively degraded with temperature warming. By 2091-2100, permafrost extent was decreased 30-75% and active layer thickness increased about 55-125 cm, compared to 1991-2010. Evapotranspiration (ET) and net primary productivity (NPP) also increased about 15-55%. However, higher ET resulted in soil dryness. On the other hand, the increased NPP enhanced soil organic matter, which increased soil water-holding capacity and limited soil warming due to its insulation

Rapid disturbances in Arctic permafrost regions (Invited)

NASA Astrophysics Data System (ADS)

Grosse, G.; Romanovsky, V. E.; Arp, C. D.; Jones, B. M.

2013-12-01

Permafrost thaw is often perceived as a slow process dominated by press disturbances such as gradual active layer thickening. However, various pulse disturbances such as thermokarst formation can substantially increase the rate of permafrost thaw and result in rapid landscape change on sub-decadal to decadal time scales. Other disturbances associated with permafrost thaw are even more dynamic and unfold on sub-annual timescales, such as catastrophic thermokarst lake drainage. The diversity of processes results in complex feedbacks with soil carbon pools, biogeochemical cycles, hydrology, and flora and fauna, and requires a differentiated approach when quantifying how these ecosystem componentsare affected,how vulnerablethey are to rapid change, and what regional to global scale impacts result. Here we show quantitative measurements for three examples of rapid pulse disturbances in permafrost regions as observed with remote sensing data time series: The formation of a mega thaw slump (>50 ha) in syngenetic permafrost in Siberia, the formation of new thermokarst ponds in ice-rich permafrost regions in Alaska and Siberia, and the drainage of thermokarst lakes along a gradient of permafrost extent in Western Alaska. The surprising setting and unabated growth of the mega thaw slump during the last 40 years indicates that limited information on panarctic ground ice distribution, abundance, and vulnerability remains a key gap for reliable projections of thermokarst and thermo-erosion impacts, and that the natural limits on the growth and size of thaw slumps are still poorly understood. Observed thermokarst pond formation and expansion in our study regions was closely tied to ice-rich permafrost terrain, such as syngenetic Yedoma uplands, but was also found in old drained thermokarst lake basins with epigenetic permafrost and shallow drained thermokarst lake basins whose ground ice had not been depleted by the prior lake phase. The very different substrates in which new

Lunar permafrost - Dielectric identification.

NASA Technical Reports Server (NTRS)

Alvarez, R.

1973-01-01

A simulator of lunar permafrost at 100 K exhibits a dielectric relaxation centered at approximately 300 hertz. If permafrost exists in the moon between 100 and 213 K, it should present a relaxation peak at approximately 300 hertz. For temperatures up to 263 K it may go up to 20 kilohertz.

Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado.

PubMed

de Araujo, Ademir Sergio Ferreira; Bezerra, Walderly Melgaço; Dos Santos, Vilma Maria; Rocha, Sandra Mara Barbosa; Carvalho, Nilza da Silva; de Lyra, Maria do Carmo Catanho Pereira; Figueiredo, Marcia do Vale Barreto; de Almeida Lopes, Ângela Celis; Melo, Vania Maria Maciel

2017-04-01

The Cerrado biome in the Sete Cidades National Park, an Ecological Reserve in Northeastern Brazil, has conserved its native biodiversity and presents a variety of plants found in other savannas in Brazil. Despite this finding the soil microbial diversity and community structure are poorly understood. Therefore, we described soil bacterial diversity and distribution along a savanna vegetation gradient taking into account the prevailing environmental factors. The bacterial composition was retrieved by sequencing a fragment of the 16S ribosomal RNA gene. The bacterial operational taxonomic units (OTUs) were assigned to 37 different phyla, 96 classes, and 83 genera. At the phylum level, a core comprised by Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Verrucomicrobia and Planctomycetes, was detected in all areas of Cerrado. 'Cerrado stricto sensu' and 'Cerradao' share more similarities between edaphic properties and vegetation and also present more similar bacterial communities, while 'Floresta decidual' and 'Campo graminoide' show the largest environmental differences and also more distinct bacterial communities. Proteobacteria (26%), Acidobacteria (21%) and Actinobacteria (21%) were the most abundant phyla within the four areas. All the samples present similar bacteria richness (alpha diversity) and the observed differences among them (beta diversity) were more related to the abundance of specific taxon OTUs compared to their presence or absence. Total organic C, N and P are the main abiotic factors structuring the bacterial communities. In summary, our findings show the bacterial community structure was clearly different across the Cerrado gradient, but that these environments share a bacterial phylum-core comprising Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Planctomycetes with other Brazilian savannas.

Sub-Ice Microalgal and Bacterial Communities in Freshwater Lake Baikal, Russia.

PubMed

Bashenkhaeva, Maria V; Zakharova, Yulia R; Petrova, Darya P; Khanaev, Igor V; Galachyants, Yuri P; Likhoshway, Yelena V

2015-10-01

The sub-ice environment of Lake Baikal represents a special ecotope where strongly increasing microbial biomass causes an "ice-bloom" contributing therefore to the ecosystem functioning and global element turnover under low temperature in the world's largest freshwater lake. In this work, we analyzed bacterial and microalgal communities and their succession in the sub-ice environment in March-April 2010-2012. It was found out that two dinoflagellate species (Gymnodinium baicalense var. minor and Peridinium baicalense Kisselew et Zwetkow) and four diatom species (Aulacoseira islandica, A. baicalensis, Synedra acus subsp. radians, and Synedra ulna) predominated in the microalgal communities. Interestingly, among all microalgae, the diatom A. islandica showed the highest number of physically attached bacterial cells (up to 67 ± 16 bacteria per alga). Bacterial communities analyzed with pyrosequencing of 16S rRNA gene fragments were diverse and represented by 161 genera. Phyla Proteobacteria, Verrucomicrobia, Actinobacteria, Acidobacteria, Bacteroidetes, and Cyanobacteria represented a core community independently on microalgal composition, although the relative abundance of these bacterial phyla strongly varied across sampling sites and time points; unique OTUs from other groups were rare.

Camparison of benthic bacterial community composition in nine streams

Treesearch

Xuqing Gao; Ola A. Olapade; Laura G. Leff

2005-01-01

In this study, the abundance of major bacterial taxa (based on fluorescent in situ hybridization, FISH) and the structure of the bacterial community (based on denaturing gradient gel electrophoresis, DGGE) were determined in the benthos of 9 streams in the southeastern and midwestern United States and related to differences in environmental conditions. Taxa examined...

Molecular bacterial community analysis of clean rooms where spacecraft are assembled.

PubMed

Moissl, Christine; Osman, Shariff; La Duc, Myron T; Dekas, Anne; Brodie, Eoin; DeSantis, Todd; Desantis, Tadd; Venkateswaran, Kasthuri

2007-09-01

Molecular bacterial community composition was characterized from three geographically distinct spacecraft-associated clean rooms to determine whether such populations are influenced by the surrounding environment or the maintenance of the clean rooms. Samples were collected from facilities at the Jet Propulsion Laboratory (JPL), Kennedy Space Flight Center (KSC), and Johnson Space Center (JSC). Nine clone libraries representing different surfaces within the spacecraft facilities and three libraries from the surrounding air were created. Despite the highly desiccated, nutrient-bare conditions within these clean rooms, a broad diversity of bacteria was detected, covering all the main bacterial phyla. Furthermore, the bacterial communities were significantly different from each other, revealing only a small subset of microorganisms common to all locations (e.g. Sphingomonas, Staphylococcus). Samples from JSC assembly room surfaces showed the greatest diversity of bacteria, particularly within the Alpha- and Gammaproteobacteria and Actinobacteria. The bacterial community structure of KSC assembly surfaces revealed a high presence of proteobacterial groups, whereas the surface samples collected from the JPL assembly facility showed a predominance of Firmicutes. Our study presents the first extended molecular survey and comparison of NASA spacecraft assembly facilities, and provides new insights into the bacterial diversity of clean room environments .

Composition and variation of sediment bacterial and nirS-harboring bacterial communities at representative sites of the Bohai Gulf coastal zone, China.

PubMed

Guan, Xiangyu; Zhu, Lingling; Li, Youxun; Xie, Yuxuan; Zhao, Mingzhang; Luo, Ximing

2014-04-01

With rapid urbanization, anthropogenic activities are increasingly influencing the natural environment of the Bohai Bay. In this study, the composition and variation of bacterial and nirS-harboring bacterial communities in the coastal zone sediments of the Bohai Gulf were analyzed using PCR-based clone libraries. A total of 95 genera were detected in the bacterial communities, with Proteobacteria (72.1 %), Acidobacteria (10.5 %), Firmicutes (1.7 %), Bacteroidetes (1.4 %), Chloroflexi (0.7 %) and Planctomycetes (0.7 %) being the dominated phyla. The NirS sequences were divided into nine Clusters (A-I). Canonical correlation analysis showed that the bacterial or denitrifying communities were correlated with different environmental factors, such as total organic carbon, total nitrogen, ammonium, sulfate, etc. Furthermore, bacterial communities' composition and diversity are influenced by oil exploration, sewage discharge and other anthropogenic activities in the coastal area of the Bohai Sea. Thus, this study provided useful information on further research on regional or global environmental control and restore.

Volcanic ash supports a diverse bacterial community in a marine mesocosm

USGS Publications Warehouse

Verena Witt,; Paul M Ayris,; Damby, David; Corrado Cimarelli,; Ulrich Kueppers,; Donald B Dingwell,; Gert Wörheide,

2017-01-01

Shallow-water coral reef ecosystems, particularly those already impaired by anthropogenic pressures, may be highly sensitive to disturbances from natural catastrophic events, such as volcanic eruptions. Explosive volcanic eruptions expel large quantities of silicate ash particles into the atmosphere, which can disperse across millions of square kilometres and deposit into coral reef ecosystems. Following heavy ash deposition, mass mortality of reef biota is expected, but little is known about the recovery of post-burial reef ecosystems. Reef regeneration depends partly upon the capacity of the ash deposit to be colonised by waterborne bacterial communities and may be influenced to an unknown extent by the physiochemical properties of the ash substrate itself. To determine the potential for volcanic ash to support pioneer bacterial colonisation, we exposed five well-characterised volcanic and coral reef substrates to a marine aquarium under low light conditions for 3 months: volcanic ash, synthetic volcanic glass, carbonate reef sand, calcite sand and quartz sand. Multivariate statistical analysis of Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting data demonstrates clear segregation of volcanic substrates from the quartz and coral reef substrates over 3 months of bacterial colonisation. Overall bacterial diversity showed shared and substrate-specific bacterial communities; however, the volcanic ash substrate supported the most diverse bacterial community. These data suggest a significant influence of substrate properties (composition, granulometry and colour) on bacterial settlement. Our findings provide first insights into physicochemical controls on pioneer bacterial colonisation of volcanic ash and highlight the potential for volcanic ash deposits to support bacterial diversity in the aftermath of reef burial, on timescales that could permit cascading effects on larval settlement.

Spatial and vertical distribution of bacterial community in the northern South China Sea.

PubMed

Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Cheng, Hao

2015-10-01

Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.

Bacterial Community Profiling of Plastic Litter in the Belgian Part of the North Sea.

PubMed

De Tender, Caroline A; Devriese, Lisa I; Haegeman, Annelies; Maes, Sara; Ruttink, Tom; Dawyndt, Peter

2015-08-18

Bacterial colonization of marine plastic litter (MPL) is known for over four decades. Still, only a few studies on the plastic colonization process and its influencing factors are reported. In this study, seafloor MPL was sampled at different locations across the Belgian part of the North Sea to study bacterial community structure using 16S metabarcoding. These marine plastic bacterial communities were compared with those of sediment and seawater, and resin pellets sampled on the beach, to investigate the origin and uniqueness of plastic bacterial communities. Plastics display great variation of bacterial community composition, while each showed significant differences from those of sediment and seawater, indicating that plastics represent a distinct environmental niche. Various environmental factors correlate with the diversity of MPL bacterial composition across plastics. In addition, intrinsic plastic-related factors such as pigment content may contribute to the differences in bacterial colonization. Furthermore, the differential abundance of known primary and secondary colonizers across the various plastics may indicate different stages of bacterial colonization, and may confound comparisons of free-floating plastics. Our studies provide insights in the factors that shape plastic bacterial colonization and shed light on the possible role of plastic as transport vehicle for bacteria through the aquatic environment.

Bacterial communities and their association with the bio-drying of sewage sludge.

PubMed

Cai, Lu; Chen, Tong-Bin; Gao, Ding; Yu, Jie

2016-03-01

Bio-drying is a technology that aims to remove water from a material using the microbial heat originating from organic matter degradation. However, the evolution of bacterial communities that are associated with the drying process has not been researched systematically. This study was performed to investigate the variations of bacterial communities and the relationships among bacterial communities, water evaporation, water generation, and organic matter degradation during the bio-drying of sewage sludge. High-throughput pyrosequencing was used to analyze the bacterial communities, while water evaporation and water generation were determined based on an in situ water vapor monitoring device. The values of water evaporation, water generation, and volatile solids degradation were 412.9 g kg(-1) sewage sludge bio-drying material (SSBM), 65.0 g kg(-1) SSBM, and 70.2 g kg(-1) SSBM, respectively. Rarefaction curves and diversity indices showed that bacterial diversity plummeted after the temperature of the bio-drying pile dramatically increased on d 2, which coincided with a remarkable increase of water evaporation on d 2. Bacterial diversity increased when the pile cooled. During the thermophilic phase, in which Acinetobacter and Bacillus were the dominant genera, the rates of water evaporation, water generation, and VS degradation peaked. These results implied that the elevated temperature reshaped the bacterial communities, which played a key role in water evaporation, and the high temperature also contributed to the effective elimination of pathogens. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biogeographical distribution and diversity of bacterial communities in surface sediments of the South China Sea.

PubMed

Li, Tao; Wang, Peng

2013-05-01

This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

Evolving hydrologic connectivity in discontinuous permafrost lowlands: what it means for lake systems

NASA Astrophysics Data System (ADS)

Walvoord, M. A.; Jepsen, S. M.; Rover, J.; Voss, C. I.; Briggs, M. A.

2015-12-01

Permafrost influence on the hydrologic connectivity of surface water bodies in high-latitude lowlands is complicated by subsurface heterogeneity and the propensity of the system to change over time. In general, permafrost limits the subsurface exchange of water, solute, and nutrients between lakes and rivers. It follows that permafrost thaw could enhance subsurface hydrologic connectivity among surface water bodies, but the impact of this process on lake distribution is not well known. Changes in the extent of lakes in interior Alaska have important ecological and societal impacts since lakes provide (1) critical habitat for migratory arctic shorebirds and waterfowl, fish, and wildlife, and (2) provisional, recreational, and cultural resources for local communities. We utilize electromagnetic imaging of the shallow subsurface and remote sensing of lake level dynamics in the Yukon Flats of interior Alaska, USA, together with water balance modeling, to gain insight into the influence of discontinuous permafrost on lowland lake systems. In the study region with relatively low precipitation, observations suggest that lakes that are hydrologically isolated during normal conditions are sustained by periodic river flooding events, including ice-jam floods that occur during river ice break-up. Climatically-influenced alterations in flooding frequency and intensity, as well as depth to permafrost, are quantitatively assessed in the context of lake maintenance. Scenario modeling is used to evaluate lake level evolution under plausible changing conditions. Model results demonstrate how permafrost degradation can reduce the dependence of typical lowland lakes on flooding events. Study results also suggest that river flooding may recharge a more spatially widespread zone of lakes and wetlands under future scenarios of permafrost table deepening and enhanced subsurface hydrologic connectivity.

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

PubMed Central

Weedon, James T.; Kowalchuk, George A.; Aerts, Rien; Freriks, Stef; Röling, Wilfred F. M.; van Bodegom, Peter M.

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15% of variance explained) > temporal variation (7–11%) > climate treatment (4–9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts. PMID:28326062

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland.

PubMed

Weedon, James T; Kowalchuk, George A; Aerts, Rien; Freriks, Stef; Röling, Wilfred F M; van Bodegom, Peter M

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50-100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12-15% of variance explained) > temporal variation (7-11%) > climate treatment (4-9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates-evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China

PubMed Central

Hu, Yinhong; Dou, Xiaolin; Li, Juanyong; Li, Feng

2018-01-01

The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete), permeable pavement (bricks with round holes), shrub coverage (Buxus megistophylla Levl.), lawns (Festuca elata Keng ex E. Alexeev), and roadside trees (Sophora japonica Linn.) in Beijing, to explore the response of bacteria to impervious surfaces. The soil bacterial communities were addressed by high-throughput sequencing of the bacterial 16S rRNA gene. We found that Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were the predominant phyla in urban soils. Soil from impervious surfaces presented a lower bacterial diversity, and differed greatly from other types of land cover. Soil bacterial diversity was predominantly affected by Zn, dissolved organic carbon (DOC), and soil moisture content (SMC). The composition of the bacterial community was similar under shrub coverage, roadside trees, and lawns, but different from beneath impervious surfaces and permeable pavement. Variance partitioning analysis showed that edaphic properties contributed to 12% of the bacterial community variation, heavy metal pollution explained 3.6% of the variation, and interaction between the two explained 33% of the variance. Together, our data indicate that impervious surfaces induced changes in bacterial community composition and decrease of bacterial diversity. Interactions between edaphic properties and heavy metals were here found to change the composition of the bacterial community and diversity across

Bacterial community profile of contaminated soils in a typical antimony mining site.

PubMed

Wang, Ningning; Zhang, Suhuan; He, Mengchang

2018-01-01

The soils around the world's largest antimony mine have been contaminated by high concentrations of Sb and As, which might influence microbial diversity in the surrounding soils. The ecological effects of bioavailable Sb and As on the composition and diversity of microbial community in soils remain unknown. In this study, the relative abundance, taxonomic diversity and composition of bacterial community in soils from a typical Sb mine area, and the relationship between the bacterial community and bioavailable concentrations as well as environmental factors have been investigated comprehensively using high-throughput sequencing (HTS) and diffusive gradients in thin films (DGT). The results indicated that Proteobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Gemmatimonadetes, and Cyanobacteria were the dominant bacterial populations at phylum level in all soil samples, accounting for more than 80% of the bacteria sequenced. The abundance and diversity of bacterial community vary along a metal contamination gradient. Redundancy discriminate analysis (RDA) revealed that 74.74% of bacterial community variation in the contaminated soils was explained by six environmental factors (pH, Sb DGT , As DGT , potential ecological risk index (RI), TC, TN), among which pH, Sb DGT , and As DGT were dominant factors influencing the composition and diversity of bacteria. This study contributes to our understanding of microbial diversity in a local ecosystem and introduces the option of studying bioavailable Sb and As using DGT.

Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

PubMed

Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

2014-08-01

The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of the Federation of European Microbiological Societies.

Pyridine-type alkaloid composition affects bacterial community composition of floral nectar

PubMed Central

Aizenberg-Gershtein, Yana; Izhaki, Ido; Santhanam, Rakesh; Kumar, Pavan; Baldwin, Ian T.; Halpern, Malka

2015-01-01

Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness. PMID:26122961

Pyridine-type alkaloid composition affects bacterial community composition of floral nectar.

PubMed

Aizenberg-Gershtein, Yana; Izhaki, Ido; Santhanam, Rakesh; Kumar, Pavan; Baldwin, Ian T; Halpern, Malka

2015-06-30

Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness.

High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

PubMed Central

Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob; Feld, Louise; Holben, William E.

2014-01-01

In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition. PMID:24610853

Permafrost and organic layer interactions over a climate gradient in a discontinuous permafrost zone

NASA Astrophysics Data System (ADS)

Johnson, Kristofer D.; Harden, Jennifer W.; McGuire, A. David; Clark, Mark; Yuan, Fengming; Finley, Andrew O.

2013-09-01

Permafrost is tightly coupled to the organic soil layer, an interaction that mediates permafrost degradation in response to regional warming. We analyzed changes in permafrost occurrence and organic layer thickness (OLT) using more than 3000 soil pedons across a mean annual temperature (MAT) gradient. Cause and effect relationships between permafrost probability (PF), OLT, and other topographic factors were investigated using structural equation modeling in a multi-group analysis. Groups were defined by slope, soil texture type, and shallow (<28 cm) versus deep organic (≥28 cm) layers. The probability of observing permafrost sharply increased by 0.32 for every 10-cm OLT increase in shallow OLT soils (OLTs) due to an insulation effect, but PF decreased in deep OLT soils (OLTd) by 0.06 for every 10-cm increase. Across the MAT gradient, PF in sandy soils varied little, but PF in loamy and silty soils decreased substantially from cooler to warmer temperatures. The change in OLT was more heterogeneous across soil texture types—in some there was no change while in others OLTs soils thinned and/or OLTd soils thickened at warmer locations. Furthermore, when soil organic carbon was estimated using a relationship with thickness, the average increase in carbon in OLTd soils was almost four times greater compared to the average decrease in carbon in OLTs soils across all soil types. If soils follow a trajectory of warming that mimics the spatial gradients found today, then heterogeneities of permafrost degradation and organic layer thinning and thickening should be considered in the regional carbon balance.

Permafrost and organic layer interactions over a climate gradient in a discontinuous permafrost zone

USGS Publications Warehouse

Johnson, Kristofer D.; Harden, Jennifer W.; McGuire, A. David; Clark, Mark; Yuan, Fengming; Finley, Andrew O.

2013-01-01

Permafrost is tightly coupled to the organic soil layer, an interaction that mediates permafrost degradation in response to regional warming. We analyzed changes in permafrost occurrence and organic layer thickness (OLT) using more than 3000 soil pedons across a mean annual temperature (MAT) gradient. Cause and effect relationships between permafrost probability (PF), OLT, and other topographic factors were investigated using structural equation modeling in a multi-group analysis. Groups were defined by slope, soil texture type, and shallow (<28 cm) versus deep organic (≥28 cm) layers. The probability of observing permafrost sharply increased by 0.32 for every 10-cm OLT increase in shallow OLT soils (OLTs) due to an insulation effect, but PF decreased in deep OLT soils (OLTd) by 0.06 for every 10-cm increase. Across the MAT gradient, PF in sandy soils varied little, but PF in loamy and silty soils decreased substantially from cooler to warmer temperatures. The change in OLT was more heterogeneous across soil texture types—in some there was no change while in others OLTs soils thinned and/or OLTd soils thickened at warmer locations. Furthermore, when soil organic carbon was estimated using a relationship with thickness, the average increase in carbon in OLTd soils was almost four times greater compared to the average decrease in carbon in OLTs soils across all soil types. If soils follow a trajectory of warming that mimics the spatial gradients found today, then heterogeneities of permafrost degradation and organic layer thinning and thickening should be considered in the regional carbon balance.

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level

PubMed Central

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-01-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial–microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner. PMID:28742069

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

PubMed

Jiang, Yuji; Liu, Manqiang; Zhang, Jiabao; Chen, Yan; Chen, Xiaoyun; Chen, Lijun; Li, Huixin; Zhang, Xue-Xian; Sun, Bo

2017-12-01

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities. A functional group of alkaline phosphomonoesterase (ALP) producing bacteria was included to test the hypothesis that nematode grazing may significantly affect specific bacteria-mediated ecological functions, that is, organic phosphate cycling in soil. Results of correlation analysis, structural equation modeling and interaction networks combined with laboratory microcosm experiments consistently indicated that bacterivorous nematodes enhanced bacterial diversity, and the abundance of bacterivores was positively correlated with bacterial biomass, including ALP-producing bacterial abundance. Significantly, such effects were more pronounced in large macroaggregates than in microaggregates. There was a positive correlation between the most dominant bacterivores Protorhabditis and the ALP-producing keystone 'species' Mesorhizobium. Taken together, these findings implicate important roles of nematodes in stimulating bacterial dynamics in a spatially dependent manner.

Shifts in bacterial community structure during succession in a glacier foreland of the High Arctic.

PubMed

Kim, Mincheol; Jung, Ji Young; Laffly, Dominique; Kwon, Hye Young; Lee, Yoo Kyung

2017-01-01

Primary succession after glacier retreat has been widely studied in plant communities, but bacterial succession is still poorly understood. In particular, few studies of microbial succession have been performed in the Arctic. We investigated the shifts in bacterial community structure and soil physicochemical properties along a successional gradient in a 100-year glacier foreland of the High Arctic. Multivariate analyses revealed that time after glacier retreat played a key role in associated bacterial community structure during succession. However, environmental filtering (i.e. pH and soil temperature) also accounted for a different, but substantial, proportion of the bacterial community structure. Using the functional trait-based approach, we found that average rRNA operon (rrn) copy number of bacterial communities is high in earlier successional stages and decreased over time. This suggests that soil bacterial taxa with higher rrn copy number have a selective advantage in early successional stages due to their ability of rapidly responding to nutrient inputs in newly exposed soils after glacier retreat. Taken together, our results demonstrate that both deglaciation time and environmental filters play key roles in structuring bacterial communities and soil bacterial groups with different ecological strategies occur in different stages of succession in this glacier foreland. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bacterial community initial development in proglacial soils of Larsemann hill, East Antarctica

NASA Astrophysics Data System (ADS)

Ma, H.; Yan, W.; Shi, G.; Sun, B.; Zhang, Y.; Xiao, X.

2016-12-01

Glacial forefields are considered ideal places to explore how microbial communities will response to climate-driven environmental changes. Our knowledge of how the bacterial community activities and structure was influenced by changing environment due to glacier retreat is still very limited, especially at the initial stage of glacier retreat. The short gradient soil samples including the ice free and ice covered sites were sampled in the forehead of East Antarctica ice sheet, in Larsemann Hills. By employing the Miseq sequencing methods, 1.8 x104 high-quality sequences were gotten for each sample and the bacterial diversity including abundant bacteria and rare bacteria were studied and compared between the gradient samples. Even though in such an extreme stress condition, the bacterial diversity was high. The coefficient of variance between the five sites of abundant group was 0.886 which was higher than that of the top 20 rare group (0.159) significantly (unpaired t test, p-value<0.0001) suggesting that the abundant bacterial communities were more sensitive to the ice sheet change in the initial stage than rare bacteria did. And the abundant bacteria contributed the community structure more than the rare bacteria did. The rare group acted more like seed bank to keep the community functionality in the forehead of sheet. And the ice thickness was the major factor to affect the abundant bacterial community. Given the fact that Antarctica environment was more sensitive to the global warming, the study about abundant and rare bacteria response to condition change will be helpful to precisely predict community response to climate change in polar region. This finding will improve the understanding about the relationship between community structure and environment condition in extreme stress condition.

Bacterial Community Analysis of Drinking Water Biofilms in Southern Sweden

PubMed Central

Lührig, Katharina; Canbäck, Björn; Paul, Catherine J.; Johansson, Tomas; Persson, Kenneth M.; Rådström, Peter

2015-01-01

Next-generation sequencing of the V1–V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82–87%), with 22–40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. The biofilm communities in pipes were distinct from those in water meters, and contained sequences that were identified as Mycobacterium, Nocardia, Desulfovibrio, and Sulfuricurvum. The approach employed in the present study resolved the bacterial diversity present in these biofilm communities as well as the differences that occurred in biofilms within a single distribution system, and suggests that next-generation sequencing of 16S rRNA amplicons can show changes in bacterial biofilm communities associated with different water qualities. PMID:25739379

Endosymbiont Dominated Bacterial Communities in a Dwarf Spider

PubMed Central

Vanthournout, Bram; Hendrickx, Frederik

2015-01-01

The microbial community of spiders is little known, with previous studies focussing primarily on the medical importance of spiders as vectors of pathogenic bacteria and on the screening of known cytoplasmic endosymbiont bacteria. These screening studies have been performed by means of specific primers that only amplify a selective set of endosymbionts, hampering the detection of unreported species in spiders. In order to have a more complete overview of the bacterial species that can be present in spiders, we applied a combination of a cloning assay, DGGE profiling and high-throughput sequencing on multiple individuals of the dwarf spider Oedothorax gibbosus. This revealed a co-infection of at least three known (Wolbachia, Rickettsia and Cardinium) and the detection of a previously unreported endosymbiont bacterium (Rhabdochlamydia) in spiders. 16S rRNA gene sequences of Rhabdochlamydia matched closely with those of Candidatus R. porcellionis, which is currently only reported as a pathogen from a woodlouse and with Candidatus R. crassificans reported from a cockroach. Remarkably, this bacterium appears to present in very high proportions in one of the two populations only, with all investigated females being infected. We also recovered Acinetobacter in high abundance in one individual. In total, more than 99% of approximately 4.5M high-throughput sequencing reads were restricted to these five bacterial species. In contrast to previously reported screening studies of terrestrial arthropods, our results suggest that the bacterial communities in this spider species are dominated by, or even restricted to endosymbiont bacteria. Given the high prevalence of endosymbiont species in spiders, this bacterial community pattern could be widespread in the Araneae order. PMID:25706947

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

PubMed Central

Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; Olesen, Scott W.; Paradis, Charles; Wu, Liyou; Campbell, James H.; Fortney, Julian L.; Mehlhorn, Tonia L.; Lowe, Kenneth A.; Earles, Jennifer E.; Phillips, Jana; Joyner, Dominique C.; Elias, Dwayne A.; Bailey, Kathryn L.; Hurt, Richard A.; Preheim, Sarah P.; Sanders, Matthew C.; Yang, Joy; Mueller, Marcella A.; Brooks, Scott; Watson, David B.; Zhang, Ping; He, Zhili; Dubinsky, Eric A.; Adams, Paul D.; Arkin, Adam P.; Fields, Matthew W.; Zhou, Jizhong; Alm, Eric J.

2015-01-01

ABSTRACT Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. PMID:25968645

Changes in bacterial community after application of three different herbicides.

PubMed

Moretto, Jéssica Aparecida Silva; Altarugio, Lucas Miguel; Andrade, Pedro Avelino; Fachin, Ana Lúcia; Andreote, Fernando Dini; Stehling, Eliana Guedes

2017-07-06

The native soil microbiota is very important to maintain the quality of that environment, but with the intensive use of agrochemicals, changes in microbial biomass and formation of large quantities of toxic waste were observed in soil, groundwater and surface water. Thereby, the goal of this study was to evaluate if the selective pressure exerted by the presence of the herbicides atrazine, diuron and 2,4-D changes the bacterial community structure of an agricultural soil, using denaturing gradient gel electrophoresis technique. According to PERMANOVA analysis, a greater effect of the herbicide persistence time in the soil, the effect of the herbicide class and the effect of interaction between these two factors (persistence time and herbicide class) were observed. In conclusion, the results showed that the selective pressure exerted by the presence of these herbicides altered the composition of the local microbiota, being atrazine and diuron that most significantly affected the bacterial community in soil, and the herbicide 2,4-D was the one that less altered the microbial community and that bacterial community was reestablished first. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands.

PubMed

Böer, Simone I; Hedtkamp, Stefanie I C; van Beusekom, Justus E E; Fuhrman, Jed A; Boetius, Antje; Ramette, Alban

2009-07-01

Bacterial community structure and microbial activity were determined together with a large number of contextual environmental parameters over 2 years in subtidal sands of the German Wadden Sea in order to identify the main factors shaping microbial community structure and activity in this habitat. Seasonal changes in temperature were directly reflected in bacterial activities and total community respiration, but could not explain variations in the community structure. Strong sediment depth-related patterns were observed for bacterial abundances, carbon production rates and extracellular enzymatic activities. Bacterial community structure also showed a clear vertical variation with higher operational taxonomic unit (OTU) numbers at 10-15 cm depth than in the top 10 cm, probably because of the decreasing disturbance by hydrodynamic forces with sediment depth. The depth-related variations in bacterial community structure could be attributed to vertical changes in bacterial abundances, chlorophyll a and NO(3)(-), indicating that spatial patterns of microbes are partially environmentally controlled. Time was the most important single factor affecting microbial community structure with an OTU replacement of up to 47% over 2 years and a contribution of 34% to the total variation. A large part of this variation was not related to any environmental parameters, suggesting that temporal variations in bacterial community structure are caused by yet unknown environmental drivers and/or by stochastic events in coastal sand habitats. Principal ecosystem functions such as benthic oxygen consumption and extracellular hydrolysis of organic matter were, however, at a high level at all times, indicating functional redundancy in the microbial communities.

Characterization of Bacterial Communities and Asaia Infection with Field-Collected and Laboratory-Reared Aedes albopictus

DTIC Science & Technology

2016-08-18

Characterization of bacterial communities and Asaia infection within field-collected and 1 laboratory-reared Aedes albopictus 2 3 4 Elizabeth S...Running Head: Bacterial communities within Ae. albopictus 10 11 #Address correspondence to Elizabeth S. Andrews, elizabeth.s.andrews11.ctr@mail.mil 12...189 DISTRIBUTION STATEMENT A: Approved for public release; distribution is unlimited. UNCLASSIFIED Abstract 19 The bacterial communities within

Volcanic ash supports a diverse bacterial community in a marine mesocosm.

PubMed

Witt, V; Ayris, P M; Damby, D E; Cimarelli, C; Kueppers, U; Dingwell, D B; Wörheide, G

2017-05-01

Shallow-water coral reef ecosystems, particularly those already impaired by anthropogenic pressures, may be highly sensitive to disturbances from natural catastrophic events, such as volcanic eruptions. Explosive volcanic eruptions expel large quantities of silicate ash particles into the atmosphere, which can disperse across millions of square kilometres and deposit into coral reef ecosystems. Following heavy ash deposition, mass mortality of reef biota is expected, but little is known about the recovery of post-burial reef ecosystems. Reef regeneration depends partly upon the capacity of the ash deposit to be colonised by waterborne bacterial communities and may be influenced to an unknown extent by the physiochemical properties of the ash substrate itself. To determine the potential for volcanic ash to support pioneer bacterial colonisation, we exposed five well-characterised volcanic and coral reef substrates to a marine aquarium under low light conditions for 3 months: volcanic ash, synthetic volcanic glass, carbonate reef sand, calcite sand and quartz sand. Multivariate statistical analysis of Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting data demonstrates clear segregation of volcanic substrates from the quartz and coral reef substrates over 3 months of bacterial colonisation. Overall bacterial diversity showed shared and substrate-specific bacterial communities; however, the volcanic ash substrate supported the most diverse bacterial community. These data suggest a significant influence of substrate properties (composition, granulometry and colour) on bacterial settlement. Our findings provide first insights into physicochemical controls on pioneer bacterial colonisation of volcanic ash and highlight the potential for volcanic ash deposits to support bacterial diversity in the aftermath of reef burial, on timescales that could permit cascading effects on larval settlement. © 2017 The Authors. Geobiology Published by John Wiley

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand

PubMed Central

Griffith, Jocelyn C.; Lee, William G.; Orlovich, David A.

2017-01-01

The cultivation of grasslands can modify both bacterial community structure and impact on nutrient cycling as well as the productivity and diversity of plant communities. In this study, two pristine New Zealand grassland sites dominated by indigenous tall tussocks (Chionochloa pallens or C. teretifolia) were examined to investigate the extent and predictability of variation of the bacterial community. The contribution of free-living bacteria to biological nitrogen fixation is predicted to be ecologically significant in these soils; therefore, the diazotrophic community was also examined. The C. teretifolia site had N-poor and poorly-drained peaty soils, and the C. pallens had N-rich and well-drained fertile soils. These soils also differ in the proportion of organic carbon (C), Olsen phosphorus (P) and soil pH. The nutrient-rich soils showed increased relative abundances of some copiotrophic bacterial taxa (including members of the Proteobacteria, Bacteroidetes and Firmicutes phyla). Other copiotrophs, Actinobacteria and the oliogotrophic Acidobacteria showed increased relative abundance in nutrient-poor soils. Greater diversity based on 16S rRNA gene sequences and the Tax4Fun prediction of enhanced spore formation associated with nutrient-rich soils could indicate increased resilience of the bacterial community. The two sites had distinct diazotrophic communities with higher diversity in C. teretifolia soils that had less available nitrate and ammonium, potentially indicating increased resilience of the diazotroph community at this site. The C. teretifolia soils had more 16S rRNA gene and nifH copies per g soil than the nutrient rich site. However, the proportion of the bacterial community that was diazotrophic was similar in the two soils. We suggest that edaphic and vegetation factors are contributing to major differences in the composition and diversity of total bacterial and diazotrophic communities at these sites. We predict the differences in the communities

Coupling of snow and permafrost processes using the Basic Modeling Interface (BMI)

NASA Astrophysics Data System (ADS)

Wang, K.; Overeem, I.; Jafarov, E. E.; Piper, M.; Stewart, S.; Clow, G. D.; Schaefer, K. M.

2017-12-01

We developed a permafrost modeling tool based by implementing the Kudryavtsev empirical permafrost active layer depth model (the so-called "Ku" component). The model is specifically set up to have a basic model interface (BMI), which enhances the potential coupling to other earth surface processes model components. This model is accessible through the Web Modeling Tool in Community Surface Dynamics Modeling System (CSDMS). The Kudryavtsev model has been applied for entire Alaska to model permafrost distribution at high spatial resolution and model predictions have been verified by Circumpolar Active Layer Monitoring (CALM) in-situ observations. The Ku component uses monthly meteorological forcing, including air temperature, snow depth, and snow density, and predicts active layer thickness (ALT) and temperature on the top of permafrost (TTOP), which are important factors in snow-hydrological processes. BMI provides an easy approach to couple the models with each other. Here, we provide a case of coupling the Ku component to snow process components, including the Snow-Degree-Day (SDD) method and Snow-Energy-Balance (SEB) method, which are existing components in the hydrological model TOPOFLOW. The work flow is (1) get variables from meteorology component, set the values to snow process component, and advance the snow process component, (2) get variables from meteorology and snow component, provide these to the Ku component and advance, (3) get variables from snow process component, set the values to meteorology component, and advance the meteorology component. The next phase is to couple the permafrost component with fully BMI-compliant TOPOFLOW hydrological model, which could provide a useful tool to investigate the permafrost hydrological effect.

Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events

PubMed Central

Sison-Mangus, Marilou P.; Jiang, Sunny; Kudela, Raphael M.; Mehic, Sanjin

2016-01-01

Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6–65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12–86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental

Investigation of bacterial communities in peat land of the Gahai Lake natural conservation area

NASA Astrophysics Data System (ADS)

Bai, Yani; Wang, Jinchang; Zhan, Zhigao; Guan, Limei; Jin, Liang; Zheng, Guohua

2017-10-01

Peat is involved in the global carbon cycle and water conservation; therefore, it is implicated in global environmental change. Microorganisms play an important role in the function of peat. To investigate the bacterial communities in peat of Gahai Lake, different locations and depths were sampled and Illumina Miseq sequencing was used to analyze the microbial community. Chemical properties of peat samples were analyzed by China state standard methods (GB methods). The results showed that bacterial communities were affected by depth, with bacterial diversity and community structure at 90 and 120 cm significantly different from that at 10, 30 and 50 cm depth from the peat surface. Chemical properties of peat land including organic matter, total nitrogen and humus content did not significantly influence bacterial community structure in peat, with only one group from genus Rhizomicrobium that was significantly correlated with total nitrogen. A substantial proportion of the bacterial sequences were unclassified (1.4%), which indicates the great application potential of peat in the Gahai Lake natural conservation area in the future.

Bacterial Community Shift Drives Antibiotic Resistance Promotion during Drinking Water Chlorination.

PubMed

Jia, Shuyu; Shi, Peng; Hu, Qing; Li, Bing; Zhang, Tong; Zhang, Xu-Xiang

2015-10-20

For comprehensive insights into the effects of chlorination, a widely used disinfection technology, on bacterial community and antibiotic resistome in drinking water, this study applied high-throughput sequencing and metagenomic approaches to investigate the changing patterns of antibiotic resistance genes (ARGs) and bacterial community in a drinking water treatment and distribution system. At genus level, chlorination could effectively remove Methylophilus, Methylotenera, Limnobacter, and Polynucleobacter, while increase the relative abundance of Pseudomonas, Acidovorax, Sphingomonas, Pleomonas, and Undibacterium in the drinking water. A total of 151 ARGs within 15 types were detectable in the drinking water, and chlorination evidently increased their total relative abundance while reduced their diversity in the opportunistic bacteria (p < 0.05). Residual chlorine was identified as the key contributing factor driving the bacterial community shift and resistome alteration. As the dominant persistent ARGs in the treatment and distribution system, multidrug resistance genes (mainly encoding resistance-nodulation-cell division transportation system) and bacitracin resistance gene bacA were mainly carried by chlorine-resistant bacteria Pseudomonas and Acidovorax, which mainly contributed to the ARGs abundance increase. The strong correlation between bacterial community shift and antibiotic resistome alteration observed in this study may shed new light on the mechanism behind the chlorination effects on antibiotic resistance.

Deodorants and antiperspirants affect the axillary bacterial community.

PubMed

Callewaert, Chris; Hutapea, Prawira; Van de Wiele, Tom; Boon, Nico

2014-10-01

The use of underarm cosmetics is common practice in the Western society to obtain better body odor and/or to prevent excessive sweating. A survey indicated that 95 % of the young adult Belgians generally use an underarm deodorant or antiperspirant. The effect of deodorants and antiperspirants on the axillary bacterial community was examined on nine healthy subjects, who were restrained from using deodorant/antiperspirant for 1 month. Denaturing gradient gel electrophoresis was used to investigate the individual microbial dynamics. The microbial profiles were unique for every person. A stable bacterial community was seen when underarm cosmetics were applied on a daily basis and when no underarm cosmetics were applied. A distinct community difference was seen when the habits were changed from daily use to no use of deodorant/antiperspirant and vice versa. The richness was higher when deodorants and antiperspirants were applied. Especially when antiperspirants were applied, the microbiome showed an increase in diversity. Antiperspirant usage led toward an increase of Actinobacteria, which is an unfavorable situation with respect to body odor development. These initial results show that axillary cosmetics modify the microbial community and can stimulate odor-producing bacteria.

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

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

Howe, Adina; Ringus, Daina L.; Williams, Ryan J.

To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showedmore » significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. Finally, the contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.« less

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

DOE PAGES

Howe, Adina; Ringus, Daina L.; Williams, Ryan J.; ...

2015-10-16

To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showedmore » significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. Finally, the contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.« less

Permafrost thaw in a nested groundwater-flow system

USGS Publications Warehouse

McKenzie, Jeffery M.; Voss, Clifford I.

2013-01-01

Groundwater flow in cold regions containing permafrost accelerates climate-warming-driven thaw and changes thaw patterns. Simulation analyses of groundwater flow and heat transport with freeze/thaw in typical cold-regions terrain with nested flow indicate that early thaw rate is particularly enhanced by flow, the time when adverse environmental impacts of climate-warming-induced permafrost loss may be severest. For the slowest climate-warming rate predicted by the Intergovernmental Panel on Climate Change (IPCC), once significant groundwater flow begins, thick permafrost layers can vanish in several hundred years, but survive over 1,000 years where flow is minimal. Large-scale thaw depends mostly on the balance of heat advection and conduction in the supra-permafrost zone. Surface-water bodies underlain by open taliks allow slow sub-permafrost flow, with lesser influence on regional thaw. Advection dominance over conduction depends on permeability and topography. Groundwater flow around permafrost and flow through permafrost impact thaw differently; the latter enhances early thaw rate. Air-temperature seasonality also increases early thaw. Hydrogeologic heterogeneity and topography strongly affect thaw rates/patterns. Permafrost controls the groundwater/surface-water-geomorphology system; hence, prediction and mitigation of impacts of thaw on ecology, chemical exports and infrastructure require improved hydrogeology/permafrost characterization and understanding

Modelling the permafrost extent on the Tibetan Plateau

NASA Astrophysics Data System (ADS)

Zhao, L.; Zou, D.; Sheng, Y.; Chen, J.; Wu, T.; Wu, J.; Pang, Q.; Wang, W.

2016-12-01

The Tibetan Plateau (TP) possesses the largest areas of permafrost terrain in mid- and low-latitude regions of the world. Permafrost plays significant role in climatic, hydrological, and ecological systems, and has great influences on landforms formation, slope and engineering construction. Detailed database of distribution and characteristics of permafrost is crucial for engineering planning, water resource management, ecosystem protection, climate modeling, and carbon cycle research. Although some permafrost distribution maps were compiled in previous studies and proved very useful, due to the limited data source, ambiguous criteria, little validation, and the deficiency of high-quality spatial datasets, there are a large uncertainty in the mapping permafrost distribution. In this paper, a new permafrost map was generated mostly based on freezing and thawing indices from modified MODIS land surface temperatures (LSTs), and validated by various ground-based dataset. Soil thermal properties of five soil types across the TP estimated according to the empirical equation and in situ observed soil properties (water content and bulk density) which were obtained during the field survey. Based on these data sets, the model of Temperature at the Top Of Permafrost (TTOP) was applied to simulate permafrost distribution over the TP. The results show that permafrost, seasonally frozen ground, and unfrozen ground covered areas of 106.4´104 km2, 145.6´104 km2, and 2.9´104 km2. The ground based observations of permafrost distribution across the five investigated regions (IRs) and three highway transects (across the entire permafrost regions from north to south) have been using to validate the model. Result of validation shows that the kappa coefficient vary from 0.38 to 0.78 in average 0.57 at the five IRs and from 0.62 to 0.74 in average 0.68 within three transects. The result of TTOP modeling shows more accuracy to identify thawing regions in comparison with two maps

Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity

PubMed Central

Pent, Mari; Põldmaa, Kadri; Bahram, Mohammad

2017-01-01

Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales—the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements. PMID:28539921

Land-use changes influence soil bacterial communities in a meadow grassland in Northeast China

NASA Astrophysics Data System (ADS)

Cao, Chengyou; Zhang, Ying; Qian, Wei; Liang, Caiping; Wang, Congmin; Tao, Shuang

2017-10-01

The conversion of natural grassland into agricultural fields is an intensive anthropogenic perturbation commonly occurring in semiarid regions, and this perturbation strongly affects soil microbiota. In this study, the influences of land-use conversion on the soil properties and bacterial communities in the Horqin Grasslands in Northeast China were assessed. This study aimed to investigate (1) how the abundances of soil bacteria changed across land-use types, (2) how the structure of the soil bacterial community was altered in each land-use type, and (3) how these variations were correlated with soil physical and chemical properties. Variations in the diversities and compositions of bacterial communities and the relative abundances of dominant taxa were detected in four distinct land-use systems, namely, natural meadow grassland, paddy field, upland field, and poplar plantation, through the high-throughput Illumina MiSeq sequencing technique. The results indicated that land-use changes primarily affected the soil physical and chemical properties and bacterial community structure. Soil properties, namely, organic matter, pH, total N, total P, available N and P, and microbial biomass C, N, and P, influenced the bacterial community structure. The dominant phyla and genera were almost the same among the land-use types, but their relative abundances were significantly different. The effects of land-use changes on the structure of soil bacterial communities were more quantitative than qualitative.

Bacterial community dynamics and product distribution during pH-adjusted fermentation of vegetable wastes.

PubMed

Ye, N-F; Lü, F; Shao, L-M; Godon, J-J; He, P-J

2007-10-01

To estimate the effect of pH on the structures of bacterial community during fermentation of vegetable wastes and to investigate the relationship between bacterial community dynamics and product distribution. The bacterial communities in five batch tests controlled at different pH values [uncontrolled (about pH 4), 5, 6, 7 and 8] were monitored by denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism (SSCP). The two fingerprinting methods provided consistent results and principal component analysis indicated a close similarity of bacterial community at pH 7 and 8 in addition to those at pH 4-6. This clustering also corresponded to dominant metabolic pathway. Thus, pH 7-8 shifted from alcohol-forming to acid-forming, especially butyric acid, whereas both alcohol-forming and acid-forming dominated at pH 5-6, and at pH 4, fermentation was inhibited. Shannon-weaver index was calculated to analyse the DGGE profiles, which revealed that the bacterial diversities at pH 7 and 8 were the highest while those at pH 5 and 4 (uncontrolled) were the lowest. According to sequencing results of the bands excised from DGGE gels, lactic acid bacteria and Clostridium sp. were predominant at all pH values, but varieties in species were observed as pH changed and time prolonged. The bacterial community during fermentation was materially influenced by pH and the diverse product distribution was related to the shift of different bacterial population. The study reveals that the impact of pH on fermentation product distribution is implemented primarily by changes of bacterial community. It also provides information about the comparison of two fingerprinting methods, DGGE and SSCP.

Soil bacterial community responses to revegetation of moving sand dune in semi-arid grassland.

PubMed

Cao, Chengyou; Zhang, Ying; Cui, Zhenbo; Feng, Shuwei; Wang, Tingting; Ren, Qing

2017-08-01

Grasslands in semi-arid Northern China are widely desertified, thus inducing the formation of a large area of moving sand lands. Revegetation of the sandy land is commonly adopted to restore degraded grasslands. The structure of the soil microbial community might dramatically change during degradation and recovery because microorganisms are one of the major drivers of ecological process through their interactions with plants and soil. Assuming that soil properties are the key determinants of the structure of soil bacterial community within the same soil type, whether the vegetation type causes the significant difference in the structure of soil bacterial community during revegetation and restoration of the degraded grasslands remains poorly understood. Our study aimed to (1) investigate the response of soil bacterial communities to the changes during vegetation degradation and recovery and (2) evaluate whether the soil bacterial communities under plantations return to their native state. We detected the shifts in diversities and compositions of the soil bacterial communities and the relative abundance of dominant bacterial taxa by using the high-throughput Illumina MiSeq sequencing technique in an area covered by 32-year-old Caragana microphylla, Artemisia halodendron, Hedysarum fruticosum, Pinus sylvestris var. mongolica, Populus simonii, and Salix gordejevii sand-fixing plantations and in the native community (NC) dominated by elm, and moving sandy dune (MS). We found that the obtained operational taxonomic units by 16S rRNA gene sequencing and diversity index in MS were all significantly lower than those in NC, and the number and composition of dominant genera were significantly different between NC and MS. Interestingly, the compositions of bacterial communities and the dominant genera in different sand-fixation plantations (C. microphylla, A. halodendron, H. fruticosum, P. sylvestris var. mongolica, P. simonii, and S. gordejevii) were all similar to those of

From source to filter: changes in bacterial community composition during potable water treatment.

PubMed

Zanacic, Enisa; McMartin, Dena W; Stavrinides, John

2017-06-01

Rural communities rely on surface water reservoirs for potable water. Effective removal of chemical contaminants and bacterial pathogens from these reservoirs requires an understanding of the bacterial community diversity that is present. In this study, we carried out a 16S rRNA-based profiling approach to describe the bacterial consortia in the raw surface water entering the water treatment plants of 2 rural communities. Our results show that source water is dominated by the Proteobacteria, Bacteroidetes, and Cyanobacteria, with some evidence of seasonal effects altering the predominant groups at each location. A subsequent community analysis of transects of a biological carbon filter in the water treatment plant revealed a significant increase in the proportion of Proteobacteria, Acidobacteria, Planctomycetes, and Nitrospirae relative to raw water. Also, very few enteric coliforms were identified in either the source water or within the filter, although Mycobacterium was of high abundance and was found throughout the filter along with Aeromonas, Legionella, and Pseudomonas. This study provides valuable insight into bacterial community composition within drinking water treatment facilities, and the importance of implementing appropriate disinfection practices to ensure safe potable water for rural communities.

Growth of Carnobacterium spp. from permafrost under low pressure, temperature, and anoxic atmosphere has implications for Earth microbes on Mars.

PubMed

Nicholson, Wayne L; Krivushin, Kirill; Gilichinsky, David; Schuerger, Andrew C

2013-01-08

The ability of terrestrial microorganisms to grow in the near-surface environment of Mars is of importance to the search for life and protection of that planet from forward contamination by human and robotic exploration. Because most water on present-day Mars is frozen in the regolith, permafrosts are considered to be terrestrial analogs of the martian subsurface environment. Six bacterial isolates were obtained from a permafrost borehole in northeastern Siberia capable of growth under conditions of low temperature (0 °C), low pressure (7 mbar), and a CO(2)-enriched anoxic atmosphere. By 16S ribosomal DNA analysis, all six permafrost isolates were identified as species of the genus Carnobacterium, most closely related to C. inhibens (five isolates) and C. viridans (one isolate). Quantitative growth assays demonstrated that the six permafrost isolates, as well as nine type species of Carnobacterium (C. alterfunditum, C. divergens, C. funditum, C. gallinarum, C. inhibens, C. maltaromaticum, C. mobile, C. pleistocenium, and C. viridans) were all capable of growth under cold, low-pressure, anoxic conditions, thus extending the low-pressure extreme at which life can function.

Bacterial Community Dynamics in Full-Scale Activated Sludge Bioreactors: Operational and Ecological Factors Driving Community Assembly and Performance

PubMed Central

Valentín-Vargas, Alexis; Toro-Labrador, Gladys; Massol-Deyá, Arturo A.

2012-01-01

The assembling of bacterial communities in conventional activated sludge (CAS) bioreactors was thought, until recently, to be chaotic and mostly unpredictable. Studies done over the last decade have shown that specific, and often, predictable random and non-random factors could be responsible for that process. These studies have also motivated a “structure–function” paradigm that is yet to be resolved. Thus, elucidating the factors that affect community assembly in the bioreactors is necessary for predicting fluctuations in community structure and function. For this study activated sludge samples were collected during a one-year period from two geographically distant CAS bioreactors of different size. Combining community fingerprinting analysis and operational parameters data with a robust statistical analysis, we aimed to identify relevant links between system performance and bacterial community diversity and dynamics. In addition to revealing a significant β-diversity between the bioreactors’ communities, results showed that the largest bioreactor had a less dynamic but more efficient and diverse bacterial community throughout the study. The statistical analysis also suggests that deterministic factors, as opposed to stochastic factors, may have a bigger impact on the community structure in the largest bioreactor. Furthermore, the community seems to rely mainly on mechanisms of resistance and functional redundancy to maintain functional stability. We suggest that the ecological theories behind the Island Biogeography model and the species-area relationship were appropriate to predict the assembly of bacterial communities in these CAS bioreactors. These results are of great importance for engineers and ecologists as they reveal critical aspects of CAS systems that could be applied towards improving bioreactor design and operation. PMID:22880016

Diversity and composition of the bacterial community in Amphioxus feces.

PubMed

Pan, Minming; Yuan, Dongjuan; Chen, Shangwu; Xu, Anlong

2015-11-01

Amphioxus is a typical filter feeder animal and is confronted with a complex bacterial community in the seawater of its habitat. It has evolved a strong innate immune system to cope with the external bacterial stimulation, however, the ecological system of the bacterial community in Amphioxus remains unknown. Through massive parallel 16S rRNA gene tag pyrosequencing, the investigation indicated that the composition of wild and lab-cultured Amphioxus fecal bacteria was complex with more than 85,000 sequence tags being assigned to 12/13 phyla. The bacterial diversity between the two fecal samples was similar according to OTU richness of V4 tag, Chao1 index, Shannon index and Rarefaction curves, however, the most prominent bacteria in wild feces were genera Pseudoalteromonas (gamma Proteobacteria) and Arcobacter (epsilon Proteobacteria); the highly abundant bacteria in lab-cultured feces were other groups, including Leisingera, Phaeobacter (alpha Proteobacteria), and Vibrio (gamma Proteobacteria). Such difference indicates the complex fecal bacteria with the potential for multi-stability. The bacteria of habitat with 28 assigned phyla had the higher bacterial diversity and species richness than both fecal bacteria. Shared bacteria between wild feces and its habitat reached to approximately 90% (153/169 genera) and 28% (153/548 genera), respectively. As speculative, the less diversity of both fecal bacteria compared to its habitat partly because Amphioxus lives buried and the feces will ultimately end up in the sediment. Therefore, our study comprehensively investigates the complex bacterial community of Amphioxus and provides evidence for understanding the relationship of this basal chordate with the environment. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Light Structures Phototroph, Bacterial and Fungal Communities at the Soil Surface

PubMed Central

Davies, Lawrence O.; Schäfer, Hendrik; Marshall, Samantha; Bramke, Irene; Oliver, Robin G.; Bending, Gary D.

2013-01-01

The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0–3 mm) and bulk soil (3–12 mm) using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere. PMID:23894406

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes.

PubMed

Zhang, Yuanchen; Kastman, Erik K; Guasto, Jeffrey S; Wolfe, Benjamin E

2018-01-23

Most studies of bacterial motility have examined small-scale (micrometer-centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes.

Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

PubMed

Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

2014-12-01

Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.