Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil.

PubMed

Pratscher, Jennifer; Dumont, Marc G; Conrad, Ralf

2011-03-08

Ammonia oxidation is an essential part of the global nitrogen cycling and was long thought to be driven only by bacteria. Recent findings expanded this pathway also to the archaea. However, most questions concerning the metabolism of ammonia-oxidizing archaea, such as ammonia oxidation and potential CO(2) fixation, remain open, especially for terrestrial environments. Here, we investigated the activity of ammonia-oxidizing archaea and bacteria in an agricultural soil by comparison of RNA- and DNA-stable isotope probing (SIP). RNA-SIP demonstrated a highly dynamic and diverse community involved in CO(2) fixation and carbon assimilation coupled to ammonia oxidation. DNA-SIP showed growth of the ammonia-oxidizing bacteria but not of archaea. Furthermore, the analysis of labeled RNA found transcripts of the archaeal acetyl-CoA/propionyl-CoA carboxylase (accA/pccB) to be expressed and labeled. These findings strongly suggest that ammonia-oxidizing archaeal groups in soil autotrophically fix CO(2) using the 3-hydroxypropionate-4-hydroxybutyrate cycle, one of the two pathways recently identified for CO(2) fixation in Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH targeting the gene encoding subunit A of ammonia monooxygenase (amoA) mRNA and 16S rRNA of archaea also revealed ammonia-oxidizing archaea to be numerically relevant among the archaea in this soil. Our results demonstrate a diverse and dynamic contribution of ammonia-oxidizing archaea in soil to nitrification and CO(2) assimilation and that their importance to the overall archaeal community might be larger than previously thought.

Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil

PubMed Central

Pratscher, Jennifer; Dumont, Marc G.; Conrad, Ralf

2011-01-01

Ammonia oxidation is an essential part of the global nitrogen cycling and was long thought to be driven only by bacteria. Recent findings expanded this pathway also to the archaea. However, most questions concerning the metabolism of ammonia-oxidizing archaea, such as ammonia oxidation and potential CO2 fixation, remain open, especially for terrestrial environments. Here, we investigated the activity of ammonia-oxidizing archaea and bacteria in an agricultural soil by comparison of RNA- and DNA-stable isotope probing (SIP). RNA-SIP demonstrated a highly dynamic and diverse community involved in CO2 fixation and carbon assimilation coupled to ammonia oxidation. DNA-SIP showed growth of the ammonia-oxidizing bacteria but not of archaea. Furthermore, the analysis of labeled RNA found transcripts of the archaeal acetyl-CoA/propionyl-CoA carboxylase (accA/pccB) to be expressed and labeled. These findings strongly suggest that ammonia-oxidizing archaeal groups in soil autotrophically fix CO2 using the 3-hydroxypropionate–4-hydroxybutyrate cycle, one of the two pathways recently identified for CO2 fixation in Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH targeting the gene encoding subunit A of ammonia monooxygenase (amoA) mRNA and 16S rRNA of archaea also revealed ammonia-oxidizing archaea to be numerically relevant among the archaea in this soil. Our results demonstrate a diverse and dynamic contribution of ammonia-oxidizing archaea in soil to nitrification and CO2 assimilation and that their importance to the overall archaeal community might be larger than previously thought. PMID:21368116

Decoupling of DAMO archaea from DAMO bacteria in a methane-driven microbial fuel cell.

PubMed

Ding, Jing; Lu, Yong-Ze; Fu, Liang; Ding, Zhao-Wei; Mu, Yang; Cheng, Shuk H; Zeng, Raymond J

2017-03-01

Anaerobic oxidation of methane (AOM) contributes significantly to the global methane sink. Previously, studies of anaerobic methanotrophic (ANME) archaea have been limited as they have not been separable from their bacterial partners during the AOM process because of their dependence on the bacteria. A microbial fuel cell (MFC) is a device capable of directly transforming chemical energy to electrical energy via electrochemical reactions involving biochemical pathways. In this study, decoupling of denitrifying anaerobic methane oxidation (DAMO) archaea and DAMO bacteria was investigated in an microbial fuel cell (MFC) using methane as the fuel. The DAMO fuel cell worked successfully but demonstrated weak electrogenic capability with around 25 mV production. After 45 days' enrichment, the sequencing and fluorescence in situ hybridization results showed the DAMO archaea percentage had increased from 26.96% (inoculum) to 65.77% (electrode biofilm), while the DAMO bacteria percentage decreased from 24.39% to 2.07%. Moreover, the amount of ANME-2d had doubled in the electrode biofilm compared with the inoculum. The sequencing results also showed substantial enrichment of the Ignavibacterium and Geobacter genera. The roles of Ignavibacterium and Geobacter in the MFC system need to be further investigated. Nevertheless, these results illustrate that an MFC device may provide a possible approach to separate DAMO archaea from DAMO bacteria. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolutionary Genomics of Defense Systems in Archaea and Bacteria*

PubMed Central

Koonin, Eugene V.; Makarova, Kira S.; Wolf, Yuri I.

2018-01-01

Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death. PMID:28657885

Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

PubMed Central

May, Megan K.; Kevorkian, Richard T.; Steen, Andrew D.

2013-01-01

There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined “yield” to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly. PMID:24096423

Diversity of Archaea in Brazilian savanna soils.

PubMed

Catão, E; Castro, A P; Barreto, C C; Krüger, R H; Kyaw, C M

2013-07-01

Although the richness of Bacteria and Fungi in Cerrado' soils has been reported, here we report, for the first time, the archaeal community in Cerrado's soils. DNA extracted from soil of two distinct vegetation types, a dense subtype of sensu strict (cerrado denso) and riverbank forest (mata de galeria), was used to amplify Archaea-specific 16S rRNA gene. All of the fragments sequenced were classified as Archaea into the phylum Thaumarchaeota, predominantly affiliated to groups I.1b and I.1c. Sequences affiliated to the group I.1a were found only in the soil from riverbank forest. Soils from 'cerrado denso' had greater Archaea richness than those from 'mata de galeria' based on the richness indexes and on the rarefaction curve. β-Diversity analysis showed significant differences between the sequences from the two soil areas studied because of their different thaumarchaeal group composition. These results provide information about the third domain of life from Cerrado soils.

A bioenergetic basis for membrane divergence in archaea and bacteria.

PubMed

Sojo, Víctor; Pomiankowski, Andrew; Lane, Nick

2014-08-01

Membrane bioenergetics are universal, yet the phospholipid membranes of archaea and bacteria-the deepest branches in the tree of life-are fundamentally different. This deep divergence in membrane chemistry is reflected in other stark differences between the two domains, including ion pumping and DNA replication. We resolve this paradox by considering the energy requirements of the last universal common ancestor (LUCA). We develop a mathematical model based on the premise that LUCA depended on natural proton gradients. Our analysis shows that such gradients can power carbon and energy metabolism, but only in leaky cells with a proton permeability equivalent to fatty acid vesicles. Membranes with lower permeability (equivalent to modern phospholipids) collapse free-energy availability, precluding exploitation of natural gradients. Pumping protons across leaky membranes offers no advantage, even when permeability is decreased 1,000-fold. We hypothesize that a sodium-proton antiporter (SPAP) provided the first step towards modern membranes. SPAP increases the free energy available from natural proton gradients by ∼60%, enabling survival in 50-fold lower gradients, thereby facilitating ecological spread and divergence. Critically, SPAP also provides a steadily amplifying advantage to proton pumping as membrane permeability falls, for the first time favoring the evolution of ion-tight phospholipid membranes. The phospholipids of archaea and bacteria incorporate different stereoisomers of glycerol phosphate. We conclude that the enzymes involved took these alternatives by chance in independent populations that had already evolved distinct ion pumps. Our model offers a quantitatively robust explanation for why membrane bioenergetics are universal, yet ion pumps and phospholipid membranes arose later and independently in separate populations. Our findings elucidate the paradox that archaea and bacteria share DNA transcription, ribosomal translation, and ATP synthase, yet

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems

PubMed Central

Danovaro, Roberto; Molari, Massimiliano; Corinaldesi, Cinzia; Dell’Anno, Antonio

2016-01-01

Bacteria and archaea dominate the biomass of benthic deep-sea ecosystems at all latitudes, playing a crucial role in global biogeochemical cycles, but their macroscale patterns and macroecological drivers are still largely unknown. We show the results of the most extensive field study conducted so far to investigate patterns and drivers of the distribution and structure of benthic prokaryote assemblages from 228 samples collected at latitudes comprising 34°N to 79°N, and from ca. 400- to 5570-m depth. We provide evidence that, in deep-sea ecosystems, benthic bacterial and archaeal abundances significantly increase from middle to high latitudes, with patterns more pronounced for archaea, and particularly for Marine Group I Thaumarchaeota. Our results also reveal that different microbial components show varying sensitivities to changes in temperature conditions and food supply. We conclude that climate change will primarily affect deep-sea benthic archaea, with important consequences on global biogeochemical cycles, particularly at high latitudes. PMID:27386507

RNA degradation in Archaea and Gram-negative bacteria different from Escherichia coli.

PubMed

Evguenieva-Hackenberg, Elena; Klug, Gabriele

2009-01-01

Exoribonucleolytic and endoribonucleolytic activities are important for controlled degradation of RNA and contribute to the regulation of gene expression at the posttranscriptional level by influencing the half-lives of specific messenger RNAs. The RNA half-lives are determined by the characteristics of the RNA substrates and by the availability and the properties of the involved proteins-ribonucleases and assisting polypeptides. Much is known about RNA degradation in Eukarya and Bacteria, but there is limited information about RNA-degrading enzymes and RNA destabilizing or stabilizing elements in the domain of the Archaea. The recent progress in the understanding of the structure and function of the archaeal exosome, a protein complex with RNA-degrading and RNA-tailing capabilities, has given some first insights into the mechanisms of RNA degradation in the third domain of life and into the evolution of RNA-degrading enzymes. Moreover, other archaeal RNases with degrading potential have been described and a new mechanism for protection of the 5'-end of RNA in Archaea was discovered. Here, we summarize the current knowledge on RNA degradation in the Archaea. Additionally, RNA degradation mechanisms in Rhodobacter capsulatus and Pseudomonas syringae are compared to those in the major model organism for Gram-negatives, Escherichia coli, which dominates our view on RNA degradation in Bacteria.

Diverse antimicrobial interactions of halophilic archaea and bacteria extend over geographical distances and cross the domain barrier

PubMed Central

Atanasova, Nina S; Pietilä, Maija K; Oksanen, Hanna M

2013-01-01

The significance of antimicrobial substances, halocins, produced by halophilic archaea and bacteria thriving in hypersaline environments is relatively unknown. It is suggested that their production might increase species diversity and give transient competitive advances to the producer strain. Halocin production is considered to be common among halophilic archaea, but there is a lack of information about halocins produced by bacteria in highly saline environments. We studied the antimicrobial activity of 68 halophilic archaea and 22 bacteria isolated from numerous geographically distant hypersaline environments. Altogether 144 antimicrobial interactions were found between the strains and aside haloarchaea, halophilic bacteria from various genera were identified as halocin producers. Close to 80% of the interactions were detected between microorganisms from different genera and in few cases, even across the domain boundary. Several of the strains produced halocins with a wide inhibitory spectrum as has been observed before. Most of the antimicrobial interactions were found between strains from distant sampling sites indicating that hypersaline environments around the world have similar microorganisms with the potential to produce wide activity range antimicrobials. PMID:23929527

Effect of Feeding Palm Oil By-Products Based Diets on Total Bacteria, Cellulolytic Bacteria and Methanogenic Archaea in the Rumen of Goats

PubMed Central

Abubakr, Abdelrahim; Alimon, Abdul Razak; Yaakub, Halimatun; Abdullah, Norhani; Ivan, Michael

2014-01-01

Rumen microorganisms are responsible for digestion and utilization of dietary feeds by host ruminants. Unconventional feed resources could be used as alternatives in tropical areas where feed resources are insufficient in terms of quality and quantity. The objective of the present experiment was to evaluate the effect of diets based on palm oil (PO), decanter cake (DC) or palm kernel cake (PKC) on rumen total bacteria, selected cellulolytic bacteria, and methanogenic archaea. Four diets: control diet (CD), decanter cake diet (DCD), palm kernel cake diet (PKCD) and CD plus 5% PO diet (CPOD) were fed to rumen cannulated goats and rumen samples were collected at the start of the experimental diets (day 0) and on days 4, 6, 8, 12, 18, 24 and 30 post dietary treatments. Feeding DCD and PKCD resulted in significantly higher (P<0.05) DNA copy number of total bacteria, Fibrobacter succinogenes, Ruminococcus flavefeciens, and Ruminococcus albus. Rumen methanogenic archaea was significantly lower (P<0.05) in goats fed PKCD and CPOD and the trend showed a severe reduction on days 4 and 6 post experimental diets. In conclusion, results indicated that feeding DCD and PKC increased the populations of cellulolytic bacteria and decreased the density of methanogenic archaea in the rumen of goats. PMID:24756125

Effect of feeding palm oil by-products based diets on total bacteria, cellulolytic bacteria and methanogenic archaea in the rumen of goats.

PubMed

Abubakr, Abdelrahim; Alimon, Abdul Razak; Yaakub, Halimatun; Abdullah, Norhani; Ivan, Michael

2014-01-01

Rumen microorganisms are responsible for digestion and utilization of dietary feeds by host ruminants. Unconventional feed resources could be used as alternatives in tropical areas where feed resources are insufficient in terms of quality and quantity. The objective of the present experiment was to evaluate the effect of diets based on palm oil (PO), decanter cake (DC) or palm kernel cake (PKC) on rumen total bacteria, selected cellulolytic bacteria, and methanogenic archaea. Four diets: control diet (CD), decanter cake diet (DCD), palm kernel cake diet (PKCD) and CD plus 5% PO diet (CPOD) were fed to rumen cannulated goats and rumen samples were collected at the start of the experimental diets (day 0) and on days 4, 6, 8, 12, 18, 24 and 30 post dietary treatments. Feeding DCD and PKCD resulted in significantly higher (P<0.05) DNA copy number of total bacteria, Fibrobacter succinogenes, Ruminococcus flavefeciens, and Ruminococcus albus. Rumen methanogenic archaea was significantly lower (P<0.05) in goats fed PKCD and CPOD and the trend showed a severe reduction on days 4 and 6 post experimental diets. In conclusion, results indicated that feeding DCD and PKC increased the populations of cellulolytic bacteria and decreased the density of methanogenic archaea in the rumen of goats.

Diverse antimicrobial interactions of halophilic archaea and bacteria extend over geographical distances and cross the domain barrier.

PubMed

Atanasova, Nina S; Pietilä, Maija K; Oksanen, Hanna M

2013-10-01

The significance of antimicrobial substances, halocins, produced by halophilic archaea and bacteria thriving in hypersaline environments is relatively unknown. It is suggested that their production might increase species diversity and give transient competitive advances to the producer strain. Halocin production is considered to be common among halophilic archaea, but there is a lack of information about halocins produced by bacteria in highly saline environments. We studied the antimicrobial activity of 68 halophilic archaea and 22 bacteria isolated from numerous geographically distant hypersaline environments. Altogether 144 antimicrobial interactions were found between the strains and aside haloarchaea, halophilic bacteria from various genera were identified as halocin producers. Close to 80% of the interactions were detected between microorganisms from different genera and in few cases, even across the domain boundary. Several of the strains produced halocins with a wide inhibitory spectrum as has been observed before. Most of the antimicrobial interactions were found between strains from distant sampling sites indicating that hypersaline environments around the world have similar microorganisms with the potential to produce wide activity range antimicrobials. © 2013 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

DNA Integrity and Shock Wave Transformation Efficiency of Bacteria and Fungi

NASA Astrophysics Data System (ADS)

Loske, Achim M.; Campos-Guillén, Juan; Fernández, Francisco; Pastrana, Xóchitl; Magaña-Ortíz, Denis; Coconi-Linares, Nancy; Ortíz-Vázquez, Elizabeth; Gómez-Lim, Miguel

Delivery of DNA into bacteria and fungi is essential in medicine and biotechnology to produce metabolites, enzymes, antibiotics and proteins. So far, protocols to genetically transform bacteria and fungi are inefficient and have low reproducibility.

Bacteria and Archaea in acidic environments and a key to morphological identification

USGS Publications Warehouse

Robbins, E.I.

2000-01-01

Natural and anthropogenic acidic environments are dominated by bacteria and Archaea. As many as 86 genera or species have been identified or isolated from pH <4.5 environments. This paper reviews the worldwide literature and provide tables of morphological characteristics, habitat information and a key for light microscope identification for the non-microbiologist.

[Establishment of Assessment Method for Air Bacteria and Fungi Contamination].

PubMed

Zhang, Hua-ling; Yao, Da-jun; Zhang, Yu; Fang, Zi-liang

2016-03-15

In this paper, in order to settle existing problems in the assessment of air bacteria and fungi contamination, the indoor and outdoor air bacteria and fungi filed concentrations by impact method and settlement method in existing documents were collected and analyzed, then the goodness of chi square was used to test whether these concentration data obeyed normal distribution at the significant level of α = 0.05, and combined with the 3σ principle of normal distribution and the current assessment standards, the suggested concentrations ranges of air microbial concentrations were determined. The research results could provide a reference for developing air bacteria and fungi contamination assessment standards in the future.

The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes.

PubMed

Luijsterburg, Martijn S; White, Malcolm F; van Driel, Roel; Dame, Remus Th

2008-01-01

The genomic DNA of all organisms across the three kingdoms of life needs to be compacted and functionally organized. Key players in these processes are DNA supercoiling, macromolecular crowding and architectural proteins that shape DNA by binding to it. The architectural proteins in bacteria, archaea and eukaryotes generally do not exhibit sequence or structural conservation especially across kingdoms. Instead, we propose that they are functionally conserved. Most of these proteins can be classified according to their architectural mode of action: bending, wrapping or bridging DNA. In order for DNA transactions to occur within a compact chromatin context, genome organization cannot be static. Indeed chromosomes are subject to a whole range of remodeling mechanisms. In this review, we discuss the role of (i) DNA supercoiling, (ii) macromolecular crowding and (iii) architectural proteins in genome organization, as well as (iv) mechanisms used to remodel chromosome structure and to modulate genomic activity. We conclude that the underlying mechanisms that shape and remodel genomes are remarkably similar among bacteria, archaea and eukaryotes.

Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria.

PubMed

Jiang, Tony T; Shao, Tzu-Yu; Ang, W X Gladys; Kinder, Jeremy M; Turner, Lucien H; Pham, Giang; Whitt, Jordan; Alenghat, Theresa; Way, Sing Sing

2017-12-13

Commensal intestinal microbes are collectively beneficial in preventing local tissue injury and augmenting systemic antimicrobial immunity. However, given the near-exclusive focus on bacterial species in establishing these protective benefits, the contributions of other types of commensal microbes remain poorly defined. Here, we show that commensal fungi can functionally replace intestinal bacteria by conferring protection against injury to mucosal tissues and positively calibrating the responsiveness of circulating immune cells. Susceptibility to colitis and influenza A virus infection occurring upon commensal bacteria eradication is efficiently overturned by mono-colonization with either Candida albicans or Saccharomyces cerevisiae. The protective benefits of commensal fungi are mediated by mannans, a highly conserved component of fungal cell walls, since intestinal stimulation with this moiety alone overrides disease susceptibility in mice depleted of commensal bacteria. Thus, commensal enteric fungi safeguard local and systemic immunity by providing tonic microbial stimulation that can functionally replace intestinal bacteria. Copyright © 2017 Elsevier Inc. All rights reserved.

Bacteria in decomposing wood and their interactions with wood-decay fungi.

PubMed

Johnston, Sarah R; Boddy, Lynne; Weightman, Andrew J

2016-11-01

The fungal community within dead wood has received considerable study, but far less attention has been paid to bacteria in the same habitat. Bacteria have long been known to inhabit decomposing wood, but much remains underexplored about their identity and ecology. Bacteria within the dead wood environment must interact with wood-decay fungi, but again, very little is known about the form this takes; there are indications of both antagonistic and beneficial interactions within this fungal microbiome. Fungi are hypothesised to play an important role in shaping bacterial communities in wood, and conversely, bacteria may affect wood-decay fungi in a variety of ways. This minireview considers what is currently known about bacteria in wood and their interactions with fungi, and proposes possible associations based on examples from other habitats. It aims to identify key knowledge gaps and pressing questions for future research. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

9 CFR 113.27 - Detection of extraneous viable bacteria and fungi in live vaccines.

Code of Federal Regulations, 2010 CFR

2010-01-01

... bacteria and fungi in live vaccines. 113.27 Section 113.27 Animals and Animal Products ANIMAL AND PLANT... bacteria and fungi in live vaccines. Unless otherwise specified by the Administrator or elsewhere exempted... Seed Bacteria shall be tested for extraneous viable bacteria and fungi as prescribed in this section. A...

9 CFR 113.27 - Detection of extraneous viable bacteria and fungi in live vaccines.

Code of Federal Regulations, 2011 CFR

2011-01-01

... bacteria and fungi in live vaccines. 113.27 Section 113.27 Animals and Animal Products ANIMAL AND PLANT... bacteria and fungi in live vaccines. Unless otherwise specified by the Administrator or elsewhere exempted... Seed Bacteria shall be tested for extraneous viable bacteria and fungi as prescribed in this section. A...

Airborne bacteria and fungi associated with waste-handling work.

PubMed

Park, Donguk; Ryu, Seunghun; Kim, Shinbum; Byun, Hyaejeong; Yoon, Chungsik; Lee, Kyeongmin

2013-01-01

Municipal workers handling household waste are potentially exposed to a variety of toxic and pathogenic substances, in particular airborne bacteria, gram-negative bacteria (GNB), and fungi. However, relatively little is known about the conditions under which exposure is facilitated. This study assessed levels of airborne bacteria, GNB, and fungi, and examined these in relation to the type of waste-handling activity (collection, transfer, transport, and sorting at the waste preprocessing plant), as well as a variety of other environmental and occupational factors. Airborne microorganisms were sampled using an Andersen single-stage sampler equipped with agar plates containing the appropriate nutritional medium and then cultured to determine airborne levels. Samples were taken during collection, transfer, transport, and sorting of household waste. Multiple regression analysis was used to identify environmental and occupational factors that significantly affect airborne microorganism levels during waste-handling activities. The "type of waste-handling activity" was the only factor that significantly affected airborne levels of bacteria and GNB, accounting for 38% (P = 0.029) and 50% (P = 0.0002) of the variation observed in bacteria and GNB levels, respectively. In terms of fungi, the type of waste-handling activity (R2 = 0.76) and whether collection had also occurred on the day prior to sampling (P < 0.0001, R2 = 0.78) explained most of the observed variation. Given that the type of waste-handling activity was significantly correlated with levels of bacteria, GNB, and fungi, we suggest that various engineering, administrative, and regulatory measures should be considered to reduce the occupational exposure to airborne microorganisms in the waste-handling industry.

Effects of Fungicides on Aquatic Fungi and Bacteria

NASA Astrophysics Data System (ADS)

Conners, D. E.; Rosemond, A. D.; Black, M. C.

2005-05-01

Aquatic microorganisms play an important role in conditioning leaf litter that enters streams and serves as an important base of production for consumers. Contamination of streams by fungicides may adversely affect microorganisms and alter leaf litter processing rates. Unfortunately, microorganisms are rarely used in acute toxicity tests for fungicide evaluation and registration. We adapted the resazurin reduction assay, which is used in medical microbiology, to assess the acute toxicity of four fungicides (azoxystrobin, trifloxystrobin, kresoxim-methyl and chlorothalonil) to aquatic fungi (Articulospora tetracladia) and bacteria (Cytophaga spp.), and investigated the ability of the toxicants to inhibit leaf breakdown in microcosms. Fungi were more sensitive to fungicides than many standard test organisms (cladocerans, green algae, trout), while bacteria were often the least sensitive. All of the fungicides except kresoxim-methyl, when added to microcosms at concentrations that inhibited the fungi by 90 percent in acute tests, reduced leaf breakdown rates by an average of 14.7 percent. Thus, aquatic fungi and their associated functions in streams may be relatively sensitive to fungicides applied terrestrially that enter streams through non-point sources. These data highlight the importance of including aquatic fungi in safety assessments of pesticides for protection of microbial function.

Pathways for degradation of lignin in bacteria and fungi.

PubMed

Bugg, Timothy D H; Ahmad, Mark; Hardiman, Elizabeth M; Rahmanpour, Rahman

2011-11-01

Lignin is a heterogeneous aromatic polymer found as 10-35% of lignocellulose, found in plant cell walls. The bio-conversion of plant lignocellulose to glucose is an important part of second generation biofuel production, but the resistance of lignin to breakdown is a major obstacle in this process, hence there is considerable interest in the microbial breakdown of lignin. White-rot fungi are known to break down lignin with the aid of extracellular peroxidase and laccase enzymes. There are also reports of bacteria that can degrade lignin, and recent work indicates that bacterial lignin breakdown may be more significant than previously thought. The review will discuss the enzymes for lignin breakdown in fungi and bacteria, and the catabolic pathways for breakdown of the β-aryl ether, biphenyl and other components of lignin in bacteria and fungi. The review will also discuss small molecule phenolic breakdown products from lignin that have been identified from lignin-degrading microbes, and includes a bioinformatic analysis of the occurrence of known lignin-degradation pathways in Gram-positive and Gram-negative bacteria.

9 CFR 113.26 - Detection of viable bacteria and fungi except in live vaccine.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Detection of viable bacteria and fungi... VECTORS STANDARD REQUIREMENTS Standard Procedures § 113.26 Detection of viable bacteria and fungi except... required to be free of viable bacteria and fungi, they shall also be tested as prescribed in this section...

9 CFR 113.26 - Detection of viable bacteria and fungi except in live vaccine.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Detection of viable bacteria and fungi... VECTORS STANDARD REQUIREMENTS Standard Procedures § 113.26 Detection of viable bacteria and fungi except... required to be free of viable bacteria and fungi, they shall also be tested as prescribed in this section...

Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils

Treesearch

Xinda Lu; Peter J. Bottomley; David D. Myrold

2015-01-01

Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA-and AOB-supported nitrifi-cation determined both in soil-water slurries and in unsaturated...

Quantitative determination of H2-utilizing acetogenic and sulfate-reducing bacteria and methanogenic archaea from digestive tract of different mammals.

PubMed

Morvan, B; Bonnemoy, F; Fonty, G; Gouet, P

1996-03-01

Total number of bacteria, cellulolytic bacteria, and H2-utilizing microbial populations (methanogenic archaea, acetogenic and sulfate-reducing bacteria) were enumerated in fresh rumen samples from sheep, cattle, buffaloes, deer, llamas, and caecal samples from horses. Methanogens and sulfate reducers were found in all samples, whereas acetogenes were not detected in some samples of each animal. Archaea methanogens were the largest H2-utilizing populations in all animals, and a correlation was observed between the numbers of methanogens and those of cellulolytic microorganisms. Higher counts of acetogens were found in horses and llamas (1 x 10(4) and 4 x 10(4) cells ml-1 respectively).

Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota.

PubMed

Miragoli, Francesco; Federici, Sara; Ferrari, Susanna; Minuti, Andrea; Rebecchi, Annalisa; Bruzzese, Eugenia; Buccigrossi, Vittoria; Guarino, Alfredo; Callegari, Maria Luisa

2017-02-01

Cystic fibrosis is often associated with intestinal inflammation due to several factors, including altered gut microbiota composition. In this study, we analyzed the fecal microbiota among patients with cystic fibrosis of 10-22 years of age, and compared the findings with age-matched healthy subjects. The participating patients included 14 homozygotes and 14 heterozygotes with the delF508 mutation, and 2 heterozygotes presenting non-delF508 mutations. We used PCR-DGGE and qPCR to analyze the presence of bacteria, archaea and sulfate-reducing bacteria. Overall, our findings confirmed disruption of the cystic fibrosis gut microbiota. Principal component analysis of the qPCR data revealed no differences between homozygotes and heterozygotes, while both groups were distinct from healthy subjects who showed higher biodiversity. Archaea were under the detection limit in all homozygotes subjects, whereas methanogens were detected in 62% of both cystic fibrosis heterozygotes and healthy subjects. Our qPCR results revealed a low frequency of sulfate-reducing bacteria in the homozygote (13%) and heterozygote (13%) patients with cystic fibrosis compared with healthy subjects (87.5%). This is a pioneer study showing that patients with cystic fibrosis exhibit significant reduction of H 2 -consuming microorganisms, which could increase hydrogen accumulation in the colon and the expulsion of this gas through non-microbial routes. © FEMS 2016.

ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea

PubMed Central

Paramasivam, Nagarajan; Linke, Dirk

2011-01-01

The subcellular localization (SCL) of proteins provides important clues to their function in a cell. In our efforts to predict useful vaccine targets against Gram-negative bacteria, we noticed that misannotated start codons frequently lead to wrongly assigned SCLs. This and other problems in SCL prediction, such as the relatively high false-positive and false-negative rates of some tools, can be avoided by applying multiple prediction tools to groups of homologous proteins. Here we present ClubSub-P, an online database that combines existing SCL prediction tools into a consensus pipeline from more than 600 proteomes of fully sequenced microorganisms. On top of the consensus prediction at the level of single sequences, the tool uses clusters of homologous proteins from Gram-negative bacteria and from Archaea to eliminate false-positive and false-negative predictions. ClubSub-P can assign the SCL of proteins from Gram-negative bacteria and Archaea with high precision. The database is searchable, and can easily be expanded using either new bacterial genomes or new prediction tools as they become available. This will further improve the performance of the SCL prediction, as well as the detection of misannotated start codons and other annotation errors. ClubSub-P is available online at http://toolkit.tuebingen.mpg.de/clubsubp/ PMID:22073040

Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment.

PubMed

Wurzbacher, Christian; Fuchs, Andrea; Attermeyer, Katrin; Frindte, Katharina; Grossart, Hans-Peter; Hupfer, Michael; Casper, Peter; Monaghan, Michael T

2017-04-08

Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137 Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO 2 and CH 4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model

Substrate and nutrient limitation of ammonia-oxidizing bacteria and archaea in temperate forest soil

Treesearch

J.S. Norman; J.E. Barrett

2014-01-01

Ammonia-oxidizing microbes control the rate-limiting step of nitrification, a critical ecosystem process, which affects retention and mobility of nitrogen in soil ecosystems. This study investigated substrate (NH4þ) and nutrient (K and P) limitation of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in temperate forest soils at Coweeta Hydrologic...

9 CFR 113.25 - Culture media for detection of bacteria and fungi.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Culture media for detection of bacteria and fungi. 113.25 Section 113.25 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION... STANDARD REQUIREMENTS Standard Procedures § 113.25 Culture media for detection of bacteria and fungi. (a...

9 CFR 113.25 - Culture media for detection of bacteria and fungi.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Culture media for detection of bacteria and fungi. 113.25 Section 113.25 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION... STANDARD REQUIREMENTS Standard Procedures § 113.25 Culture media for detection of bacteria and fungi. (a...

Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology.

PubMed

Rudolph, C; Wanner, G; Huber, R

2001-05-01

We report the identification of novel archaea living in close association with bacteria in the cold (approximately 10 degrees C) sulfurous marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. These microorganisms form a characteristic, macroscopically visible structure, morphologically comparable to a string of pearls. Tiny, whitish globules (the pearls; diameter, about 0.5 to 3.0 mm) are connected to each other by thin, white-colored threads. Fluorescent in situ hybridization (FISH) studies have revealed that the outer part of the pearls is mainly composed of bacteria, with a filamentous bacterium predominating. Internally, archaeal cocci are the predominant microorganisms, with up to 10(7) cells estimated to be present in a single pearl. The archaea appear to be embedded in a polymer of unknown chemical composition. According to FISH and 16S rRNA gene sequence analysis, the archaea are affiliated with the euryarchaeal kingdom. The new euryarchaeal sequence represents a deep phylogenetic branch within the 16S rRNA tree and does not show extensive similarity to any cultivated archaea or to 16S rRNA gene sequences from environmental samples.

Bacteria, fungi and protozoa paper

EPA Pesticide Factsheets

Bacteria and fungi in source and treated drinking waterThis dataset is associated with the following publication:King , D., S. Pfaller , M. Donohue , S. Vesper , E. Villegas , M. Ware , S. Glassmeyer , M. Vogal, E. Furlong, and D. Kolpin. Microbial pathogens in source and treated waters from drinking water treatment plants in the United States and implications for human health. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 562: 987–995, (2016).

Fungi and bacteria involved in desert varnish formation

NASA Technical Reports Server (NTRS)

Taylor-George, S.; Palmer, F.; Staley, J. T.; Curtiss, B.; Adams, J. B.; Borns, D. J.

1983-01-01

Desert varnish is a coating of ferromanganese oxides and clays that develops on rock surfaces in arid to semi-arid regions. Active respiration but not photosynthesis was detected on varnished rock surfaces from the Sonoran Desert. Light microscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations, and cultivation experiments indicate that both fungi, primarily dematiaceous hyphomycetes, and bacteria are found on and within desert varnish coatings from the arid regions studied. Some fungi grow as microcolonial fungi (MCF) on rocks, and microscopic observations suggest MCF become incorporated in the varnish coating. SEM-EDAX (energy dispersive X-ray systems) analyses indicate the MCF contain 3 of the characteristic elements of varnish: iron, aluminum, and silicon. In some locations, MCF are also enriched in manganese relative to the rock substratum. Furthermore, some of the dematiaceous hyphomycetes that have been cultivated are able to oxidize manganese under laboratory conditions. It is possible that manganese-oxidizing bacteria, which are found in varnish, also play an important role in varnish formation.

Growth of saprotrophic fungi and bacteria in soil.

PubMed

Rousk, Johannes; Bååth, Erland

2011-10-01

Bacterial and fungal growth rate measurements are sensitive variables to detect changes in environmental conditions. However, while considerable progress has been made in methods to assess the species composition and biomass of fungi and bacteria, information about growth rates remains surprisingly rudimentary. We review the recent history of approaches to assess bacterial and fungal growth rates, leading up to current methods, especially focusing on leucine/thymidine incorporation to estimate bacterial growth and acetate incorporation into ergosterol to estimate fungal growth. We present the underlying assumptions for these methods, compare estimates of turnover times for fungi and bacteria based on them, and discuss issues, including for example elusive conversion factors. We review what the application of fungal and bacterial growth rate methods has revealed regarding the influence of the environmental factors of temperature, moisture (including drying/rewetting), pH, as well as the influence of substrate additions, the presence of plants and toxins. We highlight experiments exploring the competitive and facilitative interaction between bacteria and fungi enabled using growth rate methods. Finally, we predict that growth methods will be an important complement to molecular approaches to elucidate fungal and bacterial ecology, and we identify methodological concerns and how they should be addressed. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Exposure level and distribution characteristics of airborne bacteria and fungi in Seoul metropolitan subway stations.

PubMed

Kim, Ki Youn; Kim, Yoon Shin; Kim, Daekeun; Kim, Hyeon Tae

2011-01-01

The exposure level and distribution characteristics of airborne bacteria and fungi were assessed in the workers' activity areas (station office, bedroom, ticket office and driver's seat) and passengers' activity areas (station precinct, inside the passenger carriage, and platform) of the Seoul metropolitan subway. Among investigated areas, the levels of airborne bacteria and fungi in the workers' bedroom and station precincts were relatively high. No significant difference was found in the concentration of airborne bacteria and fungi between the underground and above ground activity areas of the subway. The genera identified in all subway activity areas with a 5% or greater detection rate were Staphylococcus, Micrococcus, Bacillus and Corynebacterium for airborne bacteria and Penicillium, Cladosporium, Chrysosporium, Aspergillus for airborne fungi. Staphylococcus and Micrococcus comprised over 50% of the total airborne bacteria and Penicillium and Cladosporium comprised over 60% of the total airborne fungi, thus these four genera are the predominant genera in the subway station.

Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Reeve, Wayne

2013-03-01

Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Vertical stratification of bacteria and archaea in sediments of a boreal stratified humic lake

NASA Astrophysics Data System (ADS)

Rissanen, Antti J.; Mpamah, Promise; Peura, Sari; Taipale, Sami; Biasi, Christina; Nykänen, Hannu

2015-04-01

Boreal stratified humic lakes, with steep redox gradients in the water column and in the sediment, are important sources of methane (CH4) to the atmosphere. CH4 flux from these lakes is largely controlled by the balance between CH4-production (methanogenesis), which takes place in the organic rich sediment and in the deepest water layers, and CH4-consumption (methanotrophy), which takes place mainly in the water column. While there is already some published information on the activity, diversity and community structure of bacteria in the water columns of these lakes, such information on sediment microbial communities is very scarce. This study aims to characterize the vertical variation patterns in the diversity and the structure of microbial communities in sediment of a boreal stratified lake. Particular focus is on microbes with the potential to contribute to methanogenesis (fermentative bacteria and methanogenic archaea) and to methanotrophy (methanotrophic bacteria and archaea). Two sediment cores (26 cm deep), collected from the deepest point (~6 m) of a small boreal stratified lake during winter-stratification, were divided into depth sections of 1 to 2 cm for analyses. Communities were studied from DNA extracted from sediment samples by next-generation sequencing (Ion Torrent) of polymerase chain reaction (PCR) - amplified bacterial and archaeal 16S rRNA gene amplicons. The abundance of methanogenic archaea was also specifically studied by quantitative-PCR of methyl coenzyme-M reductase gene (mcrA) amplicons. Furthermore, the community structure and the abundance of bacteria were studied by phospholipid fatty acid (PLFA) analysis. Dominant potential fermentative bacteria belonged to families Syntrophaceae, Clostridiaceae and Peptostreptococcaceae. There were considerable differences in the vertical distribution among these groups. The relative abundance of Syntrophaceae started to increase from the sediment surface, peaked at depth layer from 5 to 10 cm (up

Molecular evolution of FtsZ protein sequences encoded within the genomes of archaea, bacteria, and eukaryota.

PubMed

Vaughan, Sue; Wickstead, Bill; Gull, Keith; Addinall, Stephen G

2004-01-01

The FtsZ protein is a polymer-forming GTPase which drives bacterial cell division and is structurally and functionally related to eukaryotic tubulins. We have searched for FtsZ-related sequences in all freely accessible databases, then used strict criteria based on the tertiary structure of FtsZ and its well-characterized in vitro and in vivo properties to determine which sequences represent genuine homologues of FtsZ. We have identified 225 full-length FtsZ homologues, which we have used to document, phylum by phylum, the primary sequence characteristics of FtsZ homologues from the Bacteria, Archaea, and Eukaryota. We provide evidence for at least five independent ftsZ gene-duplication events in the bacterial kingdom and suggest the existence of three ancestoral euryarchaeal FtsZ paralogues. In addition, we identify "FtsZ-like" sequences from Bacteria and Archaea that, while showing significant sequence similarity to FtsZs, are unlikely to bind and hydrolyze GTP.

[Contribution of fungi to soil nitrous oxide emission and their research methods: a review].

PubMed

Huang, Ying; Long, Xi-En

2014-04-01

Nitrous oxide is an important greenhouse gas. Soil is one major emission source of N2O, which is a by-product of microorganisms-driven nitrification and denitrification processes. Extensive research has demonstrated archaea and bacteria are the predominant contributors in nitrification and denitrification. However, fungi may play a predominant role in the N transformation in a certain soil ecosystem. The fungal contribution to N2O production has been rarely investigated. Here, we reviewed the mechanism of N2O production by soil fungi. The mechanisms of denitrification, autotrophic and heterotrophic nitrification and their key microbes and functional genes were described, respectively. We discriminated the differences in denitrification between bacteria and fungi and discussed the methods being used to determine the contribution of fungi to soil N2O emission, including selective inhibitors, 15N stable isotope probing, isolation and pure culturing and uncultured molecular detection methods. The existing problems and research prospects were also presented.

Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil

PubMed Central

Banning, Natasha C.; Maccarone, Linda D.; Fisk, Louise M.; Murphy, Daniel V.

2015-01-01

Ammonia-oxidising archaea (AOA) and bacteria (AOB) are responsible for the rate limiting step in nitrification; a key nitrogen (N) loss pathway in agricultural systems. Dominance of AOA relative to AOB in the amoA gene pool has been reported in many ecosystems, although their relative contributions to nitrification activity are less clear. Here we examined the distribution of AOA and AOB with depth in semi-arid agricultural soils in which soil organic matter content or pH had been altered, and related their distribution to gross nitrification rates. Soil depth had a significant effect on gene abundances, irrespective of management history. Contrary to reports of AOA dominance in soils elsewhere, AOA gene copy numbers were four-fold lower than AOB in the surface (0–10 cm). AOA gene abundance increased with depth while AOB decreased, and sub-soil abundances were approximately equal (10–90 cm). The depth profile of total archaea did not mirror that of AOA, indicating the likely presence of archaea without nitrification capacity in the surface. Gross nitrification rates declined significantly with depth and were positively correlated to AOB but negatively correlated to AOA gene abundances. We conclude that AOB are most likely responsible for regulating nitrification in these semi-arid soils. PMID:26053257

Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil.

PubMed

Banning, Natasha C; Maccarone, Linda D; Fisk, Louise M; Murphy, Daniel V

2015-06-08

Ammonia-oxidising archaea (AOA) and bacteria (AOB) are responsible for the rate limiting step in nitrification; a key nitrogen (N) loss pathway in agricultural systems. Dominance of AOA relative to AOB in the amoA gene pool has been reported in many ecosystems, although their relative contributions to nitrification activity are less clear. Here we examined the distribution of AOA and AOB with depth in semi-arid agricultural soils in which soil organic matter content or pH had been altered, and related their distribution to gross nitrification rates. Soil depth had a significant effect on gene abundances, irrespective of management history. Contrary to reports of AOA dominance in soils elsewhere, AOA gene copy numbers were four-fold lower than AOB in the surface (0-10 cm). AOA gene abundance increased with depth while AOB decreased, and sub-soil abundances were approximately equal (10-90 cm). The depth profile of total archaea did not mirror that of AOA, indicating the likely presence of archaea without nitrification capacity in the surface. Gross nitrification rates declined significantly with depth and were positively correlated to AOB but negatively correlated to AOA gene abundances. We conclude that AOB are most likely responsible for regulating nitrification in these semi-arid soils.

Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows.

PubMed

Kumar, Sanjay; Indugu, Nagaraju; Vecchiarelli, Bonnie; Pitta, Dipti W

2015-01-01

The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF), protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation) and multiparous (≥second lactation) cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n = 5) and multiparous (n = 5) cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index) revealed the effect of diet (P < 0.01) on ARF composition, while archaeal communities differed between primiparous and multiparous cows (P < 0.05). Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera. Abundance of Cyllamyces and Caecomyces shifted with diet, whereas Orpinomyces was influenced by both diet and age. Methanobrevibacter constituted the most dominant archaeal genus across all samples. Co-occurrence analysis incorporating taxa from bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows, supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to diet and

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

PubMed Central

Marraffini, Luciano A.; Sontheimer, Erik J.

2010-01-01

Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. The importance of such pathways is highlighted by the extensive study of RNA interference (RNAi) and related processes in eukaryotes. In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. CRISPR sequences provide an adaptive, heritable record of past infections and express CRISPR RNAs — small RNAs that target invasive nucleic acids. Here, we review the mechanisms of CRISPR interference and its roles in microbial physiology and evolution. We also discuss potential applications of this novel interference pathway. PMID:20125085

Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

PubMed Central

Takahashi, Shunsuke; Tomita, Junko; Nishioka, Kaori; Hisada, Takayoshi; Nishijima, Miyuki

2014-01-01

For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification of 16S rDNA is a critical step. To obtain accurate microbial composition data, PCR amplification must be free of bias; however, amplifying all 16S rDNA species with equal efficiency from a sample containing a large variety of microorganisms remains challenging. Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace×Large white×Duroc) using an Illumina MiSeq next-generation sequencer. In-silico analysis showed that the newly designed universal prokaryotic primers matched approximately 98.0% of Bacteria and 94.6% of Archaea rRNA gene sequences in the Ribosomal Database Project database. For each sequencing reaction performed with the prokaryotic universal primer, an average of 69,330 (±20,482) reads were obtained, of which archaeal rRNA genes comprised approximately 1.2% to 3.2% of all prokaryotic reads. In addition, the detection frequency of Bacteria belonging to the phylum Verrucomicrobia, including members of the classes Verrucomicrobiae and Opitutae, was higher in the NGS analysis using the prokaryotic universal primer than that performed with the bacterial universal primer. Importantly, this new prokaryotic universal primer set had markedly lower bias than that of most previously designed universal primers. Our findings demonstrate that the prokaryotic universal primer set designed in the present study will permit the simultaneous detection of Bacteria and Archaea, and will therefore allow for a more comprehensive understanding of microbial community structures in environmental samples. PMID:25144201

Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures.

PubMed

Drake, Henrik; Ivarsson, Magnus; Bengtson, Stefan; Heim, Christine; Siljeström, Sandra; Whitehouse, Martin J; Broman, Curt; Belivanova, Veneta; Åström, Mats E

2017-07-04

The deep biosphere is one of the least understood ecosystems on Earth. Although most microbiological studies in this system have focused on prokaryotes and neglected microeukaryotes, recent discoveries have revealed existence of fossil and active fungi in marine sediments and sub-seafloor basalts, with proposed importance for the subsurface energy cycle. However, studies of fungi in deep continental crystalline rocks are surprisingly few. Consequently, the characteristics and processes of fungi and fungus-prokaryote interactions in this vast environment remain enigmatic. Here we report the first findings of partly organically preserved and partly mineralized fungi at great depth in fractured crystalline rock (-740 m). Based on environmental parameters and mineralogy the fungi are interpreted as anaerobic. Synchrotron-based techniques and stable isotope microanalysis confirm a coupling between the fungi and sulfate reducing bacteria. The cryptoendolithic fungi have significantly weathered neighboring zeolite crystals and thus have implications for storage of toxic wastes using zeolite barriers.Deep subsurface microorganisms play an important role in nutrient cycling, yet little is known about deep continental fungal communities. Here, the authors show organically preserved and partly mineralized fungi at 740 m depth, and find evidence of an anaerobic fungi and sulfate reducing bacteria consortium.

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria.

PubMed

Martens-Habbena, Willm; Berube, Paul M; Urakawa, Hidetoshi; de la Torre, José R; Stahl, David A

2009-10-15

The discovery of ammonia oxidation by mesophilic and thermophilic Crenarchaeota and the widespread distribution of these organisms in marine and terrestrial environments indicated an important role for them in the global nitrogen cycle. However, very little is known about their physiology or their contribution to nitrification. Here we report oligotrophic ammonia oxidation kinetics and cellular characteristics of the mesophilic crenarchaeon 'Candidatus Nitrosopumilus maritimus' strain SCM1. Unlike characterized ammonia-oxidizing bacteria, SCM1 is adapted to life under extreme nutrient limitation, sustaining high specific oxidation rates at ammonium concentrations found in open oceans. Its half-saturation constant (K(m) = 133 nM total ammonium) and substrate threshold (Archaea to oligotrophic nitrification. The remarkably high specific affinity for reduced nitrogen (68,700 l per g cells per h) of SCM1 suggests that Nitrosopumilus-like ammonia-oxidizing Archaea could successfully compete with heterotrophic bacterioplankton and phytoplankton. Together these findings support the hypothesis that nitrification is more prevalent in the marine nitrogen cycle than accounted for in current biogeochemical models.

In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria.

PubMed

de Boer, Wietse; Wagenaar, Anne-Marieke; Klein Gunnewiek, Paulien J A; van Veen, Johannes A

2007-01-01

We hypothesized that apparently non-antagonistic soil bacteria may contribute to suppression of fungi during competitive interactions with other bacteria. Four soil bacteria (Brevundimonas sp., Luteibacter sp., Pedobacter sp. and Pseudomonas sp.) that exhibited little or no visible antifungal activity on different agar media were prescribed. Single and mixed strains of these species were tested for antagonism on a nutrient-poor agar medium against the plant pathogenic fungi Fusarium culmorum and Rhizoctonia solani and the saprotrophic fungus Trichoderma harzianum. Single bacterial strains caused little to moderate growth reduction of fungi (quantified as ergosterol), most probably due to nutrient withdrawal from the media. Growth reduction of fungi by the bacterial mixture was much stronger than that by the single strains. This appeared to be mostly due to competitive interactions between the Pseudomonas and Pedobacter strains. We argue that cohabitation of these strains triggered antibiotic production via interspecific interactions and that the growth reduction of fungi was a side-effect caused by the sensitivity of the fungi to bacterial secondary metabolites. Induction of gliding behavior in the Pedobacter strain by other strains was also observed. Our results indicate that apparently non-antagonistic soil bacteria may be important contributors to soil suppressiveness and fungistasis when in a community context.

The interactions of bacteria with fungi in soil: emerging concepts.

PubMed

Haq, Irshad Ul; Zhang, Miaozhi; Yang, Pu; van Elsas, Jan Dirk

2014-01-01

In this chapter, we review the existing literature on bacterial-fungal interactions in soil, exploring the role fungi may play for soil bacteria as providers of hospitable niches. A focus is placed on the mycosphere, i.e., the narrow zone of influence of fungal hyphae on the external soil milieu, in which hypha-associated bacterial cells dwell. Evidence is brought forward for the contention that the hyphae of both mycorrhizal and saprotrophic fungi serve as providers of ecological opportunities in a grossly carbon-limited soil, as a result of their release of carbonaceous compounds next to the provision of a colonizable surface. Soil bacteria of particular nature are postulated to have adapted to such selection pressures, evolving to the extent that they acquired capabilities that allow them to thrive in the novel habitat created by the emerging fungal hyphae. The mechanisms involved in the interactions and the modes of genetic adaptation of the mycosphere dwellers are discussed, with an emphasis on one key mycosphere-adapted bacterium, Burkholderia terrae BS001. In this discussion, we interrogate the positive interactions between soil fungi and bacteria, and refrain from considering negative interactions. © 2014 Elsevier Inc. All rights reserved.

9 CFR 113.27 - Detection of extraneous viable bacteria and fungi in live vaccines.

Code of Federal Regulations, 2013 CFR

2013-01-01

... bacteria and fungi in live vaccines. 113.27 Section 113.27 Animals and Animal Products ANIMAL AND PLANT... bacteria and fungi in live vaccines. Unless otherwise specified by the Administrator or elsewhere exempted in this part, each serial and subserial of live vaccine and each lot of Master Seed Virus and Master...

9 CFR 113.27 - Detection of extraneous viable bacteria and fungi in live vaccines.

Code of Federal Regulations, 2014 CFR

2014-01-01

... bacteria and fungi in live vaccines. 113.27 Section 113.27 Animals and Animal Products ANIMAL AND PLANT... bacteria and fungi in live vaccines. Unless otherwise specified by the Administrator or elsewhere exempted in this part, each serial and subserial of live vaccine and each lot of Master Seed Virus and Master...

9 CFR 113.27 - Detection of extraneous viable bacteria and fungi in live vaccines.

Code of Federal Regulations, 2012 CFR

2012-01-01

... bacteria and fungi in live vaccines. 113.27 Section 113.27 Animals and Animal Products ANIMAL AND PLANT... bacteria and fungi in live vaccines. Unless otherwise specified by the Administrator or elsewhere exempted in this part, each serial and subserial of live vaccine and each lot of Master Seed Virus and Master...

ETV Tech Brief: Rapid Fungi and Bacteria Detection Technologies

EPA Science Inventory

Technical brief that summarizes the results for Mycometer, Inc. Mycometer®-test and Bactiquant®-test, which are rapid detection technologies for fungi and bacteria. The brief summarizes the results of the verification report and statement.

Fungi, bacteria and soil pH: the oxalate-carbonate pathway as a model for metabolic interaction.

PubMed

Martin, Gaëtan; Guggiari, Matteo; Bravo, Daniel; Zopfi, Jakob; Cailleau, Guillaume; Aragno, Michel; Job, Daniel; Verrecchia, Eric; Junier, Pilar

2012-11-01

The oxalate-carbonate pathway involves the oxidation of calcium oxalate to low-magnesium calcite and represents a potential long-term terrestrial sink for atmospheric CO(2). In this pathway, bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria, fungi and calcium oxalate amendments was studied using microcosms. In a model system with sterile soil amended with laboratory cultures of oxalotrophic bacteria and fungi, the addition of calcium oxalate induced a distinct pH shift and led to the final precipitation of calcite. However, the simultaneous presence of bacteria and fungi was essential to drive this pH shift. Growth of both oxalotrophic bacteria and fungi was confirmed by qPCR on the frc (oxalotrophic bacteria) and 16S rRNA genes, and the quantification of ergosterol (active fungal biomass) respectively. The experiment was replicated in microcosms with non-sterilized soil. In this case, the bacterial and fungal contribution to oxalate degradation was evaluated by treatments with specific biocides (cycloheximide and bronopol). Results showed that the autochthonous microflora oxidized calcium oxalate and induced a significant soil alkalinization. Moreover, data confirmed the results from the model soil showing that bacteria are essentially responsible for the pH shift, but require the presence of fungi for their oxalotrophic activity. The combined results highlight that the interaction between bacteria and fungi is essential to drive metabolic processes in complex environments such as soil. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Mrp Antiporters Have Important Roles in Diverse Bacteria and Archaea.

PubMed

Ito, Masahiro; Morino, Masato; Krulwich, Terry A

2017-01-01

Mrp (Multiple resistance and pH) antiporter was identified as a gene complementing an alkaline-sensitive mutant strain of alkaliphilic Bacillus halodurans C-125 in 1990. At that time, there was no example of a multi-subunit type Na + /H + antiporter comprising six or seven hydrophobic proteins, and it was newly designated as the monovalent cation: proton antiporter-3 (CPA3) family in the classification of transporters. The Mrp antiporter is broadly distributed among bacteria and archaea, not only in alkaliphiles. Generally, all Mrp subunits, mrpA-G , are required for enzymatic activity. Two exceptions are Mrp from the archaea Methanosarcina acetivorans and the eubacteria Natranaerobius thermophilus , which are reported to sustain Na + /H + antiport activity with the MrpA subunit alone. Two large subunits of the Mrp antiporter, MrpA and MrpD, are homologous to membrane-embedded subunits of the respiratory chain complex I, NuoL, NuoM, and NuoN, and the small subunit MrpC has homology with NuoK. The functions of the Mrp antiporter include sodium tolerance and pH homeostasis in an alkaline environment, nitrogen fixation in Schizolobium meliloti , bile salt tolerance in Bacillus subtilis and Vibrio cholerae , arsenic oxidation in Agrobacterium tumefaciens , pathogenesis in Pseudomonas aeruginosa and Staphylococcus aureus , and the conversion of energy involved in metabolism and hydrogen production in archaea. In addition, some Mrp antiporters transport K + and Ca 2+ instead of Na + , depending on the environmental conditions. Recently, the molecular structure of the respiratory chain complex I has been elucidated by others, and details of the mechanism by which it transports protons are being clarified. Based on this, several hypotheses concerning the substrate transport mechanism in the Mrp antiporter have been proposed. The MrpA and MrpD subunits, which are homologous to the proton transport subunit of complex I, are involved in the transport of protons and their

Mrp Antiporters Have Important Roles in Diverse Bacteria and Archaea

PubMed Central

Ito, Masahiro; Morino, Masato; Krulwich, Terry A.

2017-01-01

Mrp (Multiple resistance and pH) antiporter was identified as a gene complementing an alkaline-sensitive mutant strain of alkaliphilic Bacillus halodurans C-125 in 1990. At that time, there was no example of a multi-subunit type Na+/H+ antiporter comprising six or seven hydrophobic proteins, and it was newly designated as the monovalent cation: proton antiporter-3 (CPA3) family in the classification of transporters. The Mrp antiporter is broadly distributed among bacteria and archaea, not only in alkaliphiles. Generally, all Mrp subunits, mrpA–G, are required for enzymatic activity. Two exceptions are Mrp from the archaea Methanosarcina acetivorans and the eubacteria Natranaerobius thermophilus, which are reported to sustain Na+/H+ antiport activity with the MrpA subunit alone. Two large subunits of the Mrp antiporter, MrpA and MrpD, are homologous to membrane-embedded subunits of the respiratory chain complex I, NuoL, NuoM, and NuoN, and the small subunit MrpC has homology with NuoK. The functions of the Mrp antiporter include sodium tolerance and pH homeostasis in an alkaline environment, nitrogen fixation in Schizolobium meliloti, bile salt tolerance in Bacillus subtilis and Vibrio cholerae, arsenic oxidation in Agrobacterium tumefaciens, pathogenesis in Pseudomonas aeruginosa and Staphylococcus aureus, and the conversion of energy involved in metabolism and hydrogen production in archaea. In addition, some Mrp antiporters transport K+ and Ca2+ instead of Na+, depending on the environmental conditions. Recently, the molecular structure of the respiratory chain complex I has been elucidated by others, and details of the mechanism by which it transports protons are being clarified. Based on this, several hypotheses concerning the substrate transport mechanism in the Mrp antiporter have been proposed. The MrpA and MrpD subunits, which are homologous to the proton transport subunit of complex I, are involved in the transport of protons and their coupling cations

An in situ inventory of fungi and their associated migrating bacteria in forest soils using fungal highway columns.

PubMed

Simon, Anaele; Hervé, Vincent; Al-Dourobi, Andrej; Verrecchia, Eric; Junier, Pilar

2017-01-01

Soils are complex ecosystems in which fungi and bacteria co-exist and interact. Fungal highways are a kind of interaction by which bacteria use fungal hyphae to disperse in soils. Despite the fact that fungal highways have been studied in laboratory models, the diversity of fungi and bacteria interacting in this way in soils is still unknown. Fungal highway columns containing two different culture media were used as a selective method to study the identity of fungi and bacteria able to migrate along the hyphae in three forest soils. Regardless of the soil type, fungi of the genus Mortierella (phylum Zygomycota) were selected inside the columns. In contrast, a diverse community of bacteria dominated by Firmicutes and Proteobacteria was observed. The results confirm the importance of bacteria affiliated to Burkholderia as potentially associated migrating bacteria in soils and indicate that other groups such as Bacillus and Clostridium are also highly enriched in the co-colonization of a new habitat (columns) associated to Mortierella. The diversity of potentially associated migrating bacteria brings a novel perspective on the indirect metabolic capabilities that could be favored by r-strategist fungi and supports the fact that these fungi should be considered as crucial actors in soil functioning. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Substrate availability drives spatial patterns in richness of ammonia-oxidizing bacteria and archaea in temperate forest soils

Treesearch

J.S. Norman; J.E. Barrett

2016-01-01

We sought to investigate the drivers of richness of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in temperate forest soils. We sampled soils across four experimental watersheds in the Coweeta Hydrologic Laboratory, North Carolina USA. These watersheds are geographically close, but vary in soil chemistry due to differences in land use history. While we...

Chaperones and protein folding in the archaea.

PubMed

Large, Andrew T; Goldberg, Martin D; Lund, Peter A

2009-02-01

A survey of archaeal genomes for the presence of homologues of bacterial and eukaryotic chaperones reveals several interesting features. All archaea contain chaperonins, also known as Hsp60s (where Hsp is heat-shock protein). These are more similar to the type II chaperonins found in the eukaryotic cytosol than to the type I chaperonins found in bacteria, mitochondria and chloroplasts, although some archaea also contain type I chaperonin homologues, presumably acquired by horizontal gene transfer. Most archaea contain several genes for these proteins. Our studies on the type II chaperonins of the genetically tractable archaeon Haloferax volcanii have shown that only one of the three genes has to be present for the organisms to grow, but that there is some evidence for functional specialization between the different chaperonin proteins. All archaea also possess genes for prefoldin proteins and for small heat-shock proteins, but they generally lack genes for Hsp90 and Hsp100 homologues. Genes for Hsp70 (DnaK) and Hsp40 (DnaJ) homologues are only found in a subset of archaea. Thus chaperone-assisted protein folding in archaea is likely to display some unique features when compared with that in eukaryotes and bacteria, and there may be important differences in the process between euryarchaea and crenarchaea.

Marine Planktonic Archaea Take Up Amino Acids

PubMed Central

Ouverney, Cleber C.; Fuhrman, Jed A.

2000-01-01

Archaea are traditionally thought of as “extremophiles,” but recent studies have shown that marine planktonic Archaea make up a surprisingly large percentage of ocean midwater microbial communities, up to 60% of the total prokaryotes. However, the basic physiology and contribution of Archaea to community microbial activity remain unknown. We have studied Archaea from 200-m depths of the northwest Mediterranean Sea and the Pacific Ocean near California, measuring the archaeal activity under simulated natural conditions (8 to 17°C, dark and anaerobic) by means of a method called substrate tracking autoradiography fluorescence in situ hybridization (STARFISH) that simultaneously detects specific cell types by 16S rRNA probe binding and activity by microautoradiography. In the 200-m-deep Mediterranean and Pacific samples, cells binding the archaeal probes made up about 43 and 14% of the total countable cells, respectively. Our results showed that the Archaea are active in the uptake of dissolved amino acids from natural concentrations (nanomolar) with about 60% of the individuals in the archaeal communities showing measurable uptake. Bacteria showed a similar proportion of active cells. We concluded that a portion of these Archaea is heterotrophic and also appears to coexist successfully with Bacteria in the same water. PMID:11055931

Domain Cell Theory supports the independent evolution of the Eukarya, Bacteria and Archaea and the Nuclear Compartment Commonality hypothesis.

PubMed

Staley, James T

2017-06-01

In 2015, the Royal Society of London held a meeting to discuss the various hypotheses regarding the origin of the Eukarya. Although not all participants supported a hypothesis, the proposals that did fit into two broad categories: one group favoured 'Prokaryotes First' hypotheses and another addressed 'Eukaryotes First' hypotheses. Those who proposed Prokaryotes First hypotheses advocated either a fusion event between a bacterium and an archaeon that produced the first eukaryote or the direct evolution of the Eukarya from the Archaea. The Eukaryotes First proponents posit that the eukaryotes evolved initially and then, by reductive evolution, produced the Bacteria and Archaea. No mention was made of another previously published hypothesis termed the Nuclear Compartment Commonality (NuCom) hypothesis, which proposed the evolution of the Eukarya and Bacteria from nucleated ancestors (Staley 2013 Astrobiol Outreach 1 , 105 (doi:10.4172/2332-2519.1000105)). Evidence from two studies indicates that the nucleated Planctomycetes-Verrucomicrobia-Chlamydia superphylum members are the most ancient Bacteria known (Brochier & Philippe 2002 Nature 417 , 244 (doi:10.1038/417244a); Jun et al. 2010 Proc. Natl Acad. Sci. USA 107 , 133-138 (doi:10.1073/pnas.0913033107)). This review summarizes the evidence for the NuCom hypothesis and discusses how simple the NuCom hypothesis is in explaining eukaryote evolution relative to the other hypotheses. The philosophical importance of simplicity and its relationship to truth in hypotheses such as NuCom and Domain Cell Theory is presented. Domain Cell Theory is also proposed herein, which contends that each of the three cellular lineages of life, the Archaea, Bacteria and Eukarya domains, evolved independently, in support of the NuCom hypothesis. All other proposed hypotheses violate Domain Cell Theory because they posit the evolution of different cellular descendants from ancestral cellular types. © 2017 The Authors.

Identification and Quantification of Archaea Involved in Primary Endodontic Infections

PubMed Central

Vianna, M. E.; Conrads, G.; Gomes, B. P. F. A.; Horz, H. P.

2006-01-01

Members of the domain Archaea, one of the three domains of life, are a highly diverse group of prokaryotes, distinct from bacteria and eukaryotes. Despite their abundance and ubiquity on earth, including their close association with humans, animals, and plants, so far no pathogenic archaea have been described. As some archaea live in close proximity to anaerobic bacteria, for instance, in the human gut system and in periodontal pockets, the aim of our study was to assess whether archaea might possibly be involved in human endodontic infections, which are commonly polymicrobial. We analyzed 20 necrotic uniradicular teeth with radiographic evidence of apical periodontitis and with no previous endodontic treatment. Using real-time quantitative PCR based on the functional gene mcrA (encoding the methyl coenzyme M reductase, specific to methanogenic archaea) and on archaeal 16S rRNA genes, we found five cases to be positive. Direct sequencing of PCR products from both genes showed that the archaeal community was dominated by a Methanobrevibacter oralis-like phylotype. The size of the archaeal population at the diseased sites ranged from 1.3 × 105 to 6.8 × 105 16S rRNA gene target molecule numbers and accounted for up to 2.5% of the total prokaryotic community (i.e., bacteria plus archaea). Our findings show that archaea can be intimately connected with infectious diseases and thus support the hypothesis that members of the domain Archaea may have a role as human pathogens. PMID:16597851

Insertion sequence diversity in archaea.

PubMed

Filée, J; Siguier, P; Chandler, M

2007-03-01

Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.

The capacity of some newly bacteria and fungi for biodegradation of herbicide trifluralin under agiated culture media.

PubMed

Erguven, G O; Bayhan, H; Ikizoglu, B; Kanat, G; Nuhoglu, Y

2016-05-30

Bioremediation is the use of microorganisms to degrade environmental contaminants (pesticides, polyaromatic hydrocarbons etc.) into less toxic forms or compounds. In this study microbial biodegradation of trifluralin was performed in liquid media with 11 different types of identified fungi and bacteria cultures and their mixtures in agiated culture media. The isolated fungi and bacteria mixtures showed the highest degradation, reaching 93% in the chemical oxygen demand (COD) parameter in four days and 82% as trifluralin active ingredient in five days. Bacteria and fungi mixtures achieved 69% and 66% degradations of trifluralin active ingredient respectively. In the fungi studies, the best removal was achieved by M.Chlamydosporia at 80%, in the bacteria studies, the best removal was achieved by Bacillus simplex about 95% in five days. These different removal rates were due to the microbial differencies.

Bacteria and fungi in aerosols generated by two different types of wastewater treatment plants.

PubMed

Bauer, H; Fuerhacker, M; Zibuschka, F; Schmid, H; Puxbaum, H

2002-09-01

Raw wastewater is a potential carrier of pathogenic microorganisms and may pose a health risk when pathogenic microorganisms become aerosolized during aeration. Two different types of wastewater treatment plants were investigated, and the amounts of cultivable bacteria and fungi were measured in the emitted aerosols. Average concentrations of 17,000 CFU m(-3) of mesophilic, 2,100 CFU m(-3) of TSA-SB bacteria (bacteria associated with certain waterborne virulence factors), 1700 CFU m(-3) of mesophilic and 45 CFU m(-3) of thermotolerant fungi, were found in the aerosol emitted by the aeration tank of the activated sludge plant. In the aerosol of the fixed-film reactor 3000 CFU m(-3) mesophilic and 730CFUm(-3) TSA-SB bacteria, and 180 CFUm(-3) mesophilic and 14 CFU m(-3) thermotolerant fungi were measured. The specific emissions per population equivalent between the two types of treatment plants differed by two orders of magnitude. The microbial flux based on the open water surface area of the two treatment plants was similar. The aerosolization ratios of cultivable bacteria (expressed as CFU m(-3) aerosol/m(-3) wastewater) ranged between 8.4 x 10(-11) and 4.9 x 10(-9). The aerosolization ratio of fungi was one to three orders of magnitude higher and a significant difference between the two types of treatment plants could be observed.

[Occupational exposure to airborne fungi and bacteria in a household recycled container sorting plant ].

PubMed

Solans, Xavier; Alonso, Rosa María; Constans, Angelina; Mansilla, Alfonso

2007-06-01

Several studies have showed an association between the work in waste treatment plants and occupational health problems such as irritation of skin, eyes and mucous membranes, pulmonary diseases, gastrointestinal problems and symptoms of organic dust toxic syndrome (ODTS). These symptoms have been related to bioaerosol exposure. The aim of this study was to investigate the occupational exposure to biological agents in a plant sorting source-separated packages (plastics materials, ferric and non-ferric metals) household waste. Airborne samples were collected with M Air T Millipore sampler. The concentration of total fungi and bacteria and gram-negative bacteria were determined and the most abundant genera were identified. The results shown that the predominant airborne microorganisms were fungi, with counts greater than 12,000 cfu/m(3) and gram-negative bacteria, with a environmental concentration between 1,395 and 5,280 cfu/m(3). In both cases, these concentrations were higher than levels obtained outside of the sorting plant. Among the fungi, the predominant genera were Penicillium and Cladosporium, whereas the predominant genera of gram-negative bacteria were Escherichia, Enterobacter, Klebsiella and Serratia. The present study shows that the workers at sorting source-separated packages (plastics materials, ferric and non-ferric metals) domestic waste plant may be exposed to airborne biological agents, especially fungi and gram-negative bacteria.

tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.

PubMed Central

Marck, Christian; Grosjean, Henri

2002-01-01

From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria. PMID:12403461

Archaea in symbioses.

PubMed

Wrede, Christoph; Dreier, Anne; Kokoschka, Sebastian; Hoppert, Michael

2012-01-01

During the last few years, the analysis of microbial diversity in various habitats greatly increased our knowledge on the kingdom Archaea. At the same time, we became aware of the multiple ways in which Archaea may interact with each other and with organisms of other kingdoms. The large group of euryarchaeal methanogens and their methane oxidizing relatives, in particular, take part in essential steps of the global methane cycle. Both of these processes, which are in reverse to each other, are partially conducted in a symbiotic interaction with different partners, either ciliates and xylophagous animals or sulfate reducing bacteria. Other symbiotic interactions are mostly of unknown ecological significance but depend on highly specific mechanisms. This paper will give an overview on interactions between Archaea and other organisms and will point out the ecological relevance of these symbiotic processes, as long as these have been already recognized.

Archaea in Symbioses

PubMed Central

Wrede, Christoph; Dreier, Anne; Kokoschka, Sebastian; Hoppert, Michael

2012-01-01

During the last few years, the analysis of microbial diversity in various habitats greatly increased our knowledge on the kingdom Archaea. At the same time, we became aware of the multiple ways in which Archaea may interact with each other and with organisms of other kingdoms. The large group of euryarchaeal methanogens and their methane oxidizing relatives, in particular, take part in essential steps of the global methane cycle. Both of these processes, which are in reverse to each other, are partially conducted in a symbiotic interaction with different partners, either ciliates and xylophagous animals or sulfate reducing bacteria. Other symbiotic interactions are mostly of unknown ecological significance but depend on highly specific mechanisms. This paper will give an overview on interactions between Archaea and other organisms and will point out the ecological relevance of these symbiotic processes, as long as these have been already recognized. PMID:23326206

Ammonia-oxidizing bacteria and archaea within biofilters of a commercial recirculating marine aquaculture system.

PubMed

Huang, Zhitao; Jiang, Yuli; Song, Xiefa; Hallerman, Eric; Peng, Lei; Dong, Dengpan; Ma, Teng; Zhai, Jieming; Li, Wensheng

2018-02-10

While biofilters are widely used to metabolize ammonia and other wastes in marine recirculating aquaculture systems, the ammonia-oxidizing bacterial and archaeal communities have not been characterized across a diversity of production systems. Using a metagenomics approach, we characterized the ammonia-oxidizing microbiological community of biofilters in a commercial recirculating marine aquaculture system producing hybrid grouper (Epinephelus lanceolatus × E. fuscoguttatus). Cloning and sequencing of the amoA gene showed that nitrifying bacteria included Nitrosomonas europea, N. stercoris, N. cryotolerans, N. eutropha, N. estuarii, eight strains of N. marina, and 15 strains not associated with described species. Nitrifying archaea included eight strains of Nitrosopumilus maritimus, N. koreensis, N. piranensis, N. adriaticus, undescribed congeners, and other undescribed archaea. The species composition of the bacterial and especially the archaeal communities was beyond that yet reported for aquaculture biofilters. While ammonia flux through the respective communities has yet to be estimated, the diverse environmental adaptations of the bacterial and archaeal communities suggest resilience of function under a range of environmental conditions.

Bioenergetics of the Archaea

PubMed Central

Schäfer, Günter; Engelhard, Martin; Müller, Volker

1999-01-01

In the late 1970s, on the basis of rRNA phylogeny, Archaea (archaebacteria) was identified as a distinct domain of life besides Bacteria (eubacteria) and Eucarya. Though forming a separate domain, archaea display an enormous diversity of lifestyles and metabolic capabilities. Many archaeal species are adapted to extreme environments with respect to salinity, temperatures around the boiling point of water, and/or extremely alkaline or acidic pH. This has posed the challenge of studying the molecular and mechanistic bases on which these organisms can cope with such adverse conditions. This review considers our cumulative knowledge on archaeal mechanisms of primary energy conservation, in relationship to those of bacteria and eucarya. Although the universal principle of chemiosmotic energy conservation also holds for Archaea, distinct features have been discovered with respect to novel ion-transducing, membrane-residing protein complexes and the use of novel cofactors in bioenergetics of methanogenesis. From aerobically respiring archaea, unusual electron-transporting supercomplexes could be isolated and functionally resolved, and a proposal on the organization of archaeal electron transport chains has been presented. The unique functions of archaeal rhodopsins as sensory systems and as proton or chloride pumps have been elucidated on the basis of recent structural information on the atomic scale. Whereas components of methanogenesis and of phototrophic energy transduction in halobacteria appear to be unique to archaea, respiratory complexes and the ATP synthase exhibit some chimeric features with respect to their evolutionary origin. Nevertheless, archaeal ATP synthases are to be considered distinct members of this family of secondary energy transducers. A major challenge to future investigations is the development of archaeal genetic transformation systems, in order to gain access to the regulation of bioenergetic systems and to overproducers of archaeal membrane

Bacteria and fungi inactivation by photocatalysis under UVA irradiation: liquid and gas phase.

PubMed

Rodrigues-Silva, Caio; Miranda, Sandra M; Lopes, Filipe V S; Silva, Mário; Dezotti, Márcia; Silva, Adrián M T; Faria, Joaquim L; Boaventura, Rui A R; Vilar, Vítor J P; Pinto, Eugénia

2017-03-01

In the last decade, environmental risks associated with wastewater treatment plants (WWTPs) have become a concern in the scientific community due to the absence of specific legislation governing the occupational exposure limits (OEL) for microorganisms present in indoor air. Thus, it is necessary to develop techniques to effectively inactivate microorganisms present in the air of WWTPs facilities. In the present work, ultraviolet light A radiation was used as inactivation tool. The microbial population was not visibly reduced in the bioaerosol by ultraviolet light A (UVA) photolysis. The UVA photocatalytic process for the inactivation of microorganisms (bacteria and fungi, ATCC strains and isolates from indoor air samples of a WWTP) using titanium dioxide (TiO 2 P25) and zinc oxide (ZnO) was tested in both liquid-phase and airborne conditions. In the slurry conditions at liquid phase, P25 showed a better performance in inactivation. For this reason, gas-phase assays were performed in a tubular photoreactor packed with cellulose acetate monolithic structures coated with P25. The survival rate of microorganisms under study decreased with the catalyst load and the UVA exposure time. Inactivation of fungi was slower than resistant bacteria, followed by Gram-positive bacteria and Gram-negative bacteria. Graphical abstract Inactivation of fungi and bacteria in gas phase by photocatalitic process performed in a tubular photoreactor packed with cellulose acetate monolith structures coated with TiO 2 .

High diversity of airborne fungi in the hospital environment as revealed by meta-sequencing-based microbiome analysis

PubMed Central

Tong, Xunliang; Xu, Hongtao; Zou, Lihui; Cai, Meng; Xu, Xuefeng; Zhao, Zuotao; Xiao, Fei; Li, Yanming

2017-01-01

Invasive fungal infections acquired in the hospital have progressively emerged as an important cause of life-threatening infection. In particular, airborne fungi in hospitals are considered critical pathogens of hospital-associated infections. To identify the causative airborne microorganisms, high-volume air samplers were utilized for collection, and species identification was performed using a culture-based method and DNA sequencing analysis with the Illumina MiSeq and HiSeq 2000 sequencing systems. Few bacteria were grown after cultivation in blood agar. However, using microbiome sequencing, the relative abundance of fungi, Archaea species, bacteria and viruses was determined. The distribution characteristics of fungi were investigated using heat map analysis of four departments, including the Respiratory Intensive Care Unit, Intensive Care Unit, Emergency Room and Outpatient Department. The prevalence of Aspergillus among fungi was the highest at the species level, approximately 17% to 61%, and the prevalence of Aspergillus fumigatus among Aspergillus species was from 34% to 50% in the four departments. Draft genomes of microorganisms isolated from the hospital environment were obtained by sequence analysis, indicating that investigation into the diversity of airborne fungi may provide reliable results for hospital infection control and surveillance. PMID:28045065

Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya.

PubMed

Wardle, Josephine; Burgers, Peter M J; Cann, Isaac K O; Darley, Kate; Heslop, Pauline; Johansson, Erik; Lin, Li-Jung; McGlynn, Peter; Sanvoisin, Jonathan; Stith, Carrie M; Connolly, Bernard A

2008-02-01

Family B DNA polymerases from archaea such as Pyrococcus furiosus, which live at temperatures approximately 100 degrees C, specifically recognize uracil in DNA templates and stall replication in response to this base. Here it is demonstrated that interaction with uracil is not restricted to hyperthermophilic archaea and that the polymerase from mesophilic Methanosarcina acetivorans shows identical behaviour. The family B DNA polymerases replicate the genomes of archaea, one of the three fundamental domains of life. This publication further shows that the DNA replicating polymerases from the other two domains, bacteria (polymerase III) and eukaryotes (polymerases delta and epsilon for nuclear DNA and polymerase gamma for mitochondrial) are also unable to recognize uracil. Uracil occurs in DNA as a result of deamination of cytosine, either in G:C base-pairs or, more rapidly, in single stranded regions produced, for example, during replication. The resulting G:U mis-pairs/single stranded uracils are promutagenic and, unless repaired, give rise to G:C to A:T transitions in 50% of the progeny. The confinement of uracil recognition to polymerases of the archaeal domain is discussed in terms of the DNA repair pathways necessary for the elimination of uracil.

Bacteria can mobilize nematode-trapping fungi to kill nematodes

PubMed Central

Wang, Xin; Li, Guo-Hong; Zou, Cheng-Gang; Ji, Xing-Lai; Liu, Tong; Zhao, Pei-Ji; Liang, Lian-Ming; Xu, Jian-Ping; An, Zhi-Qiang; Zheng, Xi; Qin, Yue-Ke; Tian, Meng-Qing; Xu, You-Yao; Ma, Yi-Cheng; Yu, Ze-Fen; Huang, Xiao-Wei; Liu, Shu-Qun; Niu, Xue-Mei; Yang, Jin-Kui; Huang, Ying; Zhang, Ke-Qin

2014-01-01

In their natural habitat, bacteria are consumed by bacterivorous nematodes; however, they are not simply passive preys. Here we report a defensive mechanism used by certain bacteria to mobilize nematode-trapping fungi to kill nematodes. These bacteria release urea, which triggers a lifestyle switch in the fungus Arthrobotrys oligospora from saprophytic to nematode–predatory form; this predacious form is characterized by formation of specialized cellular structures or ‘traps’. The bacteria significantly promote the elimination of nematodes by A. oligospora. Disruption of genes involved in urea transport and metabolism in A. oligospora abolishes the urea-induced trap formation. Furthermore, the urea metabolite ammonia functions as a signal molecule in the fungus to initiate the lifestyle switch to form trap structures. Our findings highlight the importance of multiple predator–prey interactions in prey defense mechanisms. PMID:25514608

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

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

Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas

The number of genomes from uncultivated microbes will soon surpass the number of isolate genomes in public databases (Hugenholtz, Skarshewski, & Parks, 2016). Technological advancements in high-throughput sequencing and assembly, including single-cell genomics and the computational extraction of genomes from metagenomes (GFMs), are largely responsible. Here we propose community standards for reporting the Minimum Information about a Single-Cell Genome (MIxS-SCG) and Minimum Information about Genomes extracted From Metagenomes (MIxS-GFM) specific for Bacteria and Archaea. The standards have been developed in the context of the International Genomics Standards Consortium (GSC) community (Field et al., 2014) and can be viewed as amore » supplement to other GSC checklists including the Minimum Information about a Genome Sequence (MIGS), Minimum information about a Metagenomic Sequence(s) (MIMS) (Field et al., 2008) and Minimum Information about a Marker Gene Sequence (MIMARKS) (P. Yilmaz et al., 2011). Community-wide acceptance of MIxS-SCG and MIxS-GFM for Bacteria and Archaea will enable broad comparative analyses of genomes from the majority of taxa that remain uncultivated, improving our understanding of microbial function, ecology, and evolution.« less

Diversity, specificity and phylogenetic relationships of endohyphal bacteria in fungi that inhabit tropical seeds and leaves

USDA-ARS?s Scientific Manuscript database

Fungi that recruit to seeds in the soil can influence seed dispersal, dormancy, germination, and survival. Bacteria that inhabit fungi can alter fungal phenotypes and the outcomes of plant-fungus interactions, but their prevalence in seed-associated fungi has not been evaluated. The aims of this stu...

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

PubMed Central

Wrighton, Kelly C; Castelle, Cindy J; Varaljay, Vanessa A; Satagopan, Sriram; Brown, Christopher T; Wilkins, Michael J; Thomas, Brian C; Sharon, Itai; Williams, Kenneth H; Tabita, F Robert; Banfield, Jillian F

2016-01-01

Metagenomic studies recently uncovered form II/III RubisCO genes, originally thought to only occur in archaea, from uncultivated bacteria of the candidate phyla radiation (CPR). There are no isolated CPR bacteria and these organisms are predicted to have limited metabolic capacities. Here we expand the known diversity of RubisCO from CPR lineages. We report a form of RubisCO, distantly similar to the archaeal form III RubisCO, in some CPR bacteria from the Parcubacteria (OD1), WS6 and Microgenomates (OP11) phyla. In addition, we significantly expand the Peregrinibacteria (PER) II/III RubisCO diversity and report the first II/III RubisCO sequences from the Microgenomates and WS6 phyla. To provide a metabolic context for these RubisCOs, we reconstructed near-complete (>93%) PER genomes and the first closed genome for a WS6 bacterium, for which we propose the phylum name Dojkabacteria. Genomic and bioinformatic analyses suggest that the CPR RubisCOs function in a nucleoside pathway similar to that proposed in Archaea. Detection of form II/III RubisCO and nucleoside metabolism gene transcripts from a PER supports the operation of this pathway in situ. We demonstrate that the PER form II/III RubisCO is catalytically active, fixing CO2 to physiologically complement phototrophic growth in a bacterial photoautotrophic RubisCO deletion strain. We propose that the identification of these RubisCOs across a radiation of obligately fermentative, small-celled organisms hints at a widespread, simple metabolic platform in which ribose may be a prominent currency. PMID:27137126

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

DOE PAGES

Wrighton, Kelly C.; Castelle, Cindy J.; Varaljay, Vanessa A.; ...

2016-05-03

Metagenomic studies recently uncovered form II/III RubisCO genes, originally thought to only occur in archaea, from uncultivated bacteria of the candidate phyla radiation (CPR). There are no isolated CPR bacteria and these organisms are predicted to have limited metabolic capacities. Here we expand the known diversity of RubisCO from CPR lineages. We report a form of RubisCO, distantly similar to the archaeal form III RubisCO, in some CPR bacteria from the Parcubacteria (OD1), WS6 and Microgenomates (OP11) phyla. In addition, we significantly expand the Peregrinibacteria (PER) II/III RubisCO diversity and report the first II/III RubisCO sequences from the Microgenomates andmore » WS6 phyla. To provide a metabolic context for these RubisCOs, we reconstructed near-complete ( > 93%) PER genomes and the first closed genome for a WS6 bacterium, for which we propose the phylum name Dojkabacteria. Genomic and bioinformatic analyses suggest that the CPR RubisCOs function in a nucleoside pathway similar to that proposed in Archaea. Detection of form II/III RubisCO and nucleoside metabolism gene transcripts from a PER supports the operation of this pathway in situ. We demonstrate that the PER form II/III RubisCO is catalytically active, fixing CO 2 to physiologically complement phototrophic growth in a bacterial photoautotrophic RubisCO deletion strain. We propose that the identification of these RubisCOs across a radiation of obligately fermentative, small-celled organisms hints at a widespread, simple metabolic platform in which ribose may be a prominent currency.« less

Fungi, β-glucan, and bacteria in nasal lavage of greenhouse workers and their relation to occupational exposure.

PubMed

Madsen, Anne Mette; Tendal, Kira; Thilsing, Trine; Frederiksen, Margit W; Baelum, Jesper; Hansen, Jørgen V

2013-10-01

The nose and mouth are the first regions of the respiratory tract in contact with airborne microorganisms. Occupational exposures to airborne microorganisms are associated with inflammation and different symptoms of the airways. The purpose of this study is to investigate the relation between occupational exposure to fungi, β-glucan, and bacteria and contents of fungi, β-glucan, and bacteria in nasal lavage (NAL) of greenhouse workers. We also studied whether contents of microorganisms in NAL were related to gender, time of the work week, and runny nose. NAL samples (n = 135) were taken Monday morning and Thursday at noon and personal exposure to inhalable bioaerosols was measured during a working day. The content of fungi and β-glucan in NAL of men was affected by their exposure to fungi and β-glucan. The content of fungi, β-glucan, and bacteria in NAL was higher Thursday at noon than Monday morning. The ratios of fungi in NAL between Thursday at noon and Monday morning were 14 (median value) for men and 3.5 for women. Gender had no effect on the exposure level but had a significant effect on the content of fungi, β-glucan, and bacteria in NAL, with the highest contents in NAL of men. On Thursdays, the median content of fungi in NAL samples of men without runny noses was 9408 cfu per NAL sample, whereas the same content for women was 595 cfu per NAL sample. Workers with runny noses had fewer fungi in NAL than workers without runny noses. A higher content of β-glucan per fungal spore was found in NAL than in the air. This indicates that mainly the larger fungal spores or pollen grains deposit in the nose. The difference between genders and the fact that the content of fungi in NAL was significantly affected by the exposure indicate that the two genders are affected by the same exposure level differently.

A prophage tail-like protein is deployed by Burkholderia bacteria to feed on fungi.

PubMed

Swain, Durga Madhab; Yadav, Sunil Kumar; Tyagi, Isha; Kumar, Rahul; Kumar, Rajeev; Ghosh, Srayan; Das, Joyati; Jha, Gopaljee

2017-09-01

Some bacteria can feed on fungi, a phenomenon known as mycophagy. Here we show that a prophage tail-like protein (Bg_9562) is essential for mycophagy in Burkholderia gladioli strain NGJ1. The purified protein causes hyphal disintegration and inhibits growth of several fungal species. Disruption of the Bg_9562 gene abolishes mycophagy. Bg_9562 is a potential effector secreted by a type III secretion system (T3SS) and is translocated into fungal mycelia during confrontation. Heterologous expression of Bg_9562 in another bacterial species, Ralstonia solanacearum, confers mycophagous ability in a T3SS-dependent manner. We propose that the ability to feed on fungi conferred by Bg_9562 may help the bacteria to survive in certain ecological niches. Furthermore, considering its broad-spectrum antifungal activity, the protein may be potentially useful in biotechnological applications to control fungal diseases.Some bacteria can feed on live fungi through unclear mechanisms. Here, the authors show that a T3SS-secreted protein, which is homologous to phage tail proteins, allows a Burkholderia gladioli strain to kill and feed on various fungal species.

Phytate degradation by fungi and bacteria that inhabit sawdust and coffee residue composts.

PubMed

Fathallh Eida, Mohamed; Nagaoka, Toshinori; Wasaki, Jun; Kouno, Kenji

2013-01-01

Phytate is the primary source of organic phosphorus, but it cannot be directly utilized by plants and is strongly adsorbed by the soil, reducing bioavailability. Composting is a process used to improve the bioavailability of phytate in organic wastes through degradation by microorganisms. In this study, we aimed to investigate the phytate-degrading ability of fungi and bacteria that inhabit sawdust compost and coffee residue compost, and their contribution to the composting process. In the plate assay, the fungi that formed clear zones around their colonies belonged to the genera Mucor, Penicillium, Galactomyces, Coniochaeta, Aspergillus, and Fusarium, while the bacteria belonged to the genera Pseudomonas, Enterobacter, Chitinophaga, and Rahnella. Eight fungal isolates (genera Mucor, Penicillium, Galactomyces, and Coniochaeta) and four bacterial isolates (genera Pseudomonas, Enterobacter, and Rahnella) were selected to evaluate phytase activity in their liquid culture and their ability to degrade phytate in organic materials composed of mushroom media residue and rice bran. The selected fungi degraded phytate in organic materials to varying degrees. Penicillium isolates showed the highest degradation ability and Coniochaeta isolate exhibited relatively high degradation ability. The clear zone diameters of these fungal isolates displayed significantly positive and negative correlations with inorganic and phytate phosphorus contents in the organic materials after incubation, respectively; however, none of the selected bacteria reduced phytate phosphorus in organic materials. It is therefore possible that fungi are major contributors to phytate degradation during composting.

Phytate Degradation by Fungi and Bacteria that Inhabit Sawdust and Coffee Residue Composts

PubMed Central

Eida, Mohamed Fathallh; Nagaoka, Toshinori; Wasaki, Jun; Kouno, Kenji

2013-01-01

Phytate is the primary source of organic phosphorus, but it cannot be directly utilized by plants and is strongly adsorbed by the soil, reducing bioavailability. Composting is a process used to improve the bioavailability of phytate in organic wastes through degradation by microorganisms. In this study, we aimed to investigate the phytate-degrading ability of fungi and bacteria that inhabit sawdust compost and coffee residue compost, and their contribution to the composting process. In the plate assay, the fungi that formed clear zones around their colonies belonged to the genera Mucor, Penicillium, Galactomyces, Coniochaeta, Aspergillus, and Fusarium, while the bacteria belonged to the genera Pseudomonas, Enterobacter, Chitinophaga, and Rahnella. Eight fungal isolates (genera Mucor, Penicillium, Galactomyces, and Coniochaeta) and four bacterial isolates (genera Pseudomonas, Enterobacter, and Rahnella) were selected to evaluate phytase activity in their liquid culture and their ability to degrade phytate in organic materials composed of mushroom media residue and rice bran. The selected fungi degraded phytate in organic materials to varying degrees. Penicillium isolates showed the highest degradation ability and Coniochaeta isolate exhibited relatively high degradation ability. The clear zone diameters of these fungal isolates displayed significantly positive and negative correlations with inorganic and phytate phosphorus contents in the organic materials after incubation, respectively; however, none of the selected bacteria reduced phytate phosphorus in organic materials. It is therefore possible that fungi are major contributors to phytate degradation during composting. PMID:23100024

Protein Ser/Thr/Tyr phosphorylation in the Archaea.

PubMed

Kennelly, Peter J

2014-04-04

The third domain of life, the Archaea (formerly Archaebacteria), is populated by a physiologically diverse set of microorganisms, many of which reside at the ecological extremes of our global environment. Although ostensibly prokaryotic in morphology, the Archaea share much closer evolutionary ties with the Eukarya than with the superficially more similar Bacteria. Initial genomic, proteomic, and biochemical analyses have revealed the presence of "eukaryotic" protein kinases and phosphatases and an intriguing set of serine-, threonine-, and tyrosine-phosphorylated proteins in the Archaea that may offer new insights into this important regulatory mechanism.

Phospholipid Evidence for Methanogenic Archaea and Sulfate-reducing Bacteria in Coalbed Methane Wells in the Powder River Basin, Wyoming

NASA Astrophysics Data System (ADS)

Glossner, A.; Flores, R. M.; Mandernack, K.

2008-12-01

The Powder River Basin (PRB) comprises roughly 22,000 mi2 in northeastern Wyoming and southeastern Montana; it is a major source of coal and natural gas in the Rocky Mountain and Great Plains regions. The coalbed methane (CBM) produced from Paleocene Fort Union Formation coals in the PRB is thought primarily to be of bacterial origin due to its low δ13C values of -51 to -82 permil. Determination of the timing of methanogenesis, however, requires a methodology suitable for distinguishing viable methanogenic microorganisms. Here we provide evidence of living methanogenic Archaea and sulfate- reducing bacteria collected from co-produced water from CBM wells using phospholipid fatty acid (PLFA) and phospholipid ether lipid (PLEL) analyses. Twelve producing wells were sampled in May, 2007, using a high- pressure filtering apparatus. PLFAs were analyzed as fatty acid methyl esters and PLELs analyzed by their liberated core components using gas chromatography/mass spectrometry. Phospholipid analyses revealed an ecosystem dominated by Archaea, as the Archaeal isoprenoid, phytane, was the dominant phospholipid observed in nine of the wells sampled. Total microbial biomass estimates ranged from 1.1 ×106 cells/L to 8.3 ×107 cells/L, with the proportion of Archaeal cells ranging from 77.5 to 99.7 percent. In addition, the biomarkers 10me16:0, and cy17:0, considered to be biomarkers for genera of sulfate-reducing bacteria, were observed in several wells. The dominance of lipids from living Archaea in co- produced waters from CBM wells provides evidence supporting a recent origin of gas in the PRB coals.

Comparison of phenanthrene removal by Aspergillus niger ATC 16404 (filamentous fungi) and Pseudomonas putida KT2442 (bacteria) in enriched nutrient-liquid medium

NASA Astrophysics Data System (ADS)

Hamzah, N.; Kamil, N. A. F. M.; Singhal, N.; Padhye, L.; Swift, S.

2018-04-01

Polycyclic Aromatic Hydrocarbons (PAHs) is one of the persistent and carcinogenic pollutants that needs to be eliminated from the environment. The study on degradation of PAHs by bacteria is thoroughly discussed in literature. Many strains of bacteria were chosen in order to eliminate the PAHs compound in the environment. However, there are less study on the filamentous fungi although fungi appears to be an abundant population and as dominant group in PAHs contaminated soil habitats [1], [2]. This study was conducted to determine and compare the Phenanthrene (PHE) removal by fungi and bacteria in excessive nutrient-liquid culture. Then, the survival for both strains was investigated in the presence of PHE and finally, the analysis on the fungi-PHE interaction was carried out. In condition of excessive nutrient, the removal of PHE was evaluated for fungi and bacteria in batch experiment for 5 days. PHE removal for A.niger and P.putida were found to be 97% and 20% respectively after 5 days. The presence of PHE was negatively inhibits the grow of the bacteria and the fungus. The PHE uptake mechanism for A.niger was observed to be a passive transport mechanism with 45 μg per g fungus dry weight within 24 hr of incubation. As a conclusion, filamentous fungi have the potent role in the removal of PHE as well as bacteria but depending on the strains and the condition of the environment. Fungi is known to co-metabolize the PHE meanwhile, PHE can be used as sole carbon for bacteria. This preliminary result is significant in understanding the bacteria-fungi-PHE interaction to enhance the degradation of PAHs for co-culture study in the future.

Phylogenetic analysis of Archaea in the deep-sea sediments of west Pacific Warm Pool.

PubMed

Wang, Peng; Xiao, Xiang; Wang, Fengping

2005-06-01

Archaea are known to play important roles in carbon cycling in marine sediments. The main compositions of archaeal community in five deep-sea sediment samples collected from west Pacific Warm Pool area (WP-0, WP-1, WP-2, WP-3, WP-4), and in five sediment layers (1 cm-, 3 cm-, 6 cm-, 10 cm-, 12 cm- layer) of the 12 cm sediment core of WP-0 were checked and compared by denaturing gradient gel electrophoresis and 16 S rRNA gene sequencing. It was revealed that all the deep-sea sediment samples checked contained members of non-thermophilic marine group I crenarchaeota as the predominant archaeal group. To further detect groups of archaea possibly relating with C1 metabolism, PCR amplification was carried out using primers targeting methane-oxidizing archaea. Although no methane-oxidizing archaea was detected, a group of novel archaea (named as WPA) was instead identified from all these five WP samples by clone analysis. They could be placed in the euryarchaeota kingdom, separated into two distinct groups, the main group was peripherally related with methanogens, the other group related with Thermoplasma. The vertical distributions of WPA, archaea and bacteria along the WP-0 sediment column were determined by quantitative-PCR. It was found that bacteria dominated at all depths, the numbers of bacteria were 10-10(4) times more than those of archaea. The proportion of archaea versus bacteria had a depth related increasing tendency, it was lowest at the first layer (0.01%), reached highest at the 12 cm- layer (10%). WPA only constituted a small proportion of the archaeal community (0.05% to 5%) of west Pacific Warm Pool sediment.

Fungi and bacteria. [fungicide and bactericide measures for spacecraft in tropical regions

NASA Technical Reports Server (NTRS)

Daniels, G. E.

1973-01-01

Spacecraft equipment is usually protected from fungi and bacteria by incorporating a fungicide-bactericide in the material, by a fungicide-bactericide spray, or by reducing the relative humidity to a degree where growth will not take place. A unique method to protect delicate, expensive bearings in equipment was to maintain a pressure (with dry air or nitrogen) slightly above the outside atmosphere (few millibars) within the working parts of the equipment, thus preventing fungi from entering equipment.

Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants.

PubMed

Xie, Gary; Forst, Christian; Bonner, Carol; Jensen, Roy A

2002-01-01

Tryptophan synthase consists of two subunits, alpha and beta. Two distinct subgroups of beta chain exist. The major group (TrpEb_1) includes the well-studied beta chain of Salmonella typhimurium. The minor group of beta chain (TrpEb_2) is most frequently found in the Archaea. Most of the amino-acid residues important for catalysis are highly conserved between both TrpE subfamilies. Conserved amino-acid residues of TrpEb_1 that make allosteric contact with the TrpEa subunit (the alpha chain) are absent in TrpEb_2. Representatives of Archaea, Bacteria and higher plants all exist that possess both TrpEb_1 and TrpEb_2. In those prokaryotes where two trpEb genes coexist, one is usually trpEb_1 and is adjacent to trpEa, whereas the second is trpEb_2 and is usually unlinked with other tryptophan-pathway genes. TrpEb_1 is nearly always partnered with TrpEa in the tryptophan synthase reaction. However, by default at least six lineages of the Archaea are likely to use TrpEb_2 as the functional beta chain, as TrpEb_1 is absent. The six lineages show a distinctive divergence within the overall TrpEa phylogenetic tree, consistent with the lack of selection for amino-acid residues in TrpEa that are otherwise conserved for interfacing with TrpEb_1. We suggest that the standalone function of TrpEb_2 might be to catalyze the serine deaminase reaction, an established catalytic capability of tryptophan synthase beta chains. A coincident finding of interest is that the Archaea seem to use the citramalate pathway, rather than threonine deaminase (IlvA), to initiate the pathway of isoleucine biosynthesis.

Ammonia-oxidizing archaea versus bacteria in two soil aquifer treatment systems.

PubMed

Ding, Kun; Wen, Xianghua; Li, Yuyang; Shen, Bo; Zhang, Bing

2015-02-01

So far, the contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation in wastewater treatment processes has not been well understood. In this study, two soil aquifer treatment (SATs) systems were built up to treat synthetic domestic wastewater (column 1) and secondary effluent (column 4), accomplishing an average of 95% ammonia removal during over 550 days of operation. Except at day 322, archaeal amoA genes always outnumbered bacterial amoA genes in both SATs as determined by using quantitative polymerase chain reaction (q-PCR). The ratios of archaeal amoA to 16S rRNA gene averaged at 0.70 ± 0.56 and 0.82 ± 0.62 in column 1 and column 4, respectively, indicating that all the archaea could be AOA carrying amoA gene in the SATs. The results of MiSeq-pyrosequencing targeting on archaeal and bacterial 16S rRNA genes with the primer pair of modified 515R/806R indicated that Nitrososphaera cluster affiliated with thaumarchaeal group I.1b was the dominant AOA species, while Nitrosospira cluster was the dominant ammonia-oxidizing bacteria (AOB). The statistical analysis showed significant relationship between AOA abundance (compared to AOB abundance) and inorganic and total nitrogen concentrations. Based on the mathematical model calculation for microbial growth, AOA had much greater capacity of ammonia oxidation as compared to the specific influent ammonia loading for AOA in the SATs, implying that a small fraction of the total AOA would actively work to oxidize ammonia chemoautotrophically whereas most of AOA would exhibit some level of functional redundancy. These results all pointed that AOA involved in microbial ammonia oxidation in the SATs.

Removal of phenanthrene from soil by co-cultures of bacteria and fungi pregrown on sugarcane bagasse pith.

PubMed

Chávez-Gómez, B; Quintero, R; Esparza-García, F; Mesta-Howard, A M; Zavala Díaz de la Serna, F J; Hernández-Rodríguez, C H; Gillén, T; Poggi-Varaldo, H M; Barrera-Cortés, J; Rodríguez-Vázquez, R

2003-09-01

Sixteen co-cultures composed of four bacteria and four fungi grown on sugarcane bagasse pith were tested for phenanthrene degradation in soil. The four bacteria were identified as Pseudomonas aeruginose, Ralstonia pickettii, Pseudomonas sp. and Pseudomonas cepacea. The four fungi were identified as: Penicillium sp., Trichoderma viride, Alternaria tenuis and Aspergillus terrus that were previously isolated from different hydrocarbon-contaminated soils. Fungi had a statistically significant positive (0.0001bacteria removed the compound by an order of 20%. Co-cultures B. cepacea-Penicillium sp., R. pickettii-Penicillium sp., and P. aeruginose-Penicillium sp. exhibited synergism for phenanthrene removal, reaching 72.84+/-3.85%, 73.61+/-6.38% and 69.47+/-4.91%; in 18 days, respectively.

Low Temperature Decreases the Phylogenetic Diversity of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofiltration Systems▿ †

PubMed Central

Urakawa, Hidetoshi; Tajima, Yoshiyuki; Numata, Yoshiyuki; Tsuneda, Satoshi

2008-01-01

The phylogenetic diversity and species richness of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were examined with aquarium biofiltration systems. Species richness, deduced from rarefaction analysis, and diversity indices indicated that the phylogenetic diversity and species richness of AOA are greater than those of AOB; the diversity of AOA and of AOB is minimized in cold-water aquaria. This finding implies that temperature is a key factor influencing the population structure and diversity of AOA and AOB in aquarium biofiltration systems. PMID:18065610

A sensitive crude oil bioassay indicates that oil spills potentially induce a change of major nitrifying prokaryotes from the archaea to the bacteria.

PubMed

Urakawa, Hidetoshi; Garcia, Juan C; Barreto, Patricia D; Molina, Gabriela A; Barreto, Jose C

2012-05-01

The sensitivity of nitrifiers to crude oil released by the BP Deepwater Horizon oil spill in Gulf of Mexico was examined using characterized ammonia-oxidizing bacteria and archaea to develop a bioassay and to gain further insight into the ecological response of these two groups of microorganisms to marine oil spills. Inhibition of nitrite production was observed among all the tested ammonia-oxidizing organisms at 100 ppb crude oil. Nitrosopumilus maritimus, a cultured representative of the abundant Marine Group I Archaea, showed 20% inhibition at 1 ppb, a much greater degree of sensitivity to petroleum than the tested ammonia-oxidizing and heterotrophic bacteria. The differing susceptibility may have ecological significance since a shift to bacterial dominance in response to an oil spill could potentially persist and alter trophic interactions influenced by availability of different nitrogen species. Copyright © 2012 Elsevier Ltd. All rights reserved.

Activity of Antarctic fungi extracts against phytopathogenic bacteria.

PubMed

Purić, J; Vieira, G; Cavalca, L B; Sette, L D; Ferreira, H; Vieira, M L C; Sass, D C

2018-06-01

This study aims to obtain secondary metabolites extracts from filamentous fungi isolated from soil and marine sediments from Antarctic ecosystems and to assess its potential antibacterial activity on Xanthomonas euvesicatoria and Xanthomonas axonopodis pv. passiflorae (phytopathogenic bacteria causing diseases in pepper and tomato and passionfruit, respectively). Among the 66 crude intracellular and extracellular extracts obtained from fungi recovered from soil and 79 obtained from marine sediment samples, 25 showed the ability to prevent the growth of X. euvesicatoria in vitro and 28 showed the ability to prevent the growth of X. axonopodis pv. passiflorae in vitro. Intracellular and extracellular extracts from soil fungi inhibited around 97% of X. euvesicatoria and 98% of X. axonopodis pv. passiflorae at 2·1 mg ml -1 . The average inhibition rates against X. euvesicatoria and X. axonopodis pv. passiflorae for intracellular and extracellular extracts from marine sediments fungi were around 96 and 97%, respectively, at 3·0 mg ml -1 . Extracts containing secondary metabolites with antimicrobial activity against X. euvesicatoria and X. axonopodis pv. passiflorae were obtained, containing possible substitutes for the products currently used to control these phytopathogens. Micro-organisms from extreme ecosystems, such as the Antarctic ecosystem, need to survive in harsh conditions with low temperatures, low nutrients and high UV radiation. Micro-organisms adapt to these conditions evolving diverse biochemical and physiological adaptations essential for survival. All this makes these micro-organisms a rich source of novel natural products based on unique chemical scaffolds. Discovering novel bioactive compounds is essential because of the rise in antibiotic-resistant micro-organisms and the emergence of new infections. Fungi from Antarctic environments have been proven to produce bioactive secondary metabolites against various micro-organisms, but few studies

Controlling weeds with fungi, bacteria and viruses: a review

PubMed Central

Harding, Dylan P.; Raizada, Manish N.

2015-01-01

Weeds are a nuisance in a variety of land uses. The increasing prevalence of both herbicide resistant weeds and bans on cosmetic pesticide use has created a strong impetus to develop novel strategies for controlling weeds. The application of bacteria, fungi and viruses to achieving this goal has received increasingly great attention over the last three decades. Proposed benefits to this strategy include reduced environmental impact, increased target specificity, reduced development costs compared to conventional herbicides and the identification of novel herbicidal mechanisms. This review focuses on examples from North America. Among fungi, the prominent genera to receive attention as bioherbicide candidates include Colletotrichum, Phoma, and Sclerotinia. Among bacteria, Xanthomonas and Pseudomonas share this distinction. The available reports on the application of viruses to controlling weeds are also reviewed. Focus is given to the phytotoxic mechanisms associated with bioherbicide candidates. Achieving consistent suppression of weeds in field conditions is a common challenge to this control strategy, as the efficacy of a bioherbicide candidate is generally more sensitive to environmental variation than a conventional herbicide. Common themes and lessons emerging from the available literature in regard to this challenge are presented. Additionally, future directions for this crop protection strategy are suggested. PMID:26379687

Improved methane production from sugarcane vinasse with filter cake in thermophilic UASB reactors, with predominance of Methanothermobacter and Methanosarcina archaea and Thermotogae bacteria.

PubMed

Barros, Valciney Gomes de; Duda, Rose Maria; Vantini, Juliana da Silva; Omori, Wellington Pine; Ferro, Maria Inês Tiraboschi; Oliveira, Roberto Alves de

2017-11-01

Biogas production from sugarcane vinasse has enormous economic, energy, and environmental management potential. However, methane production stability and biodigested vinasse quality remain key issues, requiring better nutrient and alkalinity availability, operational strategies, and knowledge of reactor microbiota. This study demonstrates increased methane production from vinasse through the use of sugarcane filter cake and improved effluent recirculation, with elevated organic loading rates (OLR) and good reactor stability. We used UASB reactors in a two-stage configuration, with OLRs up to 45gCODL -1 d -1 , and obtained methane production as high as 3LL -1 d -1 . Quantitative PCR indicated balanced amounts of bacteria and archaea in the sludge (10 9 -10 10 copiesg -1 VS), and of the predominant archaea orders, Methanobacteriales and Methanosarcinales (10 6 -10 8 copiesg -1 VS). 16S rDNA sequencing also indicated the thermophilic Thermotogae as the most abundant class of bacteria in the sludge. Copyright © 2017 Elsevier Ltd. All rights reserved.

Wide distribution of genes for tetrahydromethanopterin/methanofuran-linked C1 transfer reactions argues for their presence in the common ancestor of bacteria and archaea

DOE PAGES

Chistoserdova, Ludmila

2016-09-13

In this opinion study, I wish to highlight the fact that reactions linked to tetrahydromethanopterin (H 4MPT) and methanofuran (MF), the ones involved in methanogenesis as well as in methylotrophy, are much more widespread among both Bacteria and Archaea than originally thought.

Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei

PubMed Central

Feng, Guofang; Sun, Wei; Zhang, Fengli; Karthik, Loganathan; Li, Zhiyong

2016-01-01

Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei. PMID:27113140

Identifying and Further Understanding the Role of Bacteria and Archaea in a Basic Mine Drainage Remediation Site in Tanoma, PA

NASA Astrophysics Data System (ADS)

Sharp, G.; Mount, G.

2017-12-01

Acid mine drainage pollutes over 3000 miles of streams and ground water in Pennsylvania alone, and in response many solutions have been developed to counteract the effects of acidic mine drainage. It is estimated by USGS that restoring these watersheds would cost 5 billion-15 billion in total. As economic conditions place limits on expenditures, cost effective means of remediation will be of critical importance. One such method is passive bioremediation, and in the case of metal contamination, self-sustaining oxygenation. Our location of interest is the Tanoma Acid Mine Drainage engineered wetland near Tanoma, Pennsylvania. It is estimated that up to 5,000 gallons per minute is currently being discharged into the site. While most local remediation sites are acidic (pH <4), the Tanoma wetland allows for the study of bioremediation in more neutral pH setting (pH of 5.5-7.5). In this study, we look to further understand biologic, chemical, and hydrologic controls that contribute to the efficiency of the wetland. Our research will focus on the spatial and temporal distribution of biomass through the wetland system as well as changes in water and soil chemistry. Local biofilm (Leptothrix discophora ) are an important part of the remediation process, using iron from the water as an energy source. The bacteria reduce the iron content of the water, precipitating it onto the pond bed as Terraced Iron Formations (TIF). Terraces iron formations (TIF's) are correlated with localized biofilm-archaea densities where archaea thrive in iron rich sediments. By determining bacteria densities in the wetland through gram stain analysis, we can further understand their role in terraced iron formation creation, find localized TIF's that occur, and correlate methane production due to archaea in that location. Mapping TIF locations and identifying bacteria densities will help determine the bioremediation effects on the overall efficiency of iron reduction throughout the Tanoma AMD passive

Variations of bacteria and fungi in PM2.5 in Beijing, China

NASA Astrophysics Data System (ADS)

Du, Pengrui; Du, Rui; Ren, Weishan; Lu, Zedong; Zhang, Yang; Fu, Pingqing

2018-01-01

Bacteria and fungi present in the airborne fine particulate matter (PM2.5) play important roles in the atmosphere and provide significant impacts on human health. However, variations in the species composition and community structure have not been well understood. In this study, we sampled PM2.5 in suburban Beijing and analyzed the bacterial and fungal composition during different seasons and at different air pollution levels using gene sequencing methods. The results showed that the species richness and diversity of bacterial communities displayed a downtrend with the aggravation of air pollution. Additionally, the bacterial communities in spring samples showed the highest species richness, with average richness estimators, ACE and Chao 1, up to 14,649 and 7608, respectively, followed by winter samples (7690 and 5031, respectively) and autumn samples (4368 and 3438, respectively), whereas summer samples exhibited the lowest average ACE and Chao 1 indexes (2916 and 1900, respectively). The species richness of fungal communities followed the same seasonal pattern. The community structure of bacteria and the species composition of fungi in PM2.5 showed significant seasonal variations. The dominant bacteria were Actinobacteria (33.89%), Proteobacteria (25.72%), Firmicutes (19.87%), Cyanobacteria/Chloroplast (15.34%), and Bacteroidetes (3.19%), and Ascomycota, with an average abundance of 74.68% of all sequences, were the most abundant fungi. At the genus level, as many as 791 bacterial genera and 517 fungal genera were identified in PM2.5. The results advance our understanding of the distribution and variation of airborne microorganisms in the metropolitan surrounding areas.

Archaea.

PubMed

Eme, Laura; Doolittle, W Ford

2015-10-05

A headline on the front page of the New York Times for November 3, 1977, read "Scientists Discover a Way of Life That Predates Higher Organisms". The accompanying article described a spectacular claim by Carl Woese and George Fox to have discovered a third form of life, a new 'domain' that we now call Archaea. It's not that these microbes were unknown before, nor was it the case that their peculiarities had gone completely unnoticed. Indeed, Ralph Wolfe, in the same department at the University of Illinois as Woese, had already discovered how it was that methanogens (uniquely on the planet) make methane, and the bizarre adaptations that allow extremely halophilic archaea (then called halobacteria) and thermoacidophiles to live in the extreme environments where they do were already under investigation in many labs. But what Woese and Fox had found was that these organisms were related to each other not just in their 'extremophily' but also phylogenetically. And, most surprisingly, they were only remotely related to the rest of the prokaryotes, which we now call the domain Bacteria (Figure 1). Copyright © 2015 Elsevier Ltd. All rights reserved.

Tropical Archaea: Diversity associated with the surface microlayer of corals

USGS Publications Warehouse

Kellogg, C.A.

2004-01-01

Recent 16S rDNA studies have focused on detecting uncultivated bacteria associated with Caribbean reef corals in an effort to address the ecological roles of coral-associated microbes. Reports of Archaea associated with fishes and marine invertebrates raised the question of whether Archaea might also be part of the coral-associated microbial community. DNA analysis of mucus from 3 reef-building species of Caribbean corals, Montastraea annularis complex, Diploria strigosa and D. labyrinthiformis in the US Virgin Islands yielded 34 groups of archaeal 16S ribotypes (defined at the level of 97% similarity). The majority (75%) was most closely matched by BLAST searches to sequences derived from marine water column samples, whereas the remaining ribotypes were most similar to sequences isolated from anoxic environments (15%) and hydrothermal vents (9%). Unlike previous 16S studies of coral-associated Bacteria, the results do not suggest specific associations between particular archaeal sequences and individual coral species. Marine Archaea (Groups I, II and III) in addition to Thermoplasma-like, methanogen, and marine benthic crenarchaeote phylotypes, were detected in the mucus of tropical corals. The finding of sequences from coral-associated Archaea that are closely related to strict and facultative anaerobes, as well as to uncultivated Archaea from other types of anoxic environments, suggests that anaerobic micro-niches may exist in coral mucus layers. Archaea, with their unique biogeochemical capabilities, broaden the scope of possible interactions between corals and their associated microbial communities.

Hybrid histidine kinases in pathogenic fungi.

PubMed

Defosse, Tatiana A; Sharma, Anupam; Mondal, Alok K; Dugé de Bernonville, Thomas; Latgé, Jean-Paul; Calderone, Richard; Giglioli-Guivarc'h, Nathalie; Courdavault, Vincent; Clastre, Marc; Papon, Nicolas

2015-03-01

Histidine kinases (HK) sense and transduce via phosphorylation events many intra- and extracellular signals in bacteria, archaea, slime moulds and plants. HK are also widespread in the fungal kingdom, but their precise roles in the regulation of physiological processes remain largely obscure. Expanding genomic resources have recently given the opportunity to identify uncharacterised HK family members in yeasts and moulds and now allow proposing a complex classification of Basidiomycota, Ascomycota and lower fungi HK. A growing number of genetic approaches have progressively provided new insight into the role of several groups of HK in prominent fungal pathogens. In particular, a series of studies have revealed that members of group III HK, which occur in the highest number of fungal species and contain a unique N-terminus region consisting of multiple HAMP domain repeats, regulate morphogenesis and virulence in various human, plant and insect pathogenic fungi. This research field is further supported by recent shape-function studies providing clear correlation between structural properties and signalling states in group III HK. Since HK are absent in mammals, these represent interesting fungal target for the discovery of new antifungal drugs. © 2015 John Wiley & Sons Ltd.

Rainforest Conversion to Rubber Plantation May Not Result in Lower Soil Diversity of Bacteria, Fungi, and Nematodes.

PubMed

Kerfahi, Dorsaf; Tripathi, Binu M; Dong, Ke; Go, Rusea; Adams, Jonathan M

2016-08-01

Large areas of rainforest in Asia have been converted to plantations, with uncertain effects on soil biodiversity. Using standard metagenetic methods, we compared the soil biota of bacteria, fungi, and nematodes at three rainforest sites in Malaysia with two rubber plantation sites with similar soils and geology. We predicted the following: (1) that the rubber sites would have a lower α- and β-diversity than the rainforest sites, due to the monospecific canopy cover and intensive management with herbicides, pesticides, and fertilizers, and (2) that due to differences in the physical and biotic environment associated with cultivation, there would be distinct communities of bacteria, fungi, and nematodes. However, regarding (1), the results showed no consistent difference in α- and β-diversity of bacteria, fungi, or nematodes between rainforest and rubber plantation sites. It appears that conversion of rainforest to rubber plantations does not necessarily result in a decrease in diversity of soil biota. It may be that heterogeneity associated with the cultivation regimen compensates for loss of biotically imposed heterogeneity of the original rainforest. Regarding (2), as predicted there were statistically significant differences in community composition between rainforest and rubber plantation for bacteria, fungi, and nematodes. These differences could be related to a range of factors including light level, litter fall composition, pH, C and N, selecting a distinct set of soil taxa, and it is possible that this in itself would affect long-term soil function.

Vanadium removal from LD converter slag using bacteria and fungi.

PubMed

Mirazimi, S M J; Abbasalipour, Z; Rashchi, F

2015-04-15

Removal of vanadium from Linz-Donawits (LD) converter slag was investigated by means of three different species of microbial systems: Acidithiobacillus thiooxidans (autotrophic bacteria), Pseudomonas putida (heterotrophic bacteria) and Aspergillus niger (fungi). The bioleaching process was carried out in both one-step and two-step process and the leaching efficiencies in both cases were compared. Formation of inorganic and organic acids during the leaching process caused mobilization of vanadium. In order to reduce toxic effects of the metal species on the above mentioned microorganisms, a prolonged adaptation process was performed. Both bacteria, A. thiooxidans and P. putida were able to remove more than 90% of vanadium at slag concentrations of 1-5 g L(-1) after 15 days. Also, the maximum achievable vanadium removal in the fungal system was approximately 92% at a slag concentration of 1 g L(-1) after 22 days. Copyright © 2015 Elsevier Ltd. All rights reserved.

9 CFR 113.25 - Culture media for detection of bacteria and fungi.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 1 2013-01-01 2013-01-01 false Culture media for detection of... STANDARD REQUIREMENTS Standard Procedures § 113.25 Culture media for detection of bacteria and fungi. (a..., shall conform to such standards. In lieu of preparing the media from the individual ingredients, they...

9 CFR 113.25 - Culture media for detection of bacteria and fungi.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 1 2012-01-01 2012-01-01 false Culture media for detection of... STANDARD REQUIREMENTS Standard Procedures § 113.25 Culture media for detection of bacteria and fungi. (a..., shall conform to such standards. In lieu of preparing the media from the individual ingredients, they...

9 CFR 113.25 - Culture media for detection of bacteria and fungi.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 1 2014-01-01 2014-01-01 false Culture media for detection of... STANDARD REQUIREMENTS Standard Procedures § 113.25 Culture media for detection of bacteria and fungi. (a..., shall conform to such standards. In lieu of preparing the media from the individual ingredients, they...

Bacterioruberin and salinixanthin carotenoids of extremely halophilic Archaea and Bacteria: A Raman spectroscopic study

NASA Astrophysics Data System (ADS)

Jehlička, J.; Edwards, H. G. M.; Oren, A.

2013-04-01

Laboratory cultures of a number of red extremely halophilic Archaea (Halobacterium salinarum strains NRC-1 and R1, Halorubrum sodomense, Haloarcula valismortis) and of Salinibacter ruber, a red extremely halophilic member of the Bacteria, have been investigated by Raman spectroscopy using 514.5 nm excitation to characterize their carotenoids. The 50-carbon carotenoid α-bacterioruberin was detected as the major carotenoid in all archaeal strains. Raman spectroscopy also detected bacterioruberin as the main pigment in a red pellet of cells collected from a saltern crystallizer pond. Salinibacter contains the C40-carotenoid acyl glycoside salinixanthin (all-E, 2'S)-2'-hydroxy-1'-[6-O-(methyltetradecanoyl)-β-D-glycopyranosyloxy]-3',4'-didehydro-1',2'-dihydro-β,ψ-carotene-4-one), for which the Raman bands assignments of are given here for the first time.

Continental-scale distributions of dust-associated bacteria and fungi

PubMed Central

Barberán, Albert; Ladau, Joshua; Pollard, Katherine S.; Menninger, Holly L.; Dunn, Robert R.; Fierer, Noah

2015-01-01

It has been known for centuries that microorganisms are ubiquitous in the atmosphere, where they are capable of long-distance dispersal. Likewise, it is well-established that these airborne bacteria and fungi can have myriad effects on human health, as well as the health of plants and livestock. However, we have a limited understanding of how these airborne communities vary across different geographic regions or the factors that structure the geographic patterns of near-surface microbes across large spatial scales. We collected dust samples from the external surfaces of ∼1,200 households located across the United States to understand the continental-scale distributions of bacteria and fungi in the near-surface atmosphere. The microbial communities were highly variable in composition across the United States, but the geographic patterns could be explained by climatic and soil variables, with coastal regions of the United States sharing similar airborne microbial communities. Although people living in more urbanized areas were not found to be exposed to distinct outdoor air microbial communities compared with those living in more rural areas, our results do suggest that urbanization leads to homogenization of the airborne microbiota, with more urban communities exhibiting less continental-scale geographic variability than more rural areas. These results provide our first insight into the continental-scale distributions of airborne microbes, which is information that could be used to identify likely associations between microbial exposures in outdoor air and incidences of disease in crops, livestock, and humans. PMID:25902536

Chaophilic or chaotolerant fungi: a new category of extremophiles?

PubMed Central

Zajc, Janja; Džeroski, Sašo; Kocev, Dragi; Oren, Aharon; Sonjak, Silva; Tkavc, Rok; Gunde-Cimerman, Nina

2014-01-01

It is well known that few halophilic bacteria and archaea as well as certain fungi can grow at the highest concentrations of NaCl. However, data about possible life at extremely high concentrations of various others kosmotropic (stabilizing; like NaCl, KCl, and MgSO4) and chaotropic (destabilizing) salts (NaBr, MgCl2, and CaCl2) are scarce for prokaryotes and almost absent for the eukaryotic domain including fungi. Fungi from diverse (extreme) environments were tested for their ability to grow at the highest concentrations of kosmotropic and chaotropic salts ever recorded to support life. The majority of fungi showed preference for relatively high concentrations of kosmotropes. However, our study revealed the outstanding tolerance of several fungi to high concentrations of MgCl2 (up to 2.1 M) or CaCl2 (up to 2.0 M) without compensating kosmotropic salts. Few species, for instance Hortaea werneckii, Eurotium amstelodami, Eurotium chevalieri and Wallemia ichthyophaga, are able to thrive in media with the highest salinities of all salts (except for CaCl2 in the case of W. ichthyophaga). The upper concentration of MgCl2 to support fungal life in the absence of kosmotropes (2.1 M) is much higher than previously determined to be the upper limit for microbial growth (1.26 M). No fungal representatives showed exclusive preference for only chaotropic salts (being obligate chaophiles). Nevertheless, our study expands the knowledge of possible active life by a diverse set of fungi in biologically detrimental chaotropic environments. PMID:25566222

Diagnostic Value of PCR Analysis of Bacteria and Fungi from Blood in Empiric-Therapy-Resistant Febrile Neutropenia ▿

PubMed Central

Nakamura, Akiko; Sugimoto, Yuka; Ohishi, Kohshi; Sugawara, Yumiko; Fujieda, Atsushi; Monma, Fumihiko; Suzuki, Kei; Masuya, Masahiro; Nakase, Kazunori; Matsushima, Yoshiko; Wada, Hideo; Katayama, Naoyuki; Nobori, Tsutomu

2010-01-01

This study aimed to assess the clinical utility of PCR for the analysis of bacteria and fungi from blood for the management of febrile neutropenic patients with hematologic malignancies. Using a PCR system able to detect a broad range of bacteria and fungi, we conducted a prospective pilot study of periodic analyses of blood from patients following intensive chemotherapy. When fever occurred, it was treated with empirical antibiotic therapy, basically without knowledge of the PCR results. In 23 febrile episodes during the neutropenic period, bacteria were detected by PCR in 11 cases, while the same species were identified by blood culture in 3 cases. In 10 out of 11 PCR-positive cases, fever could be managed by empirical therapy. In the empirical-therapy-resistant case, the identification of Stenotrophomonas maltophilia by PCR led to improvement of fever. No fungi were detected by PCR in febrile cases, while Aspergillus fumigatus was detected in one afebrile patient, several days before a clinical diagnosis was made. In subsequent sporadic PCR analyses in 15 cases of febrile neutropenia, bacteria were detected by both PCR and blood culture in 7 cases and by PCR alone in 6. Fungi were not detected. While fever was improved by empirical therapy in 12 out of the 13 PCR-positive cases, the identification of Pseudomonas aeruginosa by PCR in one therapy-resistant case contributed to the successful treatment of persistent fever. Our results indicate that PCR analysis of bacteria from blood provides essential information for managing empirical-therapy-resistant febrile neutropenia. PMID:20392911

Specific interactions between arbuscular mycorrhizal fungi and plant growth-promoting bacteria--as revealed by different combinations

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

Jaderlund, Lotta; Arthurson, Veronica; Granhall, Ulf

2008-05-15

The interactions between two plant growth promoting rhizobacteria (PGPR), Pseudomonas fluorescens SBW25 and Paenibacillus brasilensis PB177, two arbuscular mycorrhizal (AM) fungi (Glomus mosseae and G. intraradices) and one pathogenic fungus (Microdochium nivale) were investigated on winter wheat (Triticum aestivum cultivar Tarso) in a greenhouse trial. PB177, but not SBW25, had strong inhibitory effects on M. nivale in dual culture plate assays. The results from the greenhouse experiment show very specific interactions; e.g. the two AM fungi react differently when interacting with the same bacteria on plants. G. intraradices (single inoculation or together with SBW25) increased plant dry weight on M.more » nivale infested plants, suggesting that the pathogenic fungus is counteracted by G. intraradices, but PB177 inhibited this positive effect. This is an example of two completely different reactions between the same AM fungus and two species of bacteria, previously known to enhance plant growth and inhibit pathogens. When searching for plant growth promoting microorganisms it is therefore important to test for the most suitable combination of plant, bacteria and fungi in order to get satisfactory plant growth benefits.« less

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

PubMed Central

Probst, Alexander J; Holman, Hoi-Ying N; DeSantis, Todd Z; Andersen, Gary L; Birarda, Giovanni; Bechtel, Hans A; Piceno, Yvette M; Sonnleitner, Maria; Venkateswaran, Kasthuri; Moissl-Eichinger, Christine

2013-01-01

Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging. PMID:23178669

Potential role of acetyl-CoA synthetase (acs) and malate dehydrogenase (mae) in the evolution of the acetate switch in Bacteria and Archaea

USGS Publications Warehouse

Barnhart, Elliott P.; McClure, Marcella A.; Johnson, Kiki; Cleveland, Sean; Hunt, Kristopher A.; Fields, Matthew W.

2015-01-01

Although many Archaea have AMP-Acs (acetyl-coenzyme A synthetase) and ADP-Acs, the extant methanogenic genus Methanosarcina is the only identified Archaeal genus that can utilize acetate via acetate kinase (Ack) and phosphotransacetylase (Pta). Despite the importance of ack as the potential urkinase in the ASKHA phosphotransferase superfamily, an origin hypothesis does not exist for the acetate kinase in Bacteria, Archaea, or Eukarya. Here we demonstrate that Archaeal AMP-Acs and ADP-Acs contain paralogous ATPase motifs previously identified in Ack, which demonstrate a novel relation between these proteins in Archaea. The identification of ATPase motif conservation and resulting structural features in AMP- and ADP-acetyl-CoA synthetase proteins in this study expand the ASKHA superfamily to include acetyl-CoA synthetase. Additional phylogenetic analysis showed that Pta and MaeB sequences had a common ancestor, and that the Pta lineage within the halophilc archaea was an ancestral lineage. These results suggested that divergence of a duplicated maeB within an ancient halophilic, archaeal lineage formed a putative pta ancestor. These results provide a potential scenario for the establishment of the Ack/Pta pathway and provide novel insight into the evolution of acetate metabolism for all three domains of life.

Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea

DOE PAGES

Barnhart, Elliott P.; McClure, Marcella A.; Johnson, Kiki; ...

2015-08-03

Although many Archaea have AMP-Acs (acetyl-coenzyme A synthetase) and ADP-Acs, the extant methanogenic genus Methanosarcina is the only identified Archaeal genus that can utilize acetate via acetate kinase (Ack) and phosphotransacetylase (Pta). Despite the importance of ack as the potential urkinase in the ASKHA phosphotransferase superfamily, an origin hypothesis does not exist for the acetate kinase in Bacteria, Archaea, or Eukarya. Here we demonstrate that Archaeal AMP-Acs and ADP-Acs contain paralogous ATPase motifs previously identified in Ack, which demonstrate a novel relation between these proteins in Archaea. The identification of ATPase motif conservation and resulting structural features in AMP- andmore » ADP-acetyl-CoA synthetase proteins in this study expand the ASKHA superfamily to include acetyl-CoA synthetase. Additional phylogenetic analysis showed that Pta and MaeB sequences had a common ancestor, and that the Pta lineage within the halophilc archaea was an ancestral lineage. Lastly, these results suggested that divergence of a duplicated maeB within an ancient halophilic, archaeal lineage formed a putative pta ancestor. These results provide a potential scenario for the establishment of the Ack/Pta pathway and provide novel insight into the evolution of acetate metabolism for all three domains of life.« less

[Diversity of beta-proteobacterial ammonia-oxidizing bacteria and ammonia-oxidizing archaea in shrimp farm sediment].

PubMed

Gao, Lihai; Lin, Weitie

2011-01-01

In order to study the diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in shrimp farm sediment. Total microbial DNA was directly extracted from the shrimp farm sediment. The clone library of amoA genes were constructed with beta-Proteobacterial-AOB and AOA specific primers. The library was screened by PCR-restriction fragment length polymorphism (RFLP) analysis and clones with unique RFLP patterns were sequenced. Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from shrimp farm sediment were affiliated with Nitrosomonas (61.54%) or Nitrosomonas-like (38. 46%) species and grouped into Nitrosomonas communis cluster, Nitrosomonas sp. Nm148 cluster, Nitrosomonas oligotropha cluster. All AOA sequences belonged to the kingdom Crenarchaeote except that one Operational Taxa Unit (OTU) sequence was Unclassified-Archaea and fell within cluster S (soil origin). AOB and AOA species composition included 13 OTUs and 9 OTUs. The clone coverage of bacterial and archaeal amoA genes was 73.47% and 90.43%. The Shannon-Wiener index, Evenness index, Simpson index and Richness index of AOB were higher than those of AOA. These findings represent the first detailed examination of archaeal amoA diversity in shrimp farm sediment and demonstrate that diverse communities of Crenarchaeote capable of ammonia oxidation are present within shrimp farm sediment, where they may be actively involved in nitrification.

Novel diesel-oil-degrading bacteria and fungi from the Ecuadorian Amazon rainforest.

PubMed

Maddela, N R; Masabanda, M; Leiva-Mora, M

2015-01-01

Isolating new diesel-oil-degrading microorganisms from crude-oil contaminated sites and evaluating their degradation capacities are vitally important in the remediation of oil-polluted environments and crude-oil exploitation. In this research, new hydrocarbon-degrading bacteria and fungi were isolated from the crude-oil contaminated soil of the oil-fields in the Amazon rainforest of north-east Ecuador by using a soil enrichment technique. Degradation analysis was tracked by gas chromatography and a flame ionization detector. Under laboratory conditions, maximum degradability of the total n-alkanes reached up to 77.34 and 62.62 removal ratios after 30 days of incubation for the evaporated diesel oil by fungi (isolate-1) and bacteria (isolate-1), respectively. The 16S/18S rDNA sequence analysis indicated that the microorganisms were most closely (99-100%) related to Bacillus cereus (isolate-1), Bacillus thuringiensis (isolate-2), Geomyces pannorum (isolate-1), and Geomyces sp. (isolate-2). Therefore, these strains enable the degradation of hydrocarbons as the sole carbon source, and these findings will benefit these strains in the remediation of oil-polluted environments and oil exploitation.

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life.

PubMed

Wampach, Linda; Heintz-Buschart, Anna; Hogan, Angela; Muller, Emilie E L; Narayanasamy, Shaman; Laczny, Cedric C; Hugerth, Luisa W; Bindl, Lutz; Bottu, Jean; Andersson, Anders F; de Beaufort, Carine; Wilmes, Paul

2017-01-01

Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus , and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides . Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

PubMed Central

Wampach, Linda; Heintz-Buschart, Anna; Hogan, Angela; Muller, Emilie E. L.; Narayanasamy, Shaman; Laczny, Cedric C.; Hugerth, Luisa W.; Bindl, Lutz; Bottu, Jean; Andersson, Anders F.; de Beaufort, Carine; Wilmes, Paul

2017-01-01

Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not

Honey Bee Health: The Potential Role of Microbes

USDA-ARS?s Scientific Manuscript database

Microbes, are a diverse group of unicellular organisms that include bacteria, fungi, archaea, protists, and sometimes viruses. Bees carry a diverse assemblage of microbes (mostly bacteria and fungi). Very few are pathogenic; most microbes are likely commensal or even beneficial to the colony. Mic...

Fungi and bacteria inventory on soybean (Glycine max (L.) merill) planting media applied by local microorganisms

NASA Astrophysics Data System (ADS)

Akhsan, Ni'matuljannah; Vionita

2017-02-01

An experiment aimed to determine the effect of application of several types of local microorganisms (MOL) and the number of doses to the development of fungi and bacteria on soybean planting media, have been conducted in Samarinda for 3 (three) months. Factorial experiment arranged in a completely randomized design and repeated three times, was used in this experiment. The first factor was the type of MOL consisted of cow dung (m1), snails (m2), banana peel (m3) and bamboo roots (m4), and the second factor was the dose MOL zero mL (d0), 100 mL (d1), 200 mL (d2), 300 mL (d3), 400 mL (d4) analyzed with Anova and Least Significance Difference (LSD) at 5%. Fungi and bacteria contained in the local microorganisms (cow dung, snails, banana peel and bamboo root) are: fungus Aspergillus sp, Penicillium sp., Trichoderma sp., cellulotic and lignolitic bacteria. An increase in the type and amount of fungus is happened for some genus. The dominant bacteria in the planting medium is a gram-negative bacteria. Cow dung seemed the best source at the dosages level of 400 ml.

Genus Distribution of Bacteria and Fungi Associated with Keratitis in a Large Eye Center Located in Southern China.

PubMed

Lin, Lixia; Lan, Weizhong; Lou, Bingsheng; Ke, Hongmin; Yang, Yuanzhe; Lin, Xiaofeng; Liang, Lingyi

2017-04-01

To investigate the genus distribution of bacteria and fungi associated with keratitis in a large eye center located in Southern China and to compare the results with existing data from other areas in China. All results of corneal microbiological examinations from 2009 to 2013 of patients who had been clinically diagnosed with bacterial or fungal keratitis were obtained chronologically and anonymously from the microbiology database at Zhongshan Ophthalmic Center. Smear/culture data were reviewed and analyzed. Antibiotic resistance of the harvested bacteria was also evaluated. Of 2973 samples, the microbial detection rate was 46.05%; in which 759 eyes (25.5%) were positive for bacteria, 796 eyes (26.8%) were positive for fungi, and 186 eyes (6.3%) were co-infected with both fungi and bacteria. The most common type of bacteria isolated was Staphylococcus epidermidis (31.9%), followed by Pseudomonas aeruginosa (12.4%). The most common type of fungus was Fusarium species (29.3%), followed by Aspergillus species (24.1%). For the bacteria harvested, mean antibiotic resistance was chloromycetin (34.6%), cephalosporins (20.0%), fluoroquinolones (18.6%), and aminoglycosides (10.5%). The genus distribution of organisms detected in keratitis cases in the largest eye center located in Southern China differs from those in other areas in China. In Southern China during the time period studied, S. epidermidis and Fusarium sp. were the most common pathogens of infectious keratitis. Monitoring the changing trend of pathogens as well as antibiotic resistance are warranted.

A short-term study on the interaction of bacteria, fungi and endosulfan in soil microcosm.

PubMed

Xie, Huijun; Gao, Fuwei; Tan, Wei; Wang, Shu-Guang

2011-12-15

Endosulfan is one of the few organic chlorine insecticides still in use today in many developing countries. It has medium toxicity for fish and aquatic invertebrates. In this study, we added different concentrations of endosulfan to a series of soil samples collected from Baihua Park in Jinan, Shandong Province, China. Interactions of exogenous endosulfan, bacteria and fungi were analyzed by monitoring the changes in microbe-specific phospholipid fatty acids (PLFA), residual endosulfan and its metabolites which include; endosulfan sulfate, endosulfan lactone and endosulfan diol during a 9 days incubation period. Our results showed that endosulfan reduced fungi biomass by 47% on average after 9 days, while bacteria biomass increased 76% on average. In addition, we found that endosulfan degraded 8.62% in natural soil (NE), 5.51% in strepolin soil (SSE) and 2.47% in sterile soil (SE). Further analysis of the endosulfan metabolites in NE and SSE, revealed that the amount of endosulfan sulfate (ES) significantly increased and that of endosulfan lactone (EL) slightly decreased in both samples after 9 days. However, that of endosulfan diol (ED) increased in NE and decreased in SSE. After collective analysis our data demonstrated that fungi and bacteria responded differently to exogeous endosulfan, in a way that could promote the formation of endosulfan diol during endosulfan degradation. Copyright © 2011 Elsevier B.V. All rights reserved.

Back To Bacteria.

ERIC Educational Resources Information Center

Flannery, Maura C.

1997-01-01

Explores new research about bacteria. Discusses bacterial genomes, archaea, unusual environments, evolution, pathogens, bacterial movement, biofilms, bacteria in the body, and a bacterial obsession. Contains 29 references. (JRH)

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

PubMed

Kyrpides, Nikos C; Hugenholtz, Philip; Eisen, Jonathan A; Woyke, Tanja; Göker, Markus; Parker, Charles T; Amann, Rudolf; Beck, Brian J; Chain, Patrick S G; Chun, Jongsik; Colwell, Rita R; Danchin, Antoine; Dawyndt, Peter; Dedeurwaerdere, Tom; DeLong, Edward F; Detter, John C; De Vos, Paul; Donohue, Timothy J; Dong, Xiu-Zhu; Ehrlich, Dusko S; Fraser, Claire; Gibbs, Richard; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Jansson, Janet K; Keasling, Jay D; Knight, Rob; Labeda, David; Lapidus, Alla; Lee, Jung-Sook; Li, Wen-Jun; Ma, Juncai; Markowitz, Victor; Moore, Edward R B; Morrison, Mark; Meyer, Folker; Nelson, Karen E; Ohkuma, Moriya; Ouzounis, Christos A; Pace, Norman; Parkhill, Julian; Qin, Nan; Rossello-Mora, Ramon; Sikorski, Johannes; Smith, David; Sogin, Mitch; Stevens, Rick; Stingl, Uli; Suzuki, Ken-Ichiro; Taylor, Dorothea; Tiedje, Jim M; Tindall, Brian; Wagner, Michael; Weinstock, George; Weissenbach, Jean; White, Owen; Wang, Jun; Zhang, Lixin; Zhou, Yu-Guang; Field, Dawn; Whitman, William B; Garrity, George M; Klenk, Hans-Peter

2014-08-01

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

Estimating growth rates of uncultivated clades of archaea and bacteria in marine sediments

NASA Astrophysics Data System (ADS)

Lloyd, K. G.

2016-12-01

The vast majority of microbes present in marine sediments have never been cultivated in laboratory conditions. It is therefore difficult to estimate the growth rates of these organisms in situ. Quantitative PCR (qPCR) and 16S rRNA gene libraries from sediments below 10 cm show very little change in abundance of these organisms with depth or with redox conditions. Therefore, we hypothesized that uncultivated clades of bacteria and archaea that are ubiquitous in marine sediments, actually grow in the upper 10 cm of marine sediments. We collected sediment cores from the White Oak River estuary, sectioned them in 1 cm intervals, and examined the changes in abundance of uncultivated microbes with depth using 16S rRNA gene libraries and qPCR. We found that some of the key clades associated with the deep subsurface microbiome, such as Bathyarchaeota and MBG-D, increase in abundance with depth, demonstrating extremely slow growth in these shallow subsurface sediments.

HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea.

PubMed

Jørgensen, Mikkel G; Pandey, Deo P; Jaskolska, Milena; Gerdes, Kenn

2009-02-01

Toxin-antitoxin (TA) loci are common in free-living bacteria and archaea. TA loci encode a stable toxin that is neutralized by a metabolically unstable antitoxin. The antitoxin can be either a protein or an antisense RNA. So far, six different TA gene families, in which the antitoxins are proteins, have been identified. Recently, Makarova et al. (K. S. Makarova, N. V. Grishin, and E. V. Koonin, Bioinformatics 22:2581-2584, 2006) suggested that the hicAB loci constitute a novel TA gene family. Using the hicAB locus of Escherichia coli K-12 as a model system, we present evidence that supports this inference: expression of the small HicA protein (58 amino acids [aa]) induced cleavage in three model mRNAs and tmRNA. Concomitantly, the global rate of translation was severely reduced. Using tmRNA as a substrate, we show that HicA-induced cleavage does not require the target RNA to be translated. Expression of HicB (145 aa) prevented HicA-mediated inhibition of cell growth. These results suggest that HicB neutralizes HicA and therefore functions as an antitoxin. As with other antitoxins (RelB and MazF), HicB could resuscitate cells inhibited by HicA, indicating that ectopic production of HicA induces a bacteriostatic rather than a bactericidal condition. Nutrient starvation induced strong hicAB transcription that depended on Lon protease. Mining of 218 prokaryotic genomes revealed that hicAB loci are abundant in bacteria and archaea.

Fungi and bacteria in mould-damaged and non-damaged office environments in a subarctic climate

NASA Astrophysics Data System (ADS)

Salonen, Heidi; Lappalainen, Sanna; Lindroos, Outi; Harju, Riitta; Reijula, Kari

The fungi and bacterial levels of the indoor air environments of 77 office buildings were measured in winter and a comparison was made between the buildings with microbe sources in their structures and those without such sources. Penicillium, yeasts, Cladosporium and non-sporing isolates were the commonest fungi detected in the indoor air and in settled dust, in both the mould-damaged and control buildings. Aspergillus ochraceus, Aspergillus glaucus and Stachybotrys chartarium were found only in environmental samples from the mould-damaged buildings. Some other fungi, with growth requiring of water activity, aw, above 0.85, occurred in both the reference and mould-damaged buildings, but such fungi were commoner in the latter type of buildings. The airborne concentrations of Penicillium, Aspergillus versicolor and yeasts were the best indicators of mould damage in the buildings studied. Penicillium species and A. versicolor were also the most abundant fungi in the material samples. This study showed that the fungi concentrations were very low (2-45 cfu m -3 90% of the concentrations being <15 cfu m -3) in the indoor air of the normal office buildings. Although the concentration range of airborne fungi was wider for the mould-damaged buildings (2-2470 cfu m -3), only about 20% of the samples exceeded 100 cfu m -3. The concentrations of airborne bacteria ranged from 12 to 540 cfu m -3 in the control buildings and from 14 to 1550 cfu m -3 in the mould-damaged buildings. A statistical analysis of the results indicated that bacteria levels are generally <600 cfu m -3 in office buildings in winter and fungi levels are <50 cfu m -3. These normal levels are applicable to subarctic climates for urban, modern office buildings when measurements are made using a six-stage impactor. These levels should not be used in evaluations of health risks, but elevated levels may indicate the presence of abnormal microbe sources in indoor air and a need for additional environmental

A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics

NASA Technical Reports Server (NTRS)

Winker, S.; Woese, C. R.

1991-01-01

The number of small subunit rRNA sequences is now great enough that the three domains Archaea, Bacteria and Eucarya (Woese et al., 1990) can be reliably defined in terms of their sequence "signatures". Approximately 50 homologous positions (or nucleotide pairs) in the small subunit rRNA characterize and distinguish among the three. In addition, the three can be recognized by a variety of nonhomologous rRNA characters, either individual positions and/or higher-order structural features. The Crenarchaeota and the Euryarchaeota, the two archaeal kingdoms, can also be defined and distinguished by their characteristic compositions at approximately fifteen positions in the small subunit rRNA molecule.

Compost bacteria and fungi that influence growth and development of Agaricus bisporus and other commercial mushrooms.

PubMed

Kertesz, Michael A; Thai, Meghann

2018-02-01

Mushrooms are an important food crop for many millions of people worldwide. The most important edible mushroom is the button mushroom (Agaricus bisporus), an excellent example of sustainable food production which is cultivated on a selective compost produced from recycled agricultural waste products. A diverse population of bacteria and fungi are involved throughout the production of Agaricus. A range of successional taxa convert the wheat straw into compost in the thermophilic composting process. These initially break down readily accessible compounds and release ammonia, and then assimilate cellulose and hemicellulose into compost microbial biomass that forms the primary source of nutrition for the Agaricus mycelium. This key process in composting is performed by a microbial consortium consisting of the thermophilic fungus Mycothermus thermophilus (Scytalidium thermophilum) and a range of thermophilic proteobacteria and actinobacteria, many of which have only recently been identified. Certain bacterial taxa have been shown to promote elongation of the Agaricus hyphae, and bacterial activity is required to induce production of the mushroom fruiting bodies during cropping. Attempts to isolate mushroom growth-promoting bacteria for commercial mushroom production have not yet been successful. Compost bacteria and fungi also cause economically important losses in the cropping process, causing a range of destructive diseases of mushroom hyphae and fruiting bodies. Recent advances in our understanding of the key bacteria and fungi in mushroom compost provide the potential to improve productivity of mushroom compost and to reduce the impact of crop disease.

Glycerol Phosphate Cytidylyltransferase Stereospecificity Is Key to Understanding the Distinct Stereochemical Compositions of Glycerophosphoinositol in Bacteria and Archaea

PubMed Central

Rodrigues, Marta V.; Borges, Nuno

2016-01-01

ABSTRACT Glycerophosphoinositol (GPI) is a compatible solute present in a few hyperthermophiles. Interestingly, different GPI stereoisomers accumulate in Bacteria and Archaea, and the basis for this domain-dependent specificity was investigated herein. The archaeon Archaeoglobus fulgidus and the bacterium Aquifex aeolicus were used as model organisms. The synthesis of GPI involves glycerol phosphate cytidylyltransferase (GCT), which catalyzes the production of CDP-glycerol from CTP and glycerol phosphate, and di-myo-inositol phosphate-phosphate synthase (DIPPS), catalyzing the formation of phosphorylated GPI from CDP-glycerol and l-myo-inositol 1-phosphate. DIPPS of A. fulgidus recognized the two CDP-glycerol stereoisomers similarly. This feature and the ability of 31P nuclear magnetic resonance (NMR) to distinguish the GPI diastereomers provided a means to study the stereospecificity of GCTs. The AF1418 gene and genes aq_185 and aq_1368 are annotated as putative GCT genes in the genomes of A. fulgidus and Aq. aeolicus, respectively. The functions of these genes were determined by assaying the activity of the respective recombinant proteins: AQ1368 and AQ185 are GCTs, while AF1418 has flavin adenine dinucleotide (FAD) synthetase activity. AQ185 is absolutely specific for sn-glycerol 3-phosphate, while AQ1368 recognizes the two enantiomers but has a 2:1 preference for sn-glycerol 3-phosphate. In contrast, the partially purified A. fulgidus GCT uses sn-glycerol 1-phosphate preferentially (4:1). Significantly, the predominant GPI stereoforms found in the bacterium and the archaeon reflect the distinct stereospecificities of the respective GCTs: i.e., A. fulgidus accumulates predominantly sn-glycero-1-phospho-3-l-myo-inositol, while Aq. aeolicus accumulates sn-glycero-3-phospho-3-l-myo-inositol. IMPORTANCE Compatible solutes of hyperthermophiles show high efficacy in thermal protection of proteins in comparison with solutes typical of mesophiles; therefore, they are

Glycerol Phosphate Cytidylyltransferase Stereospecificity Is Key to Understanding the Distinct Stereochemical Compositions of Glycerophosphoinositol in Bacteria and Archaea.

PubMed

Rodrigues, Marta V; Borges, Nuno; Santos, Helena

2017-01-01

Glycerophosphoinositol (GPI) is a compatible solute present in a few hyperthermophiles. Interestingly, different GPI stereoisomers accumulate in Bacteria and Archaea, and the basis for this domain-dependent specificity was investigated herein. The archaeon Archaeoglobus fulgidus and the bacterium Aquifex aeolicus were used as model organisms. The synthesis of GPI involves glycerol phosphate cytidylyltransferase (GCT), which catalyzes the production of CDP-glycerol from CTP and glycerol phosphate, and di-myo-inositol phosphate-phosphate synthase (DIPPS), catalyzing the formation of phosphorylated GPI from CDP-glycerol and l-myo-inositol 1-phosphate. DIPPS of A. fulgidus recognized the two CDP-glycerol stereoisomers similarly. This feature and the ability of 31 P nuclear magnetic resonance (NMR) to distinguish the GPI diastereomers provided a means to study the stereospecificity of GCTs. The AF1418 gene and genes aq_185 and aq_1368 are annotated as putative GCT genes in the genomes of A. fulgidus and Aq. aeolicus, respectively. The functions of these genes were determined by assaying the activity of the respective recombinant proteins: AQ1368 and AQ185 are GCTs, while AF1418 has flavin adenine dinucleotide (FAD) synthetase activity. AQ185 is absolutely specific for sn-glycerol 3-phosphate, while AQ1368 recognizes the two enantiomers but has a 2:1 preference for sn-glycerol 3-phosphate. In contrast, the partially purified A. fulgidus GCT uses sn-glycerol 1-phosphate preferentially (4:1). Significantly, the predominant GPI stereoforms found in the bacterium and the archaeon reflect the distinct stereospecificities of the respective GCTs: i.e., A. fulgidus accumulates predominantly sn-glycero-1-phospho-3-l-myo-inositol, while Aq. aeolicus accumulates sn-glycero-3-phospho-3-l-myo-inositol. Compatible solutes of hyperthermophiles show high efficacy in thermal protection of proteins in comparison with solutes typical of mesophiles; therefore, they are potentially useful in

Ecotoxic heavy metals transformation by bacteria and fungi in aquatic ecosystem.

PubMed

Chaturvedi, Amiy Dutt; Pal, Dharm; Penta, Santhosh; Kumar, Awanish

2015-10-01

Water is the most important and vital molecule of our planet and covers 75% of earth surface. But it is getting polluted due to high industrial growth. The heavy metals produced by industrial activities are recurrently added to it and considered as dangerous pollutants. Increasing concentration of toxic heavy metals (Pb(2+), Cd(2+), Hg(2+), Ni(2+)) in water is a severe threat for human. Heavy metal contaminated water is highly carcinogenic and poisonous at even relatively low concentrations. When they discharged in water bodies, they dissolve in the water and are distributed in the food chain. Bacteria and fungi are efficient microbes that frequently transform heavy metals and remove toxicity. The application of bacteria and fungi may offer cost benefit in water treatment plants for heavy metal transformation and directly related to public health and environmental safety issues. The heavy metals transformation rate in water is also dependent on the enzymatic capability of microorganisms. By transforming toxic heavy metals microbes sustain aquatic and terrestrial life. Therefore the application of microbiological biomass for heavy metal transformation and removal from aquatic ecosystem is highly significant and striking. This paper reviews the microbial transformation of heavy metal, microbe metal interaction and different approaches for microbial heavy metal remediation from water bodies.

Visualization and Enumeration of Marine Planktonic Archaea and Bacteria by Using Polyribonucleotide Probes and Fluorescent In Situ Hybridization

PubMed Central

DeLong, Edward F.; Taylor, Lance Trent; Marsh, Terence L.; Preston, Christina M.

1999-01-01

Fluorescent in situ hybridization (FISH) using rRNA-specific oligonucleotide probes has emerged as a popular technique for identifying individual microbial cells. In natural samples, however, the signal derived from fluor-labeled oligonucleotide probes often is undetectable above background fluorescence in many cells. To circumvent this difficulty, we applied fluorochrome-labeled polyribonucleotide probes to identify and enumerate marine planktonic archaea and bacteria. The approach greatly enhanced the sensitivity and applicability of FISH with seawater samples, allowing confident identification and enumeration of planktonic cells to ocean depths of 3,400 m. Quantitative whole-cell hybridization experiments using these probes accounted for 90 to 100% of the total 4′,6-diamidino-2-phenylindole (DAPI)-stained cells in most samples. As predicted in a previous study (R. Massana, A. E. Murray, C. M. Preston, and E. F. DeLong, Appl. Environ. Microbiol. 63:50–56, 1997), group I and II marine archaea predominate in different zones in the water column, with maximal cell densities of 105/ml. The high cell densities of archaea, extending from surface waters to abyssal depths, suggest that they represent a large and significant fraction of the total picoplankton biomass in coastal ocean waters. The data also show that the vast majority of planktonic prokaryotes contain significant numbers of ribosomes, rendering them easily detectable with polyribonucleotide probes. These results imply that the majority of planktonic cells visualized by DAPI do not represent lysed cells or “ghosts,” as was suggested in a previous report. PMID:10584017

Isolation and identification of local bacteria endophyte and screening of its antimicrobial property against pathogenic bacteria and fungi

NASA Astrophysics Data System (ADS)

Fikri, Ahmad Syairazie Ibrahim; Rahman, Irman Abdul; Nor, Norefrina Shafinaz Md; Hamzah, Ainon

2018-04-01

Endophytes are organisms, often fungi and bacteria that live in living plant cells. These organisms reside in the living tissues of the host plant in a variety of relationships, ranging from symbiotic to slightly pathogenic. The endophytes may produce a plethora of substances that have potential to be used in modern medicine, agriculture and industry. The aims of this study are to isolate, identify and screening antimicrobial activity of bacterial endophytes. The endophytes were isolated using nutrient agar, incubated at 37°C for 48 hours. Identification of the isolates were done based on morphological characteristics, biochemical tests and 16S rDNA molecular analysis. Disk diffusion method was used to screen for antimicrobial activity of metabolites from endophytes against pathogenic bacteria. Screening for antifungal activity of selected endophytes was done using dual culture method againts pathogenic fungi followed by Kirby-Bauer method. Results showed endophytes designated as B2c and B7b have positive antimicrobial activity. The metabolites from isolate B2c showed antimicrobial activity against pathogenic bacteria methicillin-resistant Staphylococcus aureus (MRSA), Staphylococcus aureus and Staphylococcus epidermis, while isolate B7b have positive activities againts MRSA, S. aureus and Pseudomonas aeruginosa. Isolates B2c displayed antifungal activity against Fusarium oxysporum, Fusarium solani, Phytophthora palmivora and Colletotrichum gloeosporioides. Identification using biochemical tests and 16S rDNA sequences identified isolate B2c as Pseudomonas resinovorans with 97% homology and isolate B7b as Bacillus subtilis with 98% homology.

Potential interactions between heterotrophic archaea and bacteria for degrading particulate organic carbon in marine water column

NASA Astrophysics Data System (ADS)

Liu, H.; Zhang, C.; Tian, J.

2017-12-01

Microbial degradation of organic matter is an essential process in marine carbon cycle, which constitutes an integral component of the marine ecosystem and influences climate change. It is still poorly known, however, how microorganisms interact in utilizing organic matter in the ocean. We have performed metagenomic and qPCR analyses of archaea and bacteria in both particle-attached (>3 mm) and free-living (0.2-3 mm) fractions from surface down to 8727 m in the Mariana Trench. The metagenomic results showed large numbers of genes related to the degradation of valine, leucine, isoleucine and lysine, which were similar between free-living and particle-attached fractions from surface to 6000 m depth intervals. However, the relative abundance of these genes decreased in particle-attached fractions and increased in the free-living fractions below 6000 m depth. This is consistent with the ecophysiology of marine group II (MGII) Euryarchaeota, which are suggested to be able to degrade proteins and lipids. Overall, significant correlation (R2 = 0.95) was observed between the abundance of particle-attached MGII and that of particle-attached heterotrophic bacteria in the Mariana Trench water column; whereas, the correlation was significantly reduced (R2 = 0.34) between free-living MGII and free-living bacteria. We hypothesize that particle-attached MGII and heterotrophic bacteria were mutually beneficial in degrading organic matter, which becomes less important between these organisms in the free-living population.

Diversity of halophilic archaea in fermented foods and human intestines and their application.

PubMed

Lee, Han-Seung

2013-12-01

Archaea are prokaryotic organisms distinct from bacteria in the structural and molecular biological sense, and these microorganisms are known to thrive mostly at extreme environments. In particular, most studies on halophilic archaea have been focused on environmental and ecological researches. However, new species of halophilic archaea are being isolated and identified from high salt-fermented foods consumed by humans, and it has been found that various types of halophilic archaea exist in food products by culture-independent molecular biological methods. In addition, even if the numbers are not quite high, DNAs of various halophilic archaea are being detected in human intestines and much interest is given to their possible roles. This review aims to summarize the types and characteristics of halophilic archaea reported to be present in foods and human intestines and to discuss their application as well.

Influence of four antimicrobials on methane-producing archaea and sulfate-reducing bacteria in anaerobic granular sludge.

PubMed

Du, Jingru; Hu, Yong; Qi, Weikang; Zhang, Yanlong; Jing, Zhaoqian; Norton, Michael; Li, Yu-You

2015-12-01

The influence of Cephalexin (CLX), Tetracycline (TC), Erythromycin (ERY) and Sulfathiazole (ST) on methane-producing archaea (MPA) and sulfate-reducing bacteria (SRB) in anaerobic sludge was investigated using acetate or ethanol as substrate. With antimicrobial concentrations below 400mgL(-1), the relative specific methanogenic activity (SMA) was above 50%, so that the antimicrobials exerted slight effects on archaea. However ERY and ST at 400mgL(-1) caused a 74.5% and 57.6% inhibition to specific sulfidogenic activity (SSA) when the sludge granules were disrupted and ethanol used as substrate. After disruption, microbial tolerance to antimicrobials decreased, but the rate at which MPA utilized acetate and ethanol increased from 0.95gCOD·(gVSS⋅d)(-1) to 1.45gCOD·(gVSS⋅d)(-1) and 0.90gCOD·(gVSS⋅d)(-1) to 1.15gCOD·(gVSS⋅d)(-1) respectively. The ethanol utilization rate for SRB also increased after disruption from 0.35gCOD·(gVSS⋅d)(-1) to 0.46gCOD·(gVSS⋅d)(-1). Removal rates for CLX approaching 20.0% and 25.0% were obtained used acetate and ethanol respectively. The disintegration of granules improved the CLX removal rate to 65% and 78%, but ST was not removed during this process. Copyright © 2014 Elsevier Ltd. All rights reserved.

Role of Alcohols in Growth, Lipid Composition, and Membrane Fluidity of Yeasts, Bacteria, and Archaea ▿

PubMed Central

Huffer, Sarah; Clark, Melinda E.; Ning, Jonathan C.; Blanch, Harvey W.; Clark, Douglas S.

2011-01-01

Increased membrane fluidity, which causes cofactor leakage and loss of membrane potential, has long been documented as a cause for decreased cell growth during exposure to ethanol, butanol, and other alcohols. Reinforcement of the membrane with more complex lipid components is thus thought to be beneficial for the generation of more tolerant organisms. In this study, organisms with more complex membranes, namely, archaea, did not maintain high growth rates upon exposure to alcohols, indicating that more complex lipids do not necessarily fortify the membrane against the fluidizing effects of alcohols. In the presence of alcohols, shifts in lipid composition to more saturated and unbranched lipids were observed in most of the organisms tested, including archaea, yeasts, and bacteria. However, these shifts did not always result in a decrease in membrane fluidity or in greater tolerance of the organism to alcohol exposure. In general, organisms tolerating the highest concentrations of alcohols maintained membrane fluidity after alcohol exposure, whereas organisms that increased membrane rigidity were less tolerant. Altered lipid composition was a common response to alcohol exposure, with the most tolerant organisms maintaining a modestly fluid membrane. Our results demonstrate that increased membrane fluidity is not the sole cause of growth inhibition and that alcohols may also denature proteins within the membrane and cytosol, adversely affecting metabolism and decreasing cell growth. PMID:21784917

Diversity of Fungi, Bacteria, and Actinomycetes on Leaves Decomposing in a Stream▿

PubMed Central

Das, Mitali; Royer, Todd V.; Leff, Laura G.

2007-01-01

Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCR-denaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycete-specific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality. PMID:17142366

Bacteria influence mountain pine beetle brood development through interactions with symbiotic and antagonistic fungi: implications for climate-driven host range expansion.

PubMed

Therrien, Janet; Mason, Charles J; Cale, Jonathan A; Adams, Aaron; Aukema, Brian H; Currie, Cameron R; Raffa, Kenneth F; Erbilgin, Nadir

2015-10-01

Bark beetles are associated with diverse communities of symbionts. Although fungi have received significant attention, we know little about how bacteria, and in particular their interactions with fungi, affect bark beetle reproduction. We tested how interactions between four bacterial associates, two symbiotic fungi, and two opportunistic fungi affect performance of mountain pine beetles (Dendroctonus ponderosae) in host tissue. We compared beetle performance in phloem of its historical host, lodgepole pine (Pinus contorta), and its novel host recently accessed through warming climate, jack pine (Pinus banksiana). Overall, beetles produced more larvae, and established longer ovipositional and larval galleries in host tissue predominantly colonized by the symbiotic fungi, Grosmannia clavigera, or Ophiostoma montium than by the opportunistic colonizer Aspergillus and to a lesser extent, Trichoderma. This occurred in both historical and naïve hosts. Impacts of bacteria on beetle reproduction depended on particular fungus-bacterium combinations and host species. Some bacteria, e.g., Pseudomonas sp. D4-22 and Hy4T4 in P. contorta and Pseudomonas sp. Hy4T4 and Stenotrophomonas in P. banksiana, reduced antagonistic effects by Aspergillus and Trichoderma resulting in more larvae and longer ovipositional and larval galleries. These effects were not selective, as bacteria also reduced beneficial effects by symbionts in both host species. Interestingly, Bacillus enhanced antagonistic effects by Aspergillus in both hosts. These results demonstrate that bacteria influence brood development of bark beetles in host tissue. They also suggest that climate-driven range expansion of D. ponderosae through the boreal forest will not be significantly constrained by requirements of, or interactions among, its microbial associates.

Effects of polluting soil with cassava mill effluent on the bacteria and fungi populations of a soil cultivated with maize.

PubMed

Ogboghodo, I A; Oluwafemi, A P; Ekeh, S M

2006-05-01

The study was carried out to investigate the effects of application of cassava mill effluent on bacteria and fungi types and population in a soil grown to maize (Zea Mays L.) Microbial populations were determined before pollution of soil with cassava mill effluent, six weeks after pollution with effluent and at the end of the experiment. Results obtained showed that bacteria and fungi populations increased with time as rates of pollution increased. It was also observed that some bacteria present in the soil at the beginning of the experiment and up to the sixth week after pollution with effluent became extinct at the end of the experiment.

Urea Uptake and Carbon Fixation by Marine Pelagic Bacteria and Archaea during the Arctic Summer and Winter Seasons

PubMed Central

Connelly, Tara L.; Baer, Steven E.; Cooper, Joshua T.; Bronk, Deborah A.

2014-01-01

How Arctic climate change might translate into alterations of biogeochemical cycles of carbon (C) and nitrogen (N) with respect to inorganic and organic N utilization is not well understood. This study combined 15N uptake rate measurements for ammonium, nitrate, and urea with 15N- and 13C-based DNA stable-isotope probing (SIP). The objective was to identify active bacterial and archeal plankton and their role in N and C uptake during the Arctic summer and winter seasons. We hypothesized that bacteria and archaea would successfully compete for nitrate and urea during the Arctic winter but not during the summer, when phytoplankton dominate the uptake of these nitrogen sources. Samples were collected at a coastal station near Barrow, AK, during August and January. During both seasons, ammonium uptake rates were greater than those for nitrate or urea, and nitrate uptake rates remained lower than those for ammonium or urea. SIP experiments indicated a strong seasonal shift of bacterial and archaeal N utilization from ammonium during the summer to urea during the winter but did not support a similar seasonal pattern of nitrate utilization. Analysis of 16S rRNA gene sequences obtained from each SIP fraction implicated marine group I Crenarchaeota (MGIC) as well as Betaproteobacteria, Firmicutes, SAR11, and SAR324 in N uptake from urea during the winter. Similarly, 13C SIP data suggested dark carbon fixation for MGIC, as well as for several proteobacterial lineages and the Firmicutes. These data are consistent with urea-fueled nitrification by polar archaea and bacteria, which may be advantageous under dark conditions. PMID:25063662

Experimental Evidence that Fungi are Dominant Microbes in Carbon Content and Growth Response to Added Soluble Organic Carbon in Moss-rich Tundra Soil.

PubMed

Anderson, O Roger; Lee, Jee Min; McGuire, Krista

2016-05-01

Global warming significantly affects Arctic tundra, including permafrost thaw and soluble C release that may differentially affect tundra microbial growth. Using laboratory experiments, we report some of the first evidence for the effects of soluble glucose-C enrichment on tundra soil prokaryotes (bacteria and archaea) and fungi, with comparisons to microbial eukaryotes. Fungal increase in C-biomass was equivalent to 10% (w/w) of the added glucose-C, and for prokaryote biomass 2% (w/w), the latter comparable to prior published results. The C-gain after 14 d was 1.3 mg/g soil for fungi, and ~200 μg/g for prokaryotes. © 2015 The Author(s) Journal of Eukaryotic Microbiology © 2015 International Society of Protistologists.

Ammonia oxidation driven by archaea rather than bacteria in the hot spring at Tengchong geothermal field, China.

NASA Astrophysics Data System (ADS)

Chen, Shun; Peng, Xiaotong; Xu, Hengchao; Li, Jiwei; Ta, Kaiwen

2015-04-01

The occurrence of microbial mediated ammonia oxidation and these organisms are present in large numbers in natural environments indicated a potential biogeochemical role for them in the global nitrogen cycle. However, very little is understood about their role and contribution to nitrification in the high temperature extreme environments. Here we explore the ammonia oxidation rates and abundance of potential ammonia-oxidizing archaea (AOA) in upper and bottom sediments from Gongxiaoshe hot spring, Tengchong, Yunnan, China. The 15N-incorporating AOA cells and cell aggregated were detected with Fluorescence in situ hybridization (FISH) and Nano secondary ion mass spectrometry (Nano-SIMS). Ammonia oxidation rates measured using 15N-NO3- pool dilution in upper and bottom sediments (without NH4+ stimulated) were 4.8 and 5.3 nmol N g-1h-1, respectively. Close relatives of the autotrophic, ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus yellowstonii' represented the most abundant OTU in both of the two spring sediments by 16S rRNA gene analysis. Furthermore, it should be noted that no ammonia-oxidizing bacterial clones detected in this study. Quantitative PCR (qPCR) indicated that AOA and 16S rRNA genes were present at 2.75-9.80×105 and 0.128-1.96×108 gene copies g-1 sediment. Based on the reaction rates and AOA abundance, we estimated the cell-specific nitrification rates were 0.41 to 0.79 fmol N archaeal cell-1 h-1, which are comparable to those observed in estuary environment. We suggest that AOA have the responsibility in nitrification in this hot spring, and these archaea rather than bacteria may be considered as a driver in nitrogen cycling in terrestrial hot ecosystems. Key words: ammonia-oxidizing archaea (AOA); nitrification; ammonia-oxidizing rate; hot spring;

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

DOE PAGES

Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A.; ...

2014-08-05

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overallmore » known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently~11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.« less

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

PubMed Central

Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A.; Woyke, Tanja; Göker, Markus; Parker, Charles T.; Amann, Rudolf; Beck, Brian J.; Chain, Patrick S. G.; Chun, Jongsik; Colwell, Rita R.; Danchin, Antoine; Dawyndt, Peter; Dedeurwaerdere, Tom; DeLong, Edward F.; Detter, John C.; De Vos, Paul; Donohue, Timothy J.; Dong, Xiu-Zhu; Ehrlich, Dusko S.; Fraser, Claire; Gibbs, Richard; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Jansson, Janet K.; Keasling, Jay D.; Knight, Rob; Labeda, David; Lapidus, Alla; Lee, Jung-Sook; Li, Wen-Jun; MA, Juncai; Markowitz, Victor; Moore, Edward R. B.; Morrison, Mark; Meyer, Folker; Nelson, Karen E.; Ohkuma, Moriya; Ouzounis, Christos A.; Pace, Norman; Parkhill, Julian; Qin, Nan; Rossello-Mora, Ramon; Sikorski, Johannes; Smith, David; Sogin, Mitch; Stevens, Rick; Stingl, Uli; Suzuki, Ken-ichiro; Taylor, Dorothea; Tiedje, Jim M.; Tindall, Brian; Wagner, Michael; Weinstock, George; Weissenbach, Jean; White, Owen; Wang, Jun; Zhang, Lixin; Zhou, Yu-Guang; Field, Dawn; Whitman, William B.; Garrity, George M.; Klenk, Hans-Peter

2014-01-01

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment. PMID:25093819

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms.

PubMed

Verhamme, Daniel T; Prosser, James I; Nicol, Graeme W

2011-06-01

The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in distinct ecological niches remain to be determined. To determine whether available ammonia concentration has a differential effect on AOA and AOB growth, soil microcosms were incubated for 28 days with ammonium at three concentrations: native (control), intermediate (20 μg NH(4)(+)-N per gram of soil) and high (200 μg NH(4)(+)-N per gram of soil). Quantitative PCR demonstrated growth of AOA at all concentrations, whereas AOB growth was prominent only at the highest concentration. Similarly, denaturing gradient gel electrophoresis (DGGE) analysis revealed changes in AOA communities at all ammonium concentrations, whereas AOB communities changed significantly only at the highest ammonium concentration. These results provide evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil.

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms

PubMed Central

Verhamme, Daniel T; Prosser, James I; Nicol, Graeme W

2011-01-01

The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in distinct ecological niches remain to be determined. To determine whether available ammonia concentration has a differential effect on AOA and AOB growth, soil microcosms were incubated for 28 days with ammonium at three concentrations: native (control), intermediate (20 μg NH4+-N per gram of soil) and high (200 μg NH4+-N per gram of soil). Quantitative PCR demonstrated growth of AOA at all concentrations, whereas AOB growth was prominent only at the highest concentration. Similarly, denaturing gradient gel electrophoresis (DGGE) analysis revealed changes in AOA communities at all ammonium concentrations, whereas AOB communities changed significantly only at the highest ammonium concentration. These results provide evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil. PMID:21228892

Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria).

PubMed Central

Edmonds, C G; Crain, P F; Gupta, R; Hashizume, T; Hocart, C H; Kowalak, J A; Pomerantz, S C; Stetter, K O; McCloskey, J A

1991-01-01

Nucleoside modification has been studied in unfractionated tRNA from 11 thermophilic archaea (archaebacteria), including phylogenetically diverse representatives of thermophilic methanogens and sulfur-metabolizing hyperthermophiles which grow optimally in the temperature range of 56 (Thermoplasma acidophilum) to 105 degrees C (Pyrodictium occultum), and for comparison from the most thermophilic bacterium (eubacterium) known, Thermotoga maritima (80 degrees C). Nine nucleosides are found to be unique to the archaea, six of which are structurally novel in being modified both in the base and by methylation in ribose and occur primarily in tRNA from the extreme thermophiles in the Crenarchaeota of the archaeal phylogenetic tree. 2-Thiothymine occurs in tRNA from Thermococcus sp., and constitutes the only known occurrence of the thymine moiety in archaeal RNA, in contrast to its near-ubiquitous presence in tRNA from bacteria and eukarya. A total of 33 modified nucleosides are rigorously characterized in archaeal tRNA in the present study, demonstrating that the structural range of posttranscriptional modifications in archaeal tRNA is more extensive than previously known. From a phylogenetic standpoint, certain tRNA modifications occur in the archaea which are otherwise unique to either the bacterial or eukaryal domain, although the overall patterns of modification are more typical of eukaryotes than bacteria. PMID:1708763

Visualization of interaction between inorganic nanoparticles and bacteria or fungi.

PubMed

Chwalibog, André; Sawosz, Ewa; Hotowy, Anna; Szeliga, Jacek; Mitura, Stanislaw; Mitura, Katarzyna; Grodzik, Marta; Orlowski, Piotr; Sokolowska, Aleksandra

2010-12-06

The objective of the present investigation was to evaluate the morphologic characteristics of self-assemblies of diamond (nano-D), silver (nano-Ag), gold (nano-Au), and platinum (nano-Pt) nanoparticles with Staphylococcus aureus (bacteria) and Candida albicans (fungi), to determine the possibility of constructing microorganism-nanoparticle vehicles. Hydrocolloids of individual nanoparticles were added to suspensions of S. aureus and C. albicans. Immediately after mixing, the samples were inspected by transmission electron microscopy. Visualization of the morphologic interaction between the nanoparticles and microorganisms showed that nano-D, which are dielectrics and exhibit a positive zeta potential, were very different from the membrane potentials of microorganisms, and uniformly surrounded the microorganisms, without causing visible damage and destruction of cells. All metal nanoparticles with negative zeta potential had cell damaging properties. Nano-Ag showed the properties of self-organization with the cells, disintegrating the cell walls and cytoplasmic membranes, and releasing a substance (probably cytoplasm) outside the cell. Arrangement of nano-Au with microorganisms did not create a system of self-organization, but instead a "noncontact" interaction between the nanoparticles and microorganisms was observed to cause damage to fungal cells. Nano-Pt caused both microorganisms to release a substance outside the cell and disintegrated the cytoplasmic membrane and cell wall. Nano-Ag, nano-Au, and nano-Pt (all metal nanoparticles) are harmful to bacteria and fungi. In contrast, nano-D bind closely to the surface of microorganisms without causing visible damage to cells, and demonstrating good self-assembling ability. The results indicate that both microorganisms could be used as potential carriers for nano-D.

The common ancestor of archaea and eukarya was not an archaeon.

PubMed

Forterre, Patrick

2013-01-01

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.

9 CFR 113.26 - Detection of viable bacteria and fungi except in live vaccine.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 1 2012-01-01 2012-01-01 false Detection of viable bacteria and fungi except in live vaccine. 113.26 Section 113.26 Animals and Animal Products ANIMAL AND PLANT HEALTH... in live vaccine. Each serial and subserial of biological product except live vaccines shall be tested...

9 CFR 113.26 - Detection of viable bacteria and fungi except in live vaccine.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 1 2014-01-01 2014-01-01 false Detection of viable bacteria and fungi except in live vaccine. 113.26 Section 113.26 Animals and Animal Products ANIMAL AND PLANT HEALTH... in live vaccine. Each serial and subserial of biological product except live vaccines shall be tested...

9 CFR 113.26 - Detection of viable bacteria and fungi except in live vaccine.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 1 2013-01-01 2013-01-01 false Detection of viable bacteria and fungi except in live vaccine. 113.26 Section 113.26 Animals and Animal Products ANIMAL AND PLANT HEALTH... in live vaccine. Each serial and subserial of biological product except live vaccines shall be tested...

Oligo-DNA Custom Macroarray for Monitoring Major Pathogenic and Non-Pathogenic Fungi and Bacteria in the Phyllosphere of Apple Trees

PubMed Central

He, Ying-Hong; Isono, Sayaka; Shibuya, Makoto; Tsuji, Masaharu; Adkar Purushothama, Charith-Raj; Tanaka, Kazuaki; Sano, Teruo

2012-01-01

Background To monitor the richness in microbial inhabitants in the phyllosphere of apple trees cultivated under various cultural and environmental conditions, we developed an oligo-DNA macroarray for major pathogenic and non-pathogenic fungi and bacteria inhabiting the phyllosphere of apple trees. Methods and Findings First, we isolated culturable fungi and bacteria from apple orchards by an agar-plate culture method, and detected 32 fungal and 34 bacterial species. Alternaria, Aureobasidium, Cladosporium, Rhodotorula, Cystofilobasidium, and Epicoccum genera were predominant among the fungi, and Bacillus, Pseudomonas, Sphingomonas, Methylobacterium, and Pantoea genera were predominant among the bacteria. Based on the data, we selected 29 major non-pathogenic and 12 phytopathogenic fungi and bacteria as the targets of macroarray. Forty-one species-specific 40-base pair long oligo-DNA sequences were selected from the nucleotide sequences of rDNA-internal transcribed spacer region for fungi and 16S rDNA for bacteria. The oligo-DNAs were fixed on nylon membrane and hybridized with digoxigenin-labeled cRNA probes prepared for each species. All arrays except those for Alternaria, Bacillus, and their related species, were specifically hybridized. The array was sensitive enough to detect 103 CFU for Aureobasidium pullulans and Bacillus cereus. Nucleotide sequencing of 100 each of independent fungal rDNA-ITS and bacterial 16S-rDNA sequences from apple tree was in agreement with the macroarray data obtained using the same sample. Finally, we analyzed the richness in the microbial inhabitants in the samples collected from apple trees in four orchards. Major apple pathogens that cause scab, Alternaria blotch, and Marssonina blotch were detected along with several non-phytopathogenic fungal and bacterial inhabitants. Conclusions The macroarray technique presented here is a strong tool to monitor the major microbial species and the community structures in the phyllosphere of

Oligo-DNA custom macroarray for monitoring major pathogenic and non-pathogenic fungi and bacteria in the phyllosphere of apple trees.

PubMed

He, Ying-Hong; Isono, Sayaka; Shibuya, Makoto; Tsuji, Masaharu; Adkar Purushothama, Charith-Raj; Tanaka, Kazuaki; Sano, Teruo

2012-01-01

To monitor the richness in microbial inhabitants in the phyllosphere of apple trees cultivated under various cultural and environmental conditions, we developed an oligo-DNA macroarray for major pathogenic and non-pathogenic fungi and bacteria inhabiting the phyllosphere of apple trees. First, we isolated culturable fungi and bacteria from apple orchards by an agar-plate culture method, and detected 32 fungal and 34 bacterial species. Alternaria, Aureobasidium, Cladosporium, Rhodotorula, Cystofilobasidium, and Epicoccum genera were predominant among the fungi, and Bacillus, Pseudomonas, Sphingomonas, Methylobacterium, and Pantoea genera were predominant among the bacteria. Based on the data, we selected 29 major non-pathogenic and 12 phytopathogenic fungi and bacteria as the targets of macroarray. Forty-one species-specific 40-base pair long oligo-DNA sequences were selected from the nucleotide sequences of rDNA-internal transcribed spacer region for fungi and 16S rDNA for bacteria. The oligo-DNAs were fixed on nylon membrane and hybridized with digoxigenin-labeled cRNA probes prepared for each species. All arrays except those for Alternaria, Bacillus, and their related species, were specifically hybridized. The array was sensitive enough to detect 10(3) CFU for Aureobasidium pullulans and Bacillus cereus. Nucleotide sequencing of 100 each of independent fungal rDNA-ITS and bacterial 16S-rDNA sequences from apple tree was in agreement with the macroarray data obtained using the same sample. Finally, we analyzed the richness in the microbial inhabitants in the samples collected from apple trees in four orchards. Major apple pathogens that cause scab, Alternaria blotch, and Marssonina blotch were detected along with several non-phytopathogenic fungal and bacterial inhabitants. The macroarray technique presented here is a strong tool to monitor the major microbial species and the community structures in the phyllosphere of apple trees and identify key species

Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi

PubMed Central

Hoppe, Björn; Kahl, Tiemo; Karasch, Peter; Wubet, Tesfaye; Bauhus, Jürgen; Buscot, François; Krüger, Dirk

2014-01-01

Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase) genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa. PMID:24505405

Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi.

PubMed

Hoppe, Björn; Kahl, Tiemo; Karasch, Peter; Wubet, Tesfaye; Bauhus, Jürgen; Buscot, François; Krüger, Dirk

2014-01-01

Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase) genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa.

Analysis on evolutionary relationship of amylases from archaea, bacteria and eukaryota.

PubMed

Yan, Shaomin; Wu, Guang

2016-02-01

Amylase is one of the earliest characterized enzymes and has many applications in clinical and industrial settings. In biotechnological industries, the amylase activity is enhanced through modifying amylase structure and through cloning and expressing targeted amylases in different species. It is important to understand how engineered amylases can survive from generation to generation. This study used phylogenetic and statistical approaches to explore general patterns of amylases evolution, including 3118 α-amylases and 280 β-amylases from archaea, eukaryota and bacteria with fully documented taxonomic lineage. First, the phylogenetic tree was created to analyze the evolution of amylases with focus on individual amylases used in biofuel industry. Second, the average pairwise p-distance was computed for each kingdom, phylum, class, order, family and genus, and its diversity implies multi-time and multi-clan evolution. Finally, the variance was further partitioned into inter-clan variance and intra-clan variance for each taxonomic group, and they represent horizontal and vertical gene transfer. Theoretically, the results show a full picture on the evolution of amylases in manners of vertical and horizontal gene transfer, and multi-time and multi-clan evolution as well. Practically, this study provides the information on the surviving chance of desired amylase in a given taxonomic group, which may potentially enhance the successful rate of cloning and expression of amylase gene in different species.

Visualization of interaction between inorganic nanoparticles and bacteria or fungi

PubMed Central

Chwalibog, André; Sawosz, Ewa; Hotowy, Anna; Szeliga, Jacek; Mitura, Stanislaw; Mitura, Katarzyna; Grodzik, Marta; Orlowski, Piotr; Sokolowska, Aleksandra

2010-01-01

Purpose The objective of the present investigation was to evaluate the morphologic characteristics of self-assemblies of diamond (nano-D), silver (nano-Ag), gold (nano-Au), and platinum (nano-Pt) nanoparticles with Staphylococcus aureus (bacteria) and Candida albicans (fungi), to determine the possibility of constructing microorganism–nanoparticle vehicles. Methods Hydrocolloids of individual nanoparticles were added to suspensions of S. aureus and C. albicans. Immediately after mixing, the samples were inspected by transmission electron microscopy. Results Visualization of the morphologic interaction between the nanoparticles and microorganisms showed that nano-D, which are dielectrics and exhibit a positive zeta potential, were very different from the membrane potentials of microorganisms, and uniformly surrounded the microorganisms, without causing visible damage and destruction of cells. All metal nanoparticles with negative zeta potential had cell damaging properties. Nano-Ag showed the properties of self-organization with the cells, disintegrating the cell walls and cytoplasmic membranes, and releasing a substance (probably cytoplasm) outside the cell. Arrangement of nano-Au with microorganisms did not create a system of self-organization, but instead a “noncontact” interaction between the nanoparticles and microorganisms was observed to cause damage to fungal cells. Nano-Pt caused both microorganisms to release a substance outside the cell and disintegrated the cytoplasmic membrane and cell wall. Conclusion Nano-Ag, nano-Au, and nano-Pt (all metal nanoparticles) are harmful to bacteria and fungi. In contrast, nano-D bind closely to the surface of microorganisms without causing visible damage to cells, and demonstrating good self-assembling ability. The results indicate that both microorganisms could be used as potential carriers for nano-D. PMID:21270959

Dust, endotoxin, fungi, and bacteria exposure as determined by work task, season, and type of plant in a flower greenhouse.

PubMed

Thilsing, Trine; Madsen, Anne Mette; Basinas, Ioannis; Schlünssen, Vivi; Tendal, Kira; Bælum, Jesper

2015-03-01

Greenhouse workers are exposed to dust, endotoxin, fungi, and bacteria potentially causing airway inflammation as well as systemic symptoms. Knowledge about determinants of exposure is a prerequisite for efficient prevention through knowledge-based reduction in exposure. The objective of this study was to assess the occupational exposure in a flower greenhouse and to investigate the impact of work tasks on the intensity and variability in exposure. Seventy-six personal full-shift exposure measurements were performed on 38 employees in a Danish flower greenhouse producing Campanula, Lavandula, Rhipsalideae, and Helleborus. The samples were gravimetrically analysed for inhalable dust. Endotoxin was assessed by the Limulus Amoebocyte Lysate test and culture-based quantification of bacteria and fungi was performed. Information on the performed tasks during sampling was extracted from the greenhouse electronic task logging system. Associations between log-transformed exposure outcomes, season, and work tasks were examined in linear mixed-effects regression with worker identity as random effect. Measured concentrations ranged between 0.04 and 2.41mg m(-3) for inhalable dust and between 0.84 and 1097 EU m(-3) for endotoxin exposure, with the highest mean levels measured during Lavandula and Campanula handling, respectively. Personal exposure to fungi ranged between 1.8×10(2) and 3.4×10(6) colony-forming units (CFU) m(-3) and to bacteria between 1.6×10(1) and 4.2×10(5) CFU m(-3). Exposure to dust, endotoxin, fungi, and bacteria differed between seasons. Packing Lavandula, sticking, potting, and grading Rhipsalideae, and all examined tasks related to Campanula production except sticking increased dust exposure. Endotoxin exposure was increased during sticking Campanula and pinching or packing Rhipsalideae, and fungi exposure was elevated by subtasks performed in the research and development area for Campanula, and by potting, packing/dumping Campanula. Sticking and

Major players on the microbial stage: why archaea are important.

PubMed

Jarrell, Ken F; Walters, Alison D; Bochiwal, Chitvan; Borgia, Juliet M; Dickinson, Thomas; Chong, James P J

2011-04-01

As microbiology undergoes a renaissance, fuelled in part by developments in new sequencing technologies, the massive diversity and abundance of microbes becomes yet more obvious. The Archaea have traditionally been perceived as a minor group of organisms forced to evolve into environmental niches not occupied by their more 'successful' and 'vigorous' counterparts, the bacteria. Here we outline some of the evidence gathered by an increasingly large and productive group of scientists that demonstrates not only that the Archaea contribute significantly to global nutrient cycling, but also that they compete successfully in 'mainstream' environments. Recent data suggest that the Archaea provide the major routes for ammonia oxidation in the environment. Archaea also have huge economic potential that to date has only been fully realized in the production of thermostable polymerases. Archaea have furnished us with key paradigms for understanding fundamentally conserved processes across all domains of life. In addition, they have provided numerous exemplars of novel biological mechanisms that provide us with a much broader view of the forms that life can take and the way in which micro-organisms can interact with other species. That this information has been garnered in a relatively short period of time, and appears to represent only a small proportion of what the Archaea have to offer, should provide further incentives to microbiologists to investigate the underlying biology of this fascinating domain.

[Experimental interaction of halophilic prokaryotes and opportunistic bacteria in brine].

PubMed

Selivanova, E A; Nemtseva, N V

2013-01-01

Study the effect of extremely halophilic archaea and moderately halophilic bacteria on preservation of opportunistic bacteria in brine. 17 strains of moderately halophilic bacteria and 2 strains of extremely halophilic archaea were isolated from continental hypersaline lake Razval of Sol-Iletsk area of Orenburg Region. Identification of pure cultures of prokaryotes was carried out taking into account their phenotype properties and based on determination of 16S RNA gene sequence. The effect of halophilic prokaryote on elimination of Escherichia coli from brine was evaluated during co-cultivation. Antagonistic activity of cell extracts of the studied microorganisms was evaluated by photometric method. A more prolonged preservation of an E. coli strain in brine in the presence of live cells of extremely halophilic archaea Halorubrum tebenquichense and moderately halophilic bacteria Marinococcus halophilus was established. Extracts of cells of extremely halophilic archaea and moderately halophilic bacteria on the contrary displayed antagonistic activity. The protective effect of live cells of halophilic prokaryotes and antagonistic activity of their cell extracts change the period of conservation of opportunistic bacteria in brine that regulates inter-microbial interactions and changes the period of self-purification that reflects the sanitary condition of a hypersaline water body.

The Co-Distribution of Nitrifying Archaea and Diazotrophic Bacteria in Geothermal Springs

NASA Astrophysics Data System (ADS)

Hamilton, T. L.; Jewell, T. N. M.; de la Torre, J. R.; Boyd, E. S.

2014-12-01

Microbial processes that regulate availability of nutrients play key roles in shaping community composition. All life requires fixed nitrogen (N), and its bioavailability is what often limits ecosystem productivity. Biological nitrogen fixation, or the reduction of dinitrogen (N2) to ammonia (NH3), is a keystone process in N limited ecosystems, providing nitrogen for members of the community. N2 fixing organisms likely represent a 'bottom up control' on the structure of communities that develop in N limited environments. N2 fixation is catalyzed by a limited number of metabolically diverse bacteria and some methanogenic archaea and occurs in a variety of physically and geochemically diverse environments. Nitrification, or the sequential oxidation of NH4+ to nitrite (NO2-) and ultimately nitrate (NO3-), is catalyzed by several lineages of Proteobacteria at temperatures of < 62°C and by members of the Thaumarcheota at temperatures up to 90°C. Nitrification can thus be considered a 'top down control' on the structure of communities that develop in N limited environments. Our research in Yellowstone National Park (YNP) reveals a strong correspondence between the distribution of ammonia oxidizing archaea (AOA) and nitrogen fixing aquificae (NFA) in nitrogen-limited geothermal hot springs over large environmental gradients. Based on the physiology of AOA and NFA, we propose that the strong co-distributional pattern results from interspecies interactions, namely competition for bioavailable ammonia. Our recent work has shown that in springs where the niche dimension of AOA and NFA overlap (e.g., Perpetual Spouter; pH 7.1, 86.4°C), the dissimilar affinities for NH4 result in AOA metabolism maintaining a low NH4(T) pool and selecting for inclusion of NFA during the assembly of these communities. Here, we examine in situ physiological interactions of AOA and NFA, tracking changes in transcript levels of key genes involved in nitrogen metabolism and carbon fixation of

The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

PubMed Central

Forterre, Patrick

2013-01-01

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other. PMID:24348094

Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline.

PubMed

Toffano-Nioche, Claire; Luo, Yufei; Kuchly, Claire; Wallon, Claire; Steinbach, Delphine; Zytnicki, Matthias; Jacq, Annick; Gautheret, Daniel

2013-09-01

RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the non-coding elements is challenging. Non-coding elements include untranslated regions (UTRs) of mRNAs, independent small RNA genes (sRNAs) and transcripts produced from the antisense strand of genes (asRNA). Here we present a computational pipeline (DETR'PROK: detection of ncRNAs in prokaryotes) based on the Galaxy framework that takes as input a mapping of deep sequencing reads and performs successive steps of clustering, comparison with existing annotation and identification of transcribed non-coding fragments classified into putative 5' UTRs, sRNAs and asRNAs. We provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coli. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Exposure to biohazards in wood dust: bacteria, fungi, endotoxins, and (1-->3)-beta-D-glucans.

PubMed

Alwis, K U; Mandryk, J; Hocking, A D

1999-09-01

Personal exposure to fungi, bacteria, endotoxin, and (1-->3)-beta-D-glucan was determined at different woodworking sites--logging sites, sawmills, woodchipping sites, and joineries. Exposure levels to fungi at logging sites and sawmills were in the range of 10(3)-10(4) cfu/m3, at the woodchipping mill, 10(3)-10(5) cfu/m3, and at joineries, 10(2)-10(4) cfu/m3. Although mean endotoxin levels were lower than the suggested threshold value of 20 ng/m3, some personal exposures at sawmills and a joinery exceeded the standard. The geometric mean personal (1-->3)-beta-D-glucan exposure level at the woodchipping mill was 2.32 ng/m3, at sawmills, 1.37 ng/m3, at logging sites, 2.02 ng/m3, and at joineries, 0.43 ng/m3. Highly significant associations were found between mean personal inhalable endotoxin exposures and Gram-negative bacteria levels (p < 0.0001), and mean personal inhalable (1-->3)-beta-D-glucan exposures and fungi levels (p = 0.0003). The prevalence of cough, phlegm, chronic bronchitis, nasal symptoms, frequent headaches, and eye and throat irritations was significantly higher among woodworkers than controls. Dose-response relationships were found between personal exposures and work-related symptoms among joinery workers and sawmill and chip mill workers.

Different effects of transgenic maize and nontransgenic maize on nitrogen-transforming archaea and bacteria in tropical soils.

PubMed

Cotta, Simone Raposo; Dias, Armando Cavalcante Franco; Marriel, Ivanildo Evódio; Andreote, Fernando Dini; Seldin, Lucy; van Elsas, Jan Dirk

2014-10-01

The composition of the rhizosphere microbiome is a result of interactions between plant roots, soil, and environmental conditions. The impact of genetic variation in plant species on the composition of the root-associated microbiota remains poorly understood. This study assessed the abundances and structures of nitrogen-transforming (ammonia-oxidizing) archaea and bacteria as well as nitrogen-fixing bacteria driven by genetic modification of their maize host plants. The data show that significant changes in the abundances (revealed by quantitative PCR) of ammonia-oxidizing bacterial and archaeal communities occurred as a result of the maize host being genetically modified. In contrast, the structures of the total communities (determined by PCR-denaturing gradient gel electrophoresis) were mainly driven by factors such as soil type and season and not by plant genotype. Thus, the abundances of ammonia-oxidizing bacterial and archaeal communities but not structures of those communities were revealed to be responsive to changes in maize genotype, allowing the suggestion that community abundances should be explored as candidate bioindicators for monitoring the possible impacts of cultivation of genetically modified plants. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Role of Mn2+ and compatible solutes in the radiation resistance of thermophilic bacteria and archaea.

PubMed

Webb, Kimberly M; DiRuggiero, Jocelyne

2012-01-01

Radiation-resistant bacteria have garnered a great deal of attention from scientists seeking to expose the mechanisms underlying their incredible survival abilities. Recent analyses showed that the resistance to ionizing radiation (IR) in the archaeon Halobacterium salinarum is dependent upon Mn-antioxidant complexes responsible for the scavenging of reactive oxygen species (ROS) generated by radiation. Here we examined the role of the compatible solutes trehalose, mannosylglycerate, and di-myo-inositol phosphate in the radiation resistance of aerobic and anaerobic thermophiles. We found that the IR resistance of the thermophilic bacteria Rubrobacter xylanophilus and Rubrobacter radiotolerans was highly correlated to the accumulation of high intracellular concentration of trehalose in association with Mn, supporting the model of Mn(2+)-dependent ROS scavenging in the aerobes. In contrast, the hyperthermophilic archaea Thermococcus gammatolerans and Pyrococcus furiosus did not contain significant amounts of intracellular Mn, and we found no significant antioxidant activity from mannosylglycerate and di-myo-inositol phosphate in vitro. We therefore propose that the low levels of IR-generated ROS under anaerobic conditions combined with highly constitutively expressed detoxification systems in these anaerobes are key to their radiation resistance and circumvent the need for the accumulation of Mn-antioxidant complexes in the cell.

Characterization of tannase protein sequences of bacteria and fungi: an in silico study.

PubMed

Banerjee, Amrita; Jana, Arijit; Pati, Bikash R; Mondal, Keshab C; Das Mohapatra, Pradeep K

2012-04-01

The tannase protein sequences of 149 bacteria and 36 fungi were retrieved from NCBI database. Among them only 77 bacterial and 31 fungal tannase sequences were taken which have different amino acid compositions. These sequences were analysed for different physical and chemical properties, superfamily search, multiple sequence alignment, phylogenetic tree construction and motif finding to find out the functional motif and the evolutionary relationship among them. The superfamily search for these tannase exposed the occurrence of proline iminopeptidase-like, biotin biosynthesis protein BioH, O-acetyltransferase, carboxylesterase/thioesterase 1, carbon-carbon bond hydrolase, haloperoxidase, prolyl oligopeptidase, C-terminal domain and mycobacterial antigens families and alpha/beta hydrolase superfamily. Some bacterial and fungal sequence showed similarity with different families individually. The multiple sequence alignment of these tannase protein sequences showed conserved regions at different stretches with maximum homology from amino acid residues 389-469 and 482-523 which could be used for designing degenerate primers or probes specific for tannase producing bacterial and fungal species. Phylogenetic tree showed two different clusters; one has only bacteria and another have both fungi and bacteria showing some relationship between these different genera. Although in second cluster near about all fungal species were found together in a corner which indicates the sequence level similarity among fungal genera. The distributions of fourteen motifs analysis revealed Motif 1 with a signature amino acid sequence of 29 amino acids, i.e. GCSTGGREALKQAQRWPHDYDGIIANNPA, was uniformly observed in 83.3 % of studied tannase sequences representing its participation with the structure and enzymatic function.

Bioremediation mechanisms of combined pollution of PAHs and heavy metals by bacteria and fungi: A mini review.

PubMed

Liu, Shao-Heng; Zeng, Guang-Ming; Niu, Qiu-Ya; Liu, Yang; Zhou, Lu; Jiang, Lu-Hua; Tan, Xiao-Fei; Xu, Piao; Zhang, Chen; Cheng, Min

2017-01-01

In recent years, knowledge in regard to bioremediation of combined pollution of polycyclic aromatic hydrocarbons (PAHs) and heavy metals by bacteria and fungi has been widely developed. This paper reviews the species of bacteria and fungi which can tackle with various types of PAHs and heavy metals entering into environment simultaneously or successively. Microbial activity, pollutants bioavailability and environmental factors (e.g. pH, temperature, low molecular weight organic acids and humic acids) can all affect the bioremediation of PAHs and heavy metals. Moreover, this paper summarizes the remediation mechanisms of PAHs and heavy metals by microbes via elucidating the interaction mechanisms of heavy metals with heavy metals, PAHs/PAHs metabolites with PAHs and PAHs with heavy metals. Based on the above reviews, this paper also discusses the potential research needs for this field. Copyright © 2016 Elsevier Ltd. All rights reserved.

Arylamine n-acetyltransferases in eukaryotic microorganisms

USDA-ARS?s Scientific Manuscript database

Microorganisms can survive highly toxic environments through numerous xenobiotic metabolizing enzymes, including arylamine N-acetyltransferases (NATs). NAT genes are present in bacteria, archaea, protists and fungi. In lower taxa of fungi, NAT genes are found in chytridiomycetes. In Dikarya, NAT gen...

Antimicrobial activity of broccoli (Brassica oleracea var. italica) cultivar Avenger against pathogenic bacteria, phytopathogenic filamentous fungi and yeast.

PubMed

Pacheco-Cano, R D; Salcedo-Hernández, R; López-Meza, J E; Bideshi, D K; Barboza-Corona, J E

2018-01-01

The objective of this study was to show whether the edible part of broccoli has antibacterial and antifungal activity against micro-organism of importance in human health and vegetable spoilage, and to test if this effect was partially due to antimicrobial peptides (AMPs). Crude extracts were obtained from florets and stems of broccoli cultivar Avenger and the inhibitory effect was demonstrated against pathogenic bacteria (Bacillus cereus, Staphylococcus xylosus, Staphylococcus aureus, Shigella flexneri, Shigella sonnei, Proteus vulgaris), phytopathogenic fungi (Colletotrichum gloeosporioides, Asperigillus niger) and yeasts (Candida albicans and Rhodotorula sp.). It was shown that samples treated with proteolytic enzymes had a reduction of approximately 60% in antibacterial activity against Staph. xylosus, suggesting that proteinaceous compounds might play a role in the inhibitory effect. Antimicrobial components in crude extracts were thermoresistant and the highest activity was observed under acidic conditions. It was shown that antifungal activity of broccoli's crude extracts might not be attributed to chitinases. Organic broccoli cultivar Avenger has antimicrobial activity against pathogenic bacteria, yeast and phytophatogenic fungi. Data suggest that this effect is partially due to AMPs. Broccoli's crude extracts have activity not only against pathogenic bacteria but also against phytophatogenic fungi of importance in agriculture. We suggest for first time that the inhibitory effect is probably due to AMPs. © 2017 The Society for Applied Microbiology.

Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

PubMed

Ozuolmez, Derya; Na, Hyunsoo; Lever, Mark A; Kjeldsen, Kasper U; Jørgensen, Bo B; Plugge, Caroline M

2015-01-01

Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.

Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

PubMed Central

Ozuolmez, Derya; Na, Hyunsoo; Lever, Mark A.; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Plugge, Caroline M.

2015-01-01

Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria. PMID:26074892

A Review of Acquired Thermotolerance, Heat Shock Proteins, and Molecular Chaperones in Archaea: Heat Shock in Archaea

DOE R&D Accomplishments Database

Trent, J. D.

1996-02-09

Acquired thermotolerance, the associated synthesis of heat-shock proteins (HSPs) under stress conditions, and the role of HSPs as molecular chaperones under normal growth conditions have been studied extensively in eukaryotes and bacteria, whereas research in these areas in archaea is only beginning. All organisms have evolved a variety of strategies for coping with high-temperature stress, and among these strategies is the increased synthesis of HSPs. The facts that both high temperatures and chemical stresses induce the HSPs and that some of the HSPs recognize and bind to unfolded proteins in vitro have led to the theory that the function of HSPs is to prevent protein aggregation in vivo. The facts that some HSPs are abundant under normal growth conditions and that they assist in protein folding in vitro have led to the theory that they assist protein folding in vivo; in this role, they are referred to as molecular chaperones. The limited research on acquired thermotolerance, HSPs, and molecular chaperones in archaea, particularly the hyperthermophilic archaea, suggests that these extremophiles provide a new perspective in these areas of research, both because they are members of a separate phylogenetic domain and because they have evolved to live under extreme conditions.

Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone

PubMed Central

Pitcher, Angela; Villanueva, Laura; Hopmans, Ellen C; Schouten, Stefan; Reichart, Gert-Jan; Sinninghe Damsté, Jaap S

2011-01-01

Ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria have emerged as significant factors in the marine nitrogen cycle and are responsible for the oxidation of ammonium to nitrite and dinitrogen gas, respectively. Potential for an interaction between these groups exists; however, their distributions are rarely determined in tandem. Here we have examined the vertical distribution of AOA and anammox bacteria through the Arabian Sea oxygen minimum zone (OMZ), one of the most intense and vertically exaggerated OMZs in the global ocean, using a unique combination of intact polar lipid (IPL) and gene-based analyses, at both DNA and RNA levels. To screen for AOA-specific IPLs, we developed a high-performance liquid chromatography/mass spectrometry/mass spectrometry method targeting hexose-phosphohexose (HPH) crenarchaeol, a common IPL of cultivated AOA. HPH-crenarchaeol showed highest abundances in the upper OMZ transition zone at oxygen concentrations of ca. 5 μ, coincident with peaks in both thaumarchaeotal 16S rDNA and amoA gene abundances and gene expression. In contrast, concentrations of anammox-specific IPLs peaked within the core of the OMZ at 600 m, where oxygen reached the lowest concentrations, and coincided with peak anammox 16S rDNA and the hydrazine oxidoreductase (hzo) gene abundances and their expression. Taken together, the data reveal a unique depth distribution of abundant AOA and anammox bacteria and the segregation of their respective niches by >400 m, suggesting no direct coupling of their metabolisms at the time and site of sampling in the Arabian Sea OMZ. PMID:21593795

Changes in N-Transforming Archaea and Bacteria in Soil during the Establishment of Bioenergy Crops

PubMed Central

Mao, Yuejian; Yannarell, Anthony C.; Mackie, Roderick I.

2011-01-01

Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community. PMID:21935454

Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil.

PubMed

Blazewicz, Steven J; Schwartz, Egbert; Firestone, Mary K

2014-05-01

The rapid increase in microbial activity that occurs when a dry soil is rewetted has been well documented and is of great interest due to implications of changing precipitation patterns on soil C dynamics. Several studies have shown minor net changes in microbial population diversity or abundance following wet-up, but the gross population dynamics of bacteria and fungi resulting from soil wet-up are virtually unknown. Here we applied DNA stable isotope probing with H218O coupled with quantitative PCR to characterize new growth, survival, and mortality of bacteria and fungi following the rewetting of a seasonally dried California annual grassland soil. Microbial activity, as determined by CO2 production, increased significantly within three hours of wet-up, yet new growth was not detected until after three hours, suggesting a pulse of nongrowth activity immediately following wet-up, likely due to osmo-regulation and resuscitation from dormancy in response to the rapid change in water potential. Total microbial abundance revealed little change throughout the seven-day post-wet incubation, but there was substantial turnover of both bacterial and fungal populations (49% and 52%, respectively). New growth was linear between 24 and 168 hours for both bacteria and fungi, with average growth rates of 2.3 x 10(8) bacterial 16S rRNA gene copies x [g dry mass](-1) x h(-1) and 4.3 x 10(7) fungal ITS copies x [g dry mass](-1) x h(-1). While bacteria and fungi differed in their mortality and survival characteristics during the seven-day incubation, mortality that occurred within the first three hours was similar, with 25% and 27% of bacterial and fungal gene copies disappearing from the pre-wet community, respectively. The rapid disappearance of gene copies indicates that cell death, occurring either during the extreme dry down period (preceding five months) or during the rapid change in water potential due to wet-up, generates a significant pool of available C that likely

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

PubMed Central

Esser, Dominik; Rauch, Bernadette

2014-01-01

SUMMARY The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented. PMID:24600042

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea

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

Skennerton, Connor T.; Chourey, Karuna; Iyer, Ramsunder

The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANMEmore » partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors. Some archaea, known as anaerobic methanotrophs, are capable of converting methane into carbon dioxide when they are growing syntopically with sulfate-reducing bacteria. This partnership is the primary mechanism for methane removal in ocean sediments; however, there is still much to learn about how this syntrophy works. Previous studies have failed to identify the metabolic intermediate, such as hydrogen or formate, that is passed between partners. However, recent analysis of

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea.

PubMed

Skennerton, Connor T; Chourey, Karuna; Iyer, Ramsunder; Hettich, Robert L; Tyson, Gene W; Orphan, Victoria J

2017-08-01

The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors. IMPORTANCE Some archaea, known as anaerobic methanotrophs, are capable of converting methane into carbon dioxide when they are growing syntopically with sulfate-reducing bacteria. This partnership is the primary mechanism for methane removal in ocean sediments; however, there is still much to learn about how this syntrophy works. Previous studies have failed to identify the metabolic intermediate, such as hydrogen or formate, that is passed between partners. However, recent analysis of

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea

DOE PAGES

Skennerton, Connor T.; Chourey, Karuna; Iyer, Ramsunder; ...

2017-08-01

The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANMEmore » partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors. Some archaea, known as anaerobic methanotrophs, are capable of converting methane into carbon dioxide when they are growing syntopically with sulfate-reducing bacteria. This partnership is the primary mechanism for methane removal in ocean sediments; however, there is still much to learn about how this syntrophy works. Previous studies have failed to identify the metabolic intermediate, such as hydrogen or formate, that is passed between partners. However, recent analysis of

Increased protein content of chickpea (Cicer arietinum L.) inoculated with arbuscular mycorrhizal fungi and nitrogen-fixing bacteria under water deficit conditions.

PubMed

Oliveira, Rui S; Carvalho, Patrícia; Marques, Guilhermina; Ferreira, Luís; Nunes, Mafalda; Rocha, Inês; Ma, Ying; Carvalho, Maria F; Vosátka, Miroslav; Freitas, Helena

2017-10-01

Chickpea (Cicer arietinum L.) is a widely cropped pulse and an important source of proteins for humans. In Mediterranean regions it is predicted that drought will reduce soil moisture and become a major issue in agricultural practice. Nitrogen (N)-fixing bacteria and arbuscular mycorrhizal (AM) fungi have the potential to improve plant growth and drought tolerance. The aim of the study was to assess the effects of N-fixing bacteria and AM fungi on the growth, grain yield and protein content of chickpea under water deficit. Plants inoculated with Mesorhizobium mediterraneum or Rhizophagus irregularis without water deficit and inoculated with M. mediterraneum under moderate water deficit had significant increases in biomass. Inoculation with microbial symbionts brought no benefits to chickpea under severe water deficit. However, under moderate water deficit grain crude protein was increased by 13%, 17% and 22% in plants inoculated with M. mediterraneum, R. irregularis and M. mediterraneum + R. irregularis, respectively. Inoculation with N-fixing bacteria and AM fungi has the potential to benefit agricultural production of chickpea under water deficit conditions and to contribute to increased grain protein content. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Does Initial Leaf Chemistry Affect the Contribution of Insects, Fungi, and Bacteria to Leaf Breakdown in a Lowland Tropical Stream?

NASA Astrophysics Data System (ADS)

Ardon, M.; Pringle, C. M.

2005-05-01

We examined effects of initial leaf chemistry of six common riparian species on the relative contribution of fungi, bacteria, and invertebrates to leaf breakdown in a lowland stream in Costa Rica. We hypothesized that fungi and bacteria would contribute more to the breakdown of species with low concentrations of secondary (tannins and phenolics) and structural (cellulose and lignin) compounds, while invertebrates would be more important in the processing of species with high concentrations of secondary and structural compounds. We incubated single species leaf bags of six common riparian species, representing a range in secondary and structural compounds, in a third-order stream at La Selva Biological Station, Costa Rica. We measured leaf chemistry during the breakdown process. We determined fungal biomass using ergosterol methods, bacteria using DAPI counts, and invertebrate biomass using length-weight regressions. We then used biomass estimates for each group to determine their contribution to the overall breakdown process. Breakdown rates ranged from very fast (Trema integerima, k = 0.23 day-1) to slow (Zygia longifolia , k = 0.011 day-1). While analyses are still under way, preliminary results support our initial hypothesis that fungi contribute more to the break down of leaves from tree species with low concentrations of secondary and structural compounds.

Acetate Metabolism in Anaerobes from the Domain Archaea

PubMed Central

Ferry, James G.

2015-01-01

Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth’s biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle by metabolizing acetate as a growth substrate or product. They are components of anaerobic microbial food chains converting complex organic matter to methane, and many fix CO2 into cell material via synthesis of acetyl-CoA. They are found in a diversity of ecological habitats ranging from the digestive tracts of insects to deep-sea hydrothermal vents, and synthesize a plethora of novel enzymes with biotechnological potential. Ecological investigations suggest that still more acetate-metabolizing species with novel properties await discovery. PMID:26068860

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

PubMed Central

Koonin, Eugene V.; Wolf, Yuri I.

2008-01-01

The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution. PMID:18948295

Gene Expression in Archaea: Studies of Transcriptional Promoters, Messenger RNA Processing, and Five Prime Untranslated Regions in "Methanocaldococcus Jannashchii"

ERIC Educational Resources Information Center

Zhang, Jian

2009-01-01

Gene expression in Archaea is less understood than those in Bacteria and Eucarya. In general, three steps are involved in gene expression--transcription, RNA processing, and translation. To expand our knowledge of these processes in Archaea, I have studied transcriptional promoters, messenger RNA processing, and 5'-untranslated regions in…

Base excision repair in Archaea: back to the future in DNA repair.

PubMed

Grasso, Stefano; Tell, Gianluca

2014-09-01

Together with Bacteria and Eukarya, Archaea represents one of the three domain of life. In contrast with the morphological difference existing between Archaea and Eukarya, these two domains are closely related. Phylogenetic analyses confirm this evolutionary relationship showing that most of the proteins involved in DNA transcription and replication are highly conserved. On the contrary, information is scanty about DNA repair pathways and their mechanisms. In the present review the most important proteins involved in base excision repair, namely glycosylases, AP lyases, AP endonucleases, polymerases, sliding clamps, flap endonucleases, and ligases, will be discussed and compared with bacterial and eukaryotic ones. Finally, possible applications and future perspectives derived from studies on Archaea and their repair pathways, will be taken into account. Copyright © 2014 Elsevier B.V. All rights reserved.

Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics

PubMed Central

Anderson, Rika E.; Sogin, Mitchell L.; Baross, John A.

2014-01-01

The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities. PMID:25279954

Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria

PubMed Central

Dyer, Betsey D.; Kahn, Michael J.; LeBlanc, Mark D.

2008-01-01

Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. Although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. Temperature optima for most of the organisms examined could be distinguished by CART analyses of tetranucleotide frequencies. This suggests that pervasive (nonlinear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved. The predominant use of GAGA and AGGA as the discriminating tetramers in CART models suggests that purine-loading and codon biases of thermophiles may explain some of the results. PMID:19054742

Nematode-trapping fungi and fungus-associated bacteria interactions: the role of bacterial diketopiperazines and biofilms on Arthrobotrys oligospora surface in hyphal morphogenesis.

PubMed

Li, Lei; Yang, Min; Luo, Jun; Qu, Qing; Chen, Ying; Liang, Lianming; Zhang, Keqin

2016-11-01

In soil, nematode-trapping fungi and bacteria often share microhabitats and interact with each other, but effects of fungus-associated bacteria on its trap formation are underestimated. We have ascertained the presence of Stenotrophomonas and Rhizobium genera associated with A. oligospora GJ-1. After A. oligospora GJ-1 without associated bacteria (cured Arthrobotrys) was co-cultivated with Stenotrophomonas and its supernatant extract, microscopic study of hyphae from co-cultivation indicated that bacterial biofilm formation on hyphae was related to trap formation in fungi and Stenotrophomonas supernatant extract. Four diketopiperazines (DKPs) were purified from Stenotrophomonas supernatant extract that could not induce traps in the cured Arthrobotrys. When cured Arthrobotrys was cultured with Stenotrophomonas and one of DKPs, polar attachment, bacterial biofilms on hyphae and trap formation in fungi were observed. After cured Arthrobotrys with bacterial biofilms was consecutively transferred several times on nutrient poor medium, trap formation disappeared with the disappearance of bacterial biofilms on hyphae. DKPs could facilitate chemotaxis of Stenotrophomonas towards fungal extract which was suggested to contribute to bacterial biofilms on hyphae. Furthermore, when cured Arthrobotrys was cultured with Stenotrophomonas and DKPs in soil, trap formation in fungi and bacterial biofilms on hyphae were also observed, and the fungal activity against nematode was enhanced. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

“Altiarchaeales”: Uncultivated Archaea from the Subsurface

PubMed Central

Probst, Alexander J.; Moissl-Eichinger, Christine

2015-01-01

Due to the limited cultivability of the vast majority of microorganisms, researchers have applied environmental genomics and other state-of-the-art technologies to gain insights into the biology of uncultivated Archaea and bacteria in their natural biotope. In this review, we summarize the scientific findings on a recently proposed order-level lineage of uncultivated Archaea called Altiarchaeales, which includes “Candidatus Altiarchaeum hamiconexum” as the most well-described representative. Ca. A. hamiconexum possesses a complex biology: thriving strictly anaerobically, this microorganism is capable of forming highly-pure biofilms, connecting the cells by extraordinary cell surface appendages (the “hami”) and has other highly unusual traits, such as a double-membrane-based cell wall. Indicated by genomic information from different biotopes, the Altiarchaeales seem to proliferate in deep, anoxic groundwater of Earth’s crust bearing a potentially very important function: carbon fixation. Although their net carbon fixation rate has not yet been determined, they appear as highly abundant organisms in their biotopes and may thus represent an important primary producer in the subsurface. In sum, the research over more than a decade on Ca. A. hamiconexum has revealed many interesting features of its lifestyle, its genomic information, metabolism and ultrastructure, making this archaeon one of the best-studied uncultivated Archaea in the literature. PMID:25984733

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

PubMed

Wolf, Yuri I; Makarova, Kira S; Yutin, Natalya; Koonin, Eugene V

2012-12-14

Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major 'highways' of horizontal gene transfer. The updated collection of arCOGs is expected to become a key resource for

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

PubMed

Mirzaei, Mohammadali Khan; Maurice, Corinne F

2017-07-01

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

Occurrence of heterotrophic bacteria and fungi in an aviation fuel handling system and its relationship with fuel fouling.

PubMed

Ferrari, M D; Neirotti, E; Albornoz, C

1998-01-01

Clean, dry and contaminant-free fuel is necessary for safe and economical aircraft operation. Microbial growth in aviation fuel handling systems can alter the quality of the product. This paper reports the occurrence of heterotrophic bacteria and fungi in a handling system of jet A-1 aviation turbine fuel. A total of 350 samples were collected during 1990-1996. The aerobic microorganisms in fuel samples were mainly fungi, 85% of samples containing < or = 100 cfu/l (range 0 (< 1 cfu/l) to 2000 cfu/l). The predominant fungi were Cladosporium and Aspergillus. Water was observed mainly in samples extracted from the drainage pipes of two tanks used frequently as intermediate storage tanks. The aerobic heterotrophic microorganisms found in water samples were mostly bacteria, counts varying from 100 to 8.8 x 10(7) cfu/ml, with 85% of samples containing 10(4)-10(7) cfu/ml. There was a preponderance of Pseudomonas spp. Bacterial contaminants belonging to the genus Flavobacterium and Aeromonas were also identified. Sulphate reducing bacteria were detected in 80% of water samples. It was not possible to assign a maximum microbial contamination level above which maintenance is required and it is suggested that analysis of successive samples from the same site are necessary for this purpose. Microbial sludges produced in the laboratory and collected from a contaminated tank bottom were analysed chemically. The data are presented and discussed. Samples collected from the supply pipes of tanks and refueller trucks during the period surveyed always met the standard specifications.

Characterization of free amino acids, bacteria and fungi in size-segregated atmospheric aerosols in boreal forest: seasonal patterns, abundances and size distributions

NASA Astrophysics Data System (ADS)

Helin, Aku; Sietiö, Outi-Maaria; Heinonsalo, Jussi; Bäck, Jaana; Riekkola, Marja-Liisa; Parshintsev, Jevgeni

2017-11-01

Primary biological aerosol particles (PBAPs) are ubiquitous in the atmosphere and constitute ˜ 30 % of atmospheric aerosol particle mass in sizes > 1 µm. PBAP components, such as bacteria, fungi and pollen, may affect the climate by acting as cloud-active particles, thus having an effect on cloud and precipitation formation processes. In this study, size-segregated aerosol samples (< 1.0, 1-2.5, 2.5-10 and > 10 µm) were collected in boreal forest (Hyytiälä, Finland) during a 9-month period covering all seasons and analysed for free amino acids (FAAs), DNA concentration and microorganism (bacteria, Pseudomonas and fungi). Measurements were performed using tandem mass spectrometry, spectrophotometry and qPCR, respectively. Meteorological parameters and statistical analysis were used to study their atmospheric implication for results. Distinct annual patterns of PBAP components were observed, late spring and autumn being seasons of dominant occurrence. Elevated abundances of FAAs and bacteria were observed during the local pollen season, whereas fungi were observed at the highest level during autumn. Meteorological parameters such as air and soil temperature, radiation and rainfall were observed to possess a close relationship with PBAP abundances on an annual scale.

Soil Bacteria and Fungi Respond on Different Spatial Scales to Invasion by the Legume Lespedeza cuneata.

PubMed

Yannarell, Anthony C; Busby, Ryan R; Denight, Michael L; Gebhart, Dick L; Taylor, Steven J

2011-01-01

The spatial scale on which microbial communities respond to plant invasions may provide important clues as to the nature of potential invader-microbe interactions. Lespedeza cuneata (Dum. Cours.) G. Don is an invasive legume that may benefit from associations with mycorrhizal fungi; however, it has also been suggested that the plant is allelopathic and may alter the soil chemistry of invaded sites through secondary metabolites in its root exudates or litter. Thus, L. cuneata invasion may interact with soil microorganisms on a variety of scales. We investigated L. cuneata-related changes to soil bacterial and fungal communities at two spatial scales using multiple sites from across its invaded N. American range. Using whole-community DNA fingerprinting, we characterized microbial community variation at the scale of entire invaded sites and at the scale of individual plants. Based on permutational multivariate analysis of variance, soil bacterial communities in heavily invaded sites were significantly different from those of uninvaded sites, but bacteria did not show any evidence of responding at very local scales around individual plants. In contrast, soil fungi did not change significantly at the scale of entire sites, but there were significant differences between fungal communities of native versus exotic plants within particular sites. The differential scaling of bacterial and fungal responses indicates that L. cuneata interacts differently with soil bacteria and soil fungi, and these microorganisms may play very different roles in the invasion process of this plant.

Chemical ecology of fungi.

PubMed

Spiteller, Peter

2015-07-01

Fungi are widespread in nature and have conquered nearly every ecological niche. Fungi occur not only in terrestrial but also in freshwater and marine environments. Moreover, fungi are known as a rich source of secondary metabolites. Despite these facts, the ecological role of many of these metabolites is still unknown and the chemical ecology of fungi has not been investigated systematically so far. This review intends to present examples of the various chemical interactions of fungi with other fungi, plants, bacteria and animals and to give an overview of the current knowledge of fungal chemical ecology.

Interaction of rhizosphere bacteria, fertilizer, and vesicular-arbuscular mycorrhizal fungi with sea oats.

PubMed

Will, M E; Sylvia, D M

1990-07-01

Plants must be established quickly on replenished beaches in order to stabilize the sand and begin the dune-building process. The objective of this research was to determine whether inoculation of sea oats (Uniola paniculata L.) with bacteria (indigenous rhizosphere bacteria and N(2) fixers) alone or in combination with vesicular-arbuscular mycorrhizal fungi would enhance plant growth in beach sand. At two fertilizer-N levels, Klebsiella pneumoniae and two Azospirillum spp. did not provide the plants with fixed atmospheric N; however, K. pneumoniae increased root and shoot growth. When a sparingly soluble P source (CaHPO(4)) was added to two sands, K. pneumoniae increased plant growth in sand with a high P content. The phosphorus content of shoots was not affected by bacterial inoculation, indicating that a mechanism other than bacterially enhanced P availability to plants was responsible for the growth increases. When sea oats were inoculated with either K. pneumoniae or Acaligenes denitrificans and a mixed Glomus inoculum, there was no consistent evidence of a synergistic effect on plant growth. Nonetheless, bacterial inoculation increased root colonization by vesicular-arbuscular mycorrhizal fungi when the fungal inoculum consisted of colonized roots but had no effect on colonization when the inoculum consisted of spores alone. K. pneumoniae was found to increase spore germination and hyphal growth of Glomus deserticola compared with the control. The use of bacterial inoculants to enhance establishment of pioneer dune plants warrants further study.

In situ DNA hybridized chain reaction (FISH-HCR) as a better method for quantification of bacteria and archaea within marine sediment

NASA Astrophysics Data System (ADS)

Buongiorno, J.; Lloyd, K. G.; Shumaker, A.; Schippers, A.; Webster, G.; Weightman, A.; Turner, S.

2015-12-01

Nearly 75% of the Earth's surface is covered by marine sediment that is home to an estimated 2.9 x 1029 microbial cells. A substantial impediment to understanding the abundance and distribution of cells within marine sediment is the lack of a consistent and reliable method for their taxon-specific quantification. Catalyzed reporter fluorescent in situ hybridization (CARD-FISH) provides taxon-specific enumeration, but this process requires passing a large enzyme through cell membranes, decreasing its precision relative to general cell counts using a small DNA stain. In 2015, Yamaguchi et al. developed FISH hybridization chain reaction (FISH-HCR) as an in situ whole cell detection method for environmental microorganisms. FISH-HCR amplifies the fluorescent signal, as does CARD-FISH, but it allows for milder cell permeation methods that might prevent yield loss. To compare FISH-HCR to CARD-FISH, we examined bacteria and archaea cell counts within two sediment cores, Lille Belt (~78 meters deep) and Landsort Deep (90 meters deep), which were retrieved from the Baltic Sea Basin during IODP Expedition 347. Preliminary analysis shows that CARD-FISH counts are below the quantification limit for most depths across both cores. By contrast, quantification of cells was possible with FISH-HCR in all examined depths. When quantification with CARD-FISH was above the limit of detection, counts with FISH-HCR were up to 11 fold higher for Bacteria and 3 fold higher for Archaea from the same sediment sample. Further, FISH-HCR counts follow the trends of on board counts nicely, indicating that FISH-HCR may better reflect the cellular abundance within marine sediment than other quantification methods, including qPCR. Using FISH-HCR, we found that archaeal cell counts were on average greater than bacterial cell counts, but within the same order of magnitude.

Archaea on Human Skin

PubMed Central

Probst, Alexander J.; Auerbach, Anna K.; Moissl-Eichinger, Christine

2013-01-01

The recent era of exploring the human microbiome has provided valuable information on microbial inhabitants, beneficials and pathogens. Screening efforts based on DNA sequencing identified thousands of bacterial lineages associated with human skin but provided only incomplete and crude information on Archaea. Here, we report for the first time the quantification and visualization of Archaea from human skin. Based on 16 S rRNA gene copies Archaea comprised up to 4.2% of the prokaryotic skin microbiome. Most of the gene signatures analyzed belonged to the Thaumarchaeota, a group of Archaea we also found in hospitals and clean room facilities. The metabolic potential for ammonia oxidation of the skin-associated Archaea was supported by the successful detection of thaumarchaeal amoA genes in human skin samples. However, the activity and possible interaction with human epithelial cells of these associated Archaea remains an open question. Nevertheless, in this study we provide evidence that Archaea are part of the human skin microbiome and discuss their potential for ammonia turnover on human skin. PMID:23776475

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork

PubMed Central

Grogan, Dennis W.

2015-01-01

Although hyperthermophilic archaea arguably have a great need for efficient DNA repair, they lack members of several DNA repair protein families broadly conserved among bacteria and eukaryotes. Conversely, the putative DNA repair genes that do occur in these archaea often do not generate the expected phenotype when deleted. The prospect that hyperthermophilic archaea have some unique strategies for coping with DNA damage and replication errors has intellectual and technological appeal, but resolving this question will require alternative coping mechanisms to be proposed and tested experimentally. This review evaluates a combination of four enigmatic properties that distinguishes the hyperthermophilic archaea from all other organisms: DNA polymerase stalling at dU, apparent lack of conventional NER, lack of MutSL homologs, and apparent essentiality of homologous recombination proteins. Hypothetical damage-coping strategies that could explain this set of properties may provide new starting points for efforts to define how archaea differ from conventional models of DNA repair and replication fidelity. PMID:26146487

Apparent Minimum Free Energy Requirements for Methanogenic Archaea and Sulfate-Reducing Bacteria in an Anoxic Marine Sediment

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Martens, Christopher S.; DeVincenzi, Don (Technical Monitor)

2000-01-01

Among the most fundamental constraints governing the distribution of microorganisms in the environment is the availability of chemical energy at biologically useful levels. To assess the minimum free energy yield that can support microbial metabolism in situ, we examined the thermodynamics of H2-consuming processes in anoxic sediments from Cape Lookout Bight, NC, USA. Depth distributions of H2 partial pressure, along with a suite of relevant concentration data, were determined in sediment cores collected in November (at 14.5 C) and August (at 27 C) and used to calculate free energy yields for methanogenesis and sulfate reduction. At both times of year, and for both processes, free energy yields gradually decreased (became less negative) with depth before reaching an apparent asymptote. Sulfate reducing bacteria exhibited an asymptote of -19.1 +/- 1.7 kj(mol SO4(2-)(sup -1) while methanogenic archaea were apparently supported by energy yields as small as -10.6 +/- 0.7 kj(mol CH4)(sup -1).

Archaea in metazoan diets: implications for food webs and biogeochemical cycling

PubMed Central

Thurber, Andrew R; Levin, Lisa A; Orphan, Victoria J; Marlow, Jeffrey J

2012-01-01

Although the importance of trophic linkages, including ‘top-down forcing', on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk δ13C=−92±4‰ polar lipids −116‰) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as ‘archivory'. PMID:22402398

Archaea in metazoan diets: implications for food webs and biogeochemical cycling.

PubMed

Thurber, Andrew R; Levin, Lisa A; Orphan, Victoria J; Marlow, Jeffrey J

2012-08-01

Although the importance of trophic linkages, including 'top-down forcing', on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk δ(13)C=-92±4‰; polar lipids -116‰) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as 'archivory'.

Metabolic plasticity for isoprenoid biosynthesis in bacteria.

PubMed

Pérez-Gil, Jordi; Rodríguez-Concepción, Manuel

2013-05-15

Isoprenoids are a large family of compounds synthesized by all free-living organisms. In most bacteria, the common precursors of all isoprenoids are produced by the MEP (methylerythritol 4-phosphate) pathway. The MEP pathway is absent from archaea, fungi and animals (including humans), which synthesize their isoprenoid precursors using the completely unrelated MVA (mevalonate) pathway. Because the MEP pathway is essential in most bacterial pathogens (as well as in the malaria parasites), it has been proposed as a promising new target for the development of novel anti-infective agents. However, bacteria show a remarkable plasticity for isoprenoid biosynthesis that should be taken into account when targeting this metabolic pathway for the development of new antibiotics. For example, a few bacteria use the MVA pathway instead of the MEP pathway, whereas others possess the two full pathways, and some parasitic strains lack both the MVA and the MEP pathways (probably because they obtain their isoprenoids from host cells). Moreover, alternative enzymes and metabolic intermediates to those of the canonical MVA or MEP pathways exist in some organisms. Recent work has also shown that resistance to a block of the first steps of the MEP pathway can easily be developed because several enzymes unrelated to isoprenoid biosynthesis can produce pathway intermediates upon spontaneous mutations. In the present review, we discuss the major advances in our knowledge of the biochemical toolbox exploited by bacteria to synthesize the universal precursors for their essential isoprenoids.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-11-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), none of the potential intermediates considered here is able to support metabolic activity matching the measured rates.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-05-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism, substrate affinity and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal was examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species causes the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), neither hydrogen nor formate is exchanged fast enough between the consortia partners to achieve measured rates of metabolic activity, but that acetate exchange might support rates that approach those observed.

Isolation and characterization of halophilic bacteria and archaea from salt ponds in Hangu Saltworks, Tianjin, China

NASA Astrophysics Data System (ADS)

Deng, Yuangao; Xu, Gaochao; Sui, Liying

2015-07-01

A total of 26 isolates were obtained from solar salt ponds of different salinities (100, 150, 200, and 250) in Hangu Saltworks Co. Ltd., Tianjin, China. Phylogenetic analysis of 16S rRNA gene sequences indicated that five bacteria genera Halomonas, Salinicoccus, Oceanobacillus, Gracibacillus, and Salimicrobium and one archaea genera Halorubrum were present. The genus Halomonas was predominant with eight strains distributed in a salinity range of 100-200, followed by Halorubrum with six strains in salinity 250. Based on the genus and original sampling salinity, eight bacterial and two archaeal isolates were selected for further morphological, physiological, and biochemical characterization. All of the bacterial strains were moderately halophilic with the optimal salinity for growth being either 50 or 100, while two archaeal strains were extremely halophilic with an optimal growth salinity of 200. Additionally, we put forth strain SM.200-5 as a new candidate Salimicrobium species based on the phylogenic analysis of the 16S rRNA gene sequence and its biochemical characteristics when compared with known related species.

Genomic insights into the metabolic potential and interactions between marine methanotrophic ANME archaea and associated bacteria

NASA Astrophysics Data System (ADS)

Orphan, V. J.; Skennerton, C.; Chadwick, G.; Haroon, F.; Tyson, G. W.; Leu, A.; Hatzenpichler, R.; Woyke, T.; Malmstrom, R.; Yu, H.; Scheller, S.

2015-12-01

Cooperative metabolic interactions between multiple groups of methanotrophic 'ANME' archaea and sulfate-reducing bacteria represent the primary sink for methane within continental margin sediments. These syntrophic associations are frequently observed as structured multi-celled consortia in methane seeps, often comprising a substantial proportion of the microbial biomass within near seafloor seep sediments. Since their discovery nearly 15 years ago, a number of distinct ANME groups and multiple sulfate-reducing bacterial partners have been described from seep environments worldwide. Attempts to reconstruct the genomes of some ANME organisms have been reported, however the ecological physiology and metabolic interactions of distinct ANME lineages and their bacterial partners remains poorly understood. Here, we used a fluorescence azide-alkyne click chemistry technique known as BONCAT combined with FAC sorting to examine patterns in microbial membership and the genomes of single, metabolically active ANME-bacterial consortia recovered from methane seep sediments. This targeted consortia-level sequencing approach revealed significant diversity in the ANME-bacterial associations in situ as well as insights into the potential syntrophic mechanisms underpinning these enigmatic methane-fueled partnerships.

Life in blue: copper resistance mechanisms of bacteria and archaea used in industrial biomining of minerals.

PubMed

Orell, Alvaro; Navarro, Claudio A; Arancibia, Rafaela; Mobarec, Juan C; Jerez, Carlos A

2010-01-01

Industrial biomining processes to extract copper, gold and other metals involve the use of extremophiles such as the acidophilic Acidithiobacillus ferrooxidans (Bacteria), and the thermoacidophilic Sulfolobus metallicus (Archaea). Together with other extremophiles these microorganisms subsist in habitats where they are exposed to copper concentrations higher than 100mM. Herein we review the current knowledge on the Cu-resistance mechanisms found in these microorganisms. Recent information suggests that biomining extremophiles respond to extremely high Cu concentrations by using simultaneously all or most of the following key elements: 1) a wide repertoire of Cu-resistance determinants; 2) duplication of some of these Cu-resistance determinants; 3) existence of novel Cu chaperones; 4) a polyP-based Cu-resistance system, and 5) an oxidative stress defense system. Further insight of the biomining community members and their individual response to copper is highly relevant, since this could provide key information to the mining industry. In turn, this information could be used to select the more fit members of the bioleaching community to attain more efficient industrial biomining processes. Copyright © 2010 Elsevier Inc. All rights reserved.

Indigenous Bacteria and Fungi Drive Traditional Kimoto Sake Fermentations

PubMed Central

Bokulich, Nicholas A.; Ohta, Moe; Lee, Morgan

2014-01-01

Sake (Japanese rice wine) production is a complex, multistage process in which fermentation is performed by a succession of mixed fungi and bacteria. This study employed high-throughput rRNA marker gene sequencing, quantitative PCR, and terminal restriction fragment length polymorphism to characterize the bacterial and fungal communities of spontaneous sake production from koji to product as well as brewery equipment surfaces. Results demonstrate a dynamic microbial succession, with koji and early moto fermentations dominated by Bacillus, Staphylococcus, and Aspergillus flavus var. oryzae, succeeded by Lactobacillus spp. and Saccharomyces cerevisiae later in the fermentations. The microbiota driving these fermentations were also prevalent in the production environment, illustrating the reservoirs and routes for microbial contact in this traditional food fermentation. Interrogating the microbial consortia of production environments in parallel with food products is a valuable approach for understanding the complete ecology of food production systems and can be applied to any food system, leading to enlightened perspectives for process control and food safety. PMID:24973064

Osmoadaptation and osmoregulation in archaea.

PubMed

Roberts, M F

2000-09-01

The response of archaea to changes in external NaCl is reviewed and compared to what is known about osmoadaptation and osmoregulation in bacteria and eukaryotes. Cells placed in altered external NaCl exhibit short term and long term responses. The earliest events are likely to be water movement through aquaporin-like channels (efflux if external NaCl has been increased, influx into the cell if the external NaCl has been decreased) and ion movement (e.g., K+ moving in the direction opposite to water flow) through channels sensitive to osmotic pressure. Accumulation of organic solutes, either by uptake from the medium or de novo synthesis, is triggered after these initial changes. Archaea have some unique organic solutes (osmolytes) that are not used by other organisms. These as well as other more common solutes have a role in stabilizing macromolecules from denaturation. Many osmolytes are distinguished by their stability in the cell and their lack of strong interactions with cellular components. A cell may respond by accumulating one or more temporary osmolytes, then over time readjust the intracellular solute distribution to what is optimal for cell growth under the new conditions. Coupled with the movement and accumulation of solutes is the induction of stress proteins (e.g., chaperonins) and, in some cases, transcriptional regulation of key enzymes. The response to NaCl stress of Methanococcus thermolithotrophicus is presented as an example of how one particular archaeon responds and adapts to altered osmotic pressure. Clearly, the detailed response of other archaea to osmotic stress will be needed in order to identify features (aside from some of the organic osmolytes) unique to the organisms in this kingdom.

A novel, multiplex, real-time PCR-based approach for the detection of the commonly occurring pathogenic fungi and bacteria.

PubMed

Horváth, Ádám; Pető, Zoltán; Urbán, Edit; Vágvölgyi, Csaba; Somogyvári, Ferenc

2013-12-23

Polymerase chain reaction (PCR)-based techniques are widely used to identify fungal and bacterial infections. There have been numerous reports of different, new, real-time PCR-based pathogen identification methods although the clinical practicability of such techniques is not yet fully clarified.The present study focuses on a novel, multiplex, real-time PCR-based pathogen identification system developed for rapid differentiation of the commonly occurring bacterial and fungal causative pathogens of bloodstream infections. A multiplex, real-time PCR approach is introduced for the detection and differentiation of fungi, Gram-positive (G+) and Gram-negative (G-) bacteria. The Gram classification is performed with the specific fluorescence resonance energy transfer (FRET) probes recommended for LightCycler capillary real-time PCR. The novelty of our system is the use of a non-specific SYBR Green dye instead of labelled anchor probes or primers, to excite the acceptor dyes on the FRET probes. In conjunction with this, the use of an intercalating dye allows the detection of fungal amplicons.With the novel pathogen detection system, fungi, G + and G- bacteria in the same reaction tube can be differentiated within an hour after the DNA preparation via the melting temperatures of the amplicons and probes in the same tube. This modified FRET technique is specific and more rapid than the gold-standard culture-based methods. The fact that fungi, G + and G- bacteria were successfully identified in the same tube within an hour after the DNA preparation permits rapid and early evidence-based management of bloodstream infections in clinical practice.

Taxonomic study of extreme halophilic archaea isolated from the "Salar de Atacama", Chile.

PubMed

Lizama, C; Monteoliva-Sánchez, M; Prado, B; Ramos-Cormenzana, A; Weckesser, J; Campos, V

2001-11-01

A large number of halophilic bacteria were isolated in 1984-1992 from the Atacama Saltern (North of Chile). For this study 82 strains of extreme halophilic archaea were selected. The characterization was performed by using the phenotypic characters including morphological, physiological, biochemical, nutritional and antimicrobial susceptibility test. The results, together with those from reference strains, were subjected to numerical analysis, using the Simple Matching (S(SM)) coefficient and clustered by the unweighted pair group method of association (UPGMA). Fifteen phena were obtained at an 70% similarity level. The results obtained reveal a high diversity among the halophilic archaea isolated. Representative strains from the phena were chosen to determine their DNA base composition and the percentage of DNA-DNA similarity compared to reference strains. The 16S rRNA studies showed that some of these strains constitutes a new taxa of extreme halophilic archaea.

Vertical profiles of community abundance and diversity of anaerobic methanotrophic archaea (ANME) and bacteria in a simple waste landfill in north China.

PubMed

Dong, Jun; Ding, Linjie; Wang, Xu; Chi, Zifang; Lei, Jiansen

2015-03-01

Anaerobic methane oxidation (AMO) is considered to be an important sink of CH4 in habitats as marine sediments. But, few studies focused on AMO in landfills which may be an important sink of CH4 derived from waste fermentation. To show evidence of AMO and to uncover function anaerobic methanotroph (ANME) community in landfill, different age waste samples were collected in Jinqianpu landfill located in north China. Through high-throughput sequencing, Methanomicrobiales and Methanosarcinales archaea associated with ANME and reverse methanogenic archaea of Methanosarcina and Methanobacterium were detected. Sulfate-reducing bacteria (SRB) (Desulfobulbus and Desulfococcus) which could couple with ANME-conducting AMO were also found. But, the community structure of ANME had no significant difference with depths. From the results of investigation, we can come to a conclusion that sulfate-dependent anaerobic methane oxidation (SR-DAMO) would be the dominant AMO process in the landfill, while iron-dependent anaerobic methane oxidation (M/IR-DAMO) process was weak though concentration of ferric iron was large in the landfill. Denitrification-dependent anaerobic methane oxidation (NR-DAMO) was negative because of lack of nitrate and relevant function microorganisms in the landfill. Results also indicate that CH4 mitigation would have higher potential by increasing electron acceptor contents and promoting the growth of relevant function microorganisms.

Antibiosis of vineyard ecosystem fungi against food-borne microorganisms.

PubMed

Cueva, Carolina; Moreno-Arribas, M Victoria; Bartolomé, Begoña; Salazar, Óscar; Vicente, M Francisca; Bills, Gerald F

2011-12-01

Fermentation extracts from fungi isolated from vineyard ecosystems were tested for antimicrobial activities against a set of test microorganisms, including five food-borne pathogens (Staphylococcus aureus EP167, Acinetobacter baumannii (clinically isolated), Pseudomonas aeruginosa PAO1, Escherichia coli O157:H7 (CECT 5947) and Candida albicans MY1055) and two probiotic bacteria (Lactobacillus plantarum LCH17 and Lactobacillus brevis LCH23). A total of 182 fungi was grown in eight different media, and the fermentation extracts were screened for antimicrobial activity. A total of 71 fungi produced extracts active against at least one pathogenic microorganism, but not against any probiotic bacteria. The Gram-positive bacterium S. aureus EP167 was more susceptible to antimicrobial fungi broth extracts than Gram-negative bacteria and pathogenic fungi. Identification of active fungi based on internal transcribed spacer rRNA sequence analysis revealed that species in the orders Pleosporales, Hypocreales and Xylariales dominated. Differences in antimicrobial selectivity were observed among isolates from the same species. Some compounds present in the active extracts were tentatively identified by liquid chromatography-mass spectrometry. Antimicrobial metabolites produced by vineyard ecosystem fungi may potentially limit colonization and spoilage of food products by food-borne pathogens, with minimal effect on probiotic bacteria. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Adaptation of the membrane in Archaea.

PubMed

Oger, Philippe M; Cario, Anaïs

2013-12-15

Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. This is achieved in bacteria and eucarya by a modification of the membrane lipid compositions, a strategy termed homeoviscous adaptation. We review here evidence for homeoviscous adaptation in Archaea, and discuss the limits of this strategy and our knowledge in this very peculiar domain of life. © 2013 Elsevier B.V. All rights reserved.

Bacteria and fungi can contribute to nutrients bioavailability and aggregate formation in degraded soils.

PubMed

Rashid, Muhammad Imtiaz; Mujawar, Liyakat Hamid; Shahzad, Tanvir; Almeelbi, Talal; Ismail, Iqbal M I; Oves, Mohammad

2016-02-01

Intensive agricultural practices and cultivation of exhaustive crops has deteriorated soil fertility and its quality in agroecosystems. According to an estimate, such practices will convert 30% of the total world cultivated soil into degraded land by 2020. Soil structure and fertility loss are one of the main causes of soil degradation. They are also considered as a major threat to crop production and food security for future generations. Implementing safe and environmental friendly technology would be viable solution for achieving sustainable restoration of degraded soils. Bacterial and fungal inocula have a potential to reinstate the fertility of degraded land through various processes. These microorganisms increase the nutrient bioavailability through nitrogen fixation and mobilization of key nutrients (phosphorus, potassium and iron) to the crop plants while remediate soil structure by improving its aggregation and stability. Success rate of such inocula under field conditions depends on their antagonistic or synergistic interaction with indigenous microbes or their inoculation with organic fertilizers. Co-inoculation of bacteria and fungi with or without organic fertilizer are more beneficial for reinstating the soil fertility and organic matter content than single inoculum. Such factors are of great importance when considering bacteria and fungi inocula for restoration of degraded soils. The overview of presented mechanisms and interactions will help agriculturists in planning sustainable management strategy for reinstating the fertility of degraded soil and assist them in reducing the negative impact of artificial fertilizers on our environment. Copyright © 2015 Elsevier GmbH. All rights reserved.

Symbiotic interaction of endophytic bacteria with arbuscular mycorrhizal fungi and its antagonistic effect on Ganoderma boninense.

PubMed

Sundram, Shamala; Meon, Sariah; Seman, Idris Abu; Othman, Radziah

2011-08-01

Endophytic bacteria (Pseudomonas aeruginosa UPMP3 and Burkholderia cepacia UMPB3), isolated from within roots of oil palm (Elaeis guineensis Jacq.) were tested for their presymbiotic effects on two arbuscular mcorrhizal fungi, Glomus intraradices UT126 and Glomus clarum BR152B). These endophytic bacteria were also tested for antagonistic effects on Ganoderma boninense PER 71, a white wood rot fungal pathogen that causes a serious disease in oil palm. Spore germination and hyphal length of each arbuscular mycorrhizal fungal (AMF) pairing with endophytic bacteria was found to be significantly higher than spores plated in the absence of bacteria. Scanning electron microscopy (SEM) showed that the endophytic bacteria were scattered, resting or embedded on the surface hyaline layer or on the degraded walls of AMF spores, possibly feeding on the outer hyaline spore wall. The antagonistic effect of the endophytic bacteria was expressed as severe morphological abnormalities in the hyphal structures of G. boninense PER 71. The effects of the endophytic bacteria on G. boninense PER 71 hyphal structures were observed clearly under SEM. Severe inter-twisting, distortion, lysis and shriveling of the hyphal structures were observed. This study found that the effect of endophytic bacteria on G. intraradices UT126 and G. clarum BR152B resembled that of a mycorrhiza helper bacteria (MHB) association because the association significantly promoted AMF spore germination and hyphal length. However, the endophytic bacteria were extremely damaging to G. boninense PER 71.

First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin

PubMed Central

Koskinen, Kaisa; Pausan, Manuela R.; Perras, Alexandra K.; Beck, Michael; Bang, Corinna; Mora, Maximilian; Schilhabel, Anke; Schmitz, Ruth

2017-01-01

ABSTRACT Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea. The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts. PMID:29138298

Health hazard evaluation report HETA 81-138-1563, Fillmore Dole Mushrooms, Castle and Cooke Foods, Fillmore, Utah. [Analyses for bacteria, fungi, formaldehyde, and vapona

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

Gunter, B.J.; Thoburn, T.W.; Lockey, J.E.

1985-01-01

Environmental and breathing-zone samples were analyzed for bacteria, fungi, formaldehyde, and 2,2-dichlorovinyldimethylphosphate (vapona) at Fillmore Dole Mushrooms, Castle and Cooke Foods, Fillmore, Utah in June, 1981. The survey was requested by the workers to evaluate respiratory problems. A total of 111 workers, including 59 Southeast Asians, were interviewed by questionnaire. There were 48 English-speaking and 18 Asian comparisons. The authors conclude that a potential hazard exists due to exposure to airborne fungi and bacteria. Formaldehyde and vapona are not a problem. Recommendations include conducting more intensive medical studies of the exposed workers and repeating the survey in about 5 years.

The Maximal C³ Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses.

PubMed

Michel, Christian J

2017-04-18

In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C 3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses. The method was based on the preferential occurrence of trinucleotides among the three frames at the gene population level. We extend here this definition at the gene level. This new statistical approach considers all the genes, i.e., of large and small lengths, with the same weight for searching the circular code X . As a consequence, the concept of circular code, in particular the reading frame retrieval, is directly associated to each gene. At the gene level, the circular code X is strengthened in the genes of bacteria, eukaryotes, plasmids, and viruses, and is now also identified in the genes of archaea. The genes of mitochondria and chloroplasts contain a subset of the circular code X . Finally, by studying viral genes, the circular code X was found in DNA genomes, RNA genomes, double-stranded genomes, and single-stranded genomes.

RecA family proteins in archaea: RadA and its cousins.

PubMed

Haldenby, Sam; White, Malcolm F; Allers, Thorsten

2009-02-01

Recombinases of the RecA family are essential for homologous recombination and underpin genome stability, by promoting the repair of double-stranded DNA breaks and the rescue of collapsed DNA replication forks. Until now, our understanding of homologous recombination has relied on studies of bacterial and eukaryotic model organisms. Archaea provide new opportunities to study how recombination operates in a lineage distinct from bacteria and eukaryotes. In the present paper, we focus on RadA, the archaeal RecA family recombinase, and its homologues in archaea and other domains. On the basis of phylogenetic analysis, we propose that a family of archaeal proteins with a single RecA domain, which are currently annotated as KaiC, be renamed aRadC.

A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea.

PubMed

Yan, Zhen; Wang, Mingyu; Ferry, James G

2017-02-07

Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO 2 -reducing methanogenic anaerobes (methanogens) from the domain Archaea Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F 420 (F 420 H 2 ) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F 420 H 2 and reduction of ferredoxin with the exergonic oxidation of F 420 H 2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting. Discovery of the archetype HdrA2B2C2 heterodisulfide reductase with categorically unique properties extends the understanding of this ancient family beyond CO 2

Diversity and stratification of archaea in a hypersaline microbial mat.

PubMed

Robertson, Charles E; Spear, John R; Harris, J Kirk; Pace, Norman R

2009-04-01

The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial mat below the fourth pond in the series identified an enormous diversity of bacteria in the mat, but archaea have received little attention. To determine the bulk contribution of archaeal phylotypes to the pond 4 study site, we determined the phylogenetic distribution of archaeal rRNA gene sequences in PCR libraries based on nominally universal primers. The ratios of bacterial/archaeal/eukaryotic rRNA genes, 90%/9%/1%, suggest that the archaeal contribution to the metabolic activities of the mat may be significant. To explore the distribution of archaea in the mat, sequences derived using archaeon-specific PCR primers were surveyed in 10 strata of the 6-cm-thick mat. The diversity of archaea overall was substantial albeit less than the diversity observed previously for bacteria. Archaeal diversity, mainly euryarchaeotes, was highest in the uppermost 2 to 3 mm of the mat and decreased rapidly with depth, where crenarchaeotes dominated. Only 3% of the sequences were specifically related to known organisms including methanogens. While some mat archaeal clades corresponded with known chemical gradients, others did not, which is likely explained by heretofore-unrecognized gradients. Some clades did not segregate by depth in the mat, indicating broad metabolic repertoires, undersampling, or both.

Protection of the vehicle cab environment against bacteria, fungi and endotoxins in composting facilities.

PubMed

Schlosser, O; Huyard, A; Rybacki, D; Do Quang, Z

2012-06-01

Microbial quality of air inside vehicle cabs is a major occupational health risk management issue in composting facilities. Large differences and discrepancies in protection factors between vehicles and between biological agents have been reported. This study aimed at estimating the mean protection efficiency of the vehicle cab environment against bioaerosols with higher precision. In-cab measurement results were also analysed to ascertain whether or not these protection systems reduce workers' exposure to tolerable levels. Five front-end loaders, one mobile mixer and two agricultural tractors pulling windrow turners were investigated. Four vehicles were fitted with a pressurisation and high efficiency particulate air (HEPA) filtration system. The four others were only equipped with pleated paper filter without pressurisation. Bacteria, fungi and endotoxins were measured in 72 pairs of air samples, simultaneously collected inside the cab and on the outside of the cab with a CIP 10-M sampler. A front-end loader, purchased a few weeks previously, fitted with a pressurisation and high efficiency particulate air (HEPA) filtration system, and with a clean cab, exhibited a mean protection efficiency of between 99.47% CI 95% [98.58-99.97%] and 99.91% [99.78-99.98%] depending on the biological agent. It is likely that the lower protection efficiency demonstrated in other vehicles was caused by penetration through the only moderately efficient filters, by the absence of pressurisation, by leakage in the filter-sealing system, and by re-suspension of particles which accumulated in dirty cabs. Mean protection efficiency in regards to bacteria and endotoxins ranged between 92.64% [81.87-97.89%] and 98.61% [97.41-99.38%], and between 92.68% [88.11-96.08%] and 98.43% [97.44-99.22%], respectively. The mean protection efficiency was the lowest when confronted with fungal spores, from 59.76% [4.19-90.75%] to 94.71% [91.07-97.37%]. The probability that in-cab exposure to fungi

Indigenous bacteria and fungi drive traditional kimoto sake fermentations.

PubMed

Bokulich, Nicholas A; Ohta, Moe; Lee, Morgan; Mills, David A

2014-09-01

Sake (Japanese rice wine) production is a complex, multistage process in which fermentation is performed by a succession of mixed fungi and bacteria. This study employed high-throughput rRNA marker gene sequencing, quantitative PCR, and terminal restriction fragment length polymorphism to characterize the bacterial and fungal communities of spontaneous sake production from koji to product as well as brewery equipment surfaces. Results demonstrate a dynamic microbial succession, with koji and early moto fermentations dominated by Bacillus, Staphylococcus, and Aspergillus flavus var. oryzae, succeeded by Lactobacillus spp. and Saccharomyces cerevisiae later in the fermentations. The microbiota driving these fermentations were also prevalent in the production environment, illustrating the reservoirs and routes for microbial contact in this traditional food fermentation. Interrogating the microbial consortia of production environments in parallel with food products is a valuable approach for understanding the complete ecology of food production systems and can be applied to any food system, leading to enlightened perspectives for process control and food safety. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Stress Genes and Proteins in the Archaea

PubMed Central

Macario, Alberto J. L.; Lange, Marianne; Ahring, Birgitte K.; De Macario, Everly Conway

1999-01-01

The field covered in this review is new; the first sequence of a gene encoding the molecular chaperone Hsp70 and the first description of a chaperonin in the archaea were reported in 1991. These findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular biology and biochemistry of life in extreme environments, and stress tolerance at the cellular and molecular levels. In the last 8 years, archaeal stress genes and proteins belonging to the families Hsp70, Hsp60 (chaperonins), Hsp40(DnaJ), and small heat-shock proteins (sHsp) have been studied. The hsp70(dnaK), hsp40(dnaJ), and grpE genes (the chaperone machine) have been sequenced in seven, four, and two species, respectively, but their expression has been examined in detail only in the mesophilic methanogen Methanosarcina mazei S-6. The proteins possess markers typical of bacterial homologs but none of the signatures distinctive of eukaryotes. In contrast, gene expression and transcription initiation signals and factors are of the eucaryal type, which suggests a hybrid archaeal-bacterial complexion for the Hsp70 system. Another remarkable feature is that several archaeal species in different phylogenetic branches do not have the gene hsp70(dnaK), an evolutionary puzzle that raises the important question of what replaces the product of this gene, Hsp70(DnaK), in protein biogenesis and refolding and for stress resistance. Although archaea are prokaryotes like bacteria, their Hsp60 (chaperonin) family is of type (group) II, similar to that of the eukaryotic cytosol; however, unlike the latter, which has several different members, the archaeal chaperonin system usually includes only two (in some species one and in others possibly three) related subunits of ∼60 kDa. These

Lipid-Based Immuno-Magnetic Separation of Archaea from a Mixed Community

NASA Astrophysics Data System (ADS)

Frickle, C. M.; Bailey, J.; Lloyd, K. G.; Shumaker, A.; Flood, B.

2014-12-01

Despite advancing techniques in microbiology, an estimated 98% of all microbial species on Earth have yet to be isolated in pure culture. Natural samples, once transferred to the lab, are commonly overgrown by "weed" species whose metabolic advantages enable them to monopolize available resources. Developing new methods for the isolation of thus-far uncultivable microorganisms would allow us to better understand their ecology, physiology and genetic potential. Physically separating target organisms from a mixed community is one approach that may allow enrichment and growth of the desired strain. Here we report on a novel method that uses known physiological variations between taxa, in this case membrane lipids, to segregate the desired organisms while keeping them alive and viable for reproduction. Magnetic antibodies bound to the molecule squalene, which is found in the cell membranes of certain archaea, but not bacteria, enable separation of archaea from bacteria in mixed samples. Viability of cells was tested by growing the separated fractions in batch culture. Efficacy and optimization of the antibody separation technique are being evaluated using qPCR and cell counts. Future work will apply this new separation technique to natural samples.

Application of real-time PCR to determination of combined effect of antibiotics on Bacteria, Methanogenic Archaea, Archaea in anaerobic sequencing batch reactors.

PubMed

Aydin, Sevcan; Ince, Bahar; Ince, Orhan

2015-06-01

This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) and sulfamethoxazole-tetracycline (ST) antibiotic combinations on the microbial community and examined the ways in which these antimicrobials impact the performance of anaerobic reactors. Quantitative real-time PCR was used to determine the effect that different antibiotic combinations had on the total and active Bacteria, Archae and Methanogenic Archae. Three primer sets that targeted metabolic genes encoding formylterahydrofolate synthetase, methyl-coenzyme M reductase and acetyl-coA synthetase were also used to determine the inhibition level on the mRNA expression of the homoacetogens, methanogens and specifically acetoclastic methanogens, respectively. These microorganisms play a vital role in the anaerobic degradation of organic waste and targeting these gene expressions offers operators or someone at a treatment plant the potential to control and the improve the anaerobic system. The results of the investigation revealed that acetogens have a competitive advantage over Archaea in the presence of ETS and ST combinations. Although the efficiency with which methane production takes place and the quantification of microbial populations in both the ETS and ST reactors decreased as antibiotic concentrations increased, the ETS batch reactor performed better than the ST batch reactor. According to the expression of genes results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the ETS and ST reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characterization of aerosolized bacteria and fungi from desert dust events in Mali, West Africa

USGS Publications Warehouse

Kellogg, C.A.; Griffin, Dale W.; Garrison, V.H.; Peak, K.K.; Royall, N.; Smith, R.R.; Shinn, E.A.

2004-01-01

Millions of metric tons of African desert dust blow across the Atlantic Ocean each year, blanketing the Caribbean and southeastern United States. Previous work in the Caribbean has shown that atmospheric samples collected during dust events contain living microbes, including plant and opportunistic human pathogens. To better understand the potential downwind public health and ecosystem effects of the dust microbes, it is important to characterize the source population. We describe 19 genera of bacteria and 3 genera of fungi isolated from air samples collected in Mali, a known source region for dust storms, and over which large dust storms travel.

Enrichment of Thermophilic Ammonia-Oxidizing Archaea from an Alkaline Hot Spring in the Great Basin, USA

NASA Astrophysics Data System (ADS)

Zhang, C.; Huang, Z.; Jiang, H.; Wiegel, J.; Li, W.; Dong, H.

2010-12-01

One of the major advances in the nitrogen cycle is the recent discovery of ammonia oxidation by archaea. While culture-independent studies have revealed occurrence of ammonia-oxidizing archaea (AOA) in nearly every surface niche on earth, most of these microorganisms have resisted isolation and so far only a few species have been identified. The Great Basin contains numerous hot springs, which are characterized by moderately high temperature (40-65 degree C) and circumneutral or alkaline pH. Unique thermophilic archaea have been identified based on molecular DNA and lipid biomarkers; some of which may be ammonia oxidizers. This study aims to isolate some of these archaea from a California hot spring that has pH around 9.0 and temperature around 42 degree C. Mat material was collected from the spring and transported on ice to the laboratory. A synthetic medium (SCM-5) was inoculated with the mat material and the culture was incubated under varying temperature (35-65 degree C) and pH (7.0-10.0) conditions using antibiotics to suppress bacterial growth. Growth of the culture was monitored by microscopy, decrease in ammonium and increase in nitrite, and increases in Crenarchaeota and AOA abundances over time. Clone libraries were constructed to compare archaeal community structures before and after the enrichment experiment. Temperature and pH profiles indicated that the culture grew optimally at pH 9.0 and temperature 45 degree C, which are consistent with the geochemical conditions of the natural environment. Phylogenetic analysis showed that the final OTU was distantly related to all known hyperthermophilic archaea. Analysis of the amoA genes showed two OTUs in the final culture; one of them was closely related to Candidatus Nitrososphaera gargensis. However, the enrichment culture always contained bacteria and attempts to separate them from archaea have failed. This highlights the difficulty in bringing AOA into pure culture and suggests that some of the AOA may

Mineral-Association and Activity of Bacteria and Archaea in the Deep Subsurface South Pacific Gyre Sediment

NASA Astrophysics Data System (ADS)

Steele, J. A.; Dekas, A. E.; Harrison, B. K.; Morono, Y.; Inagaki, F.; Ziebis, W.; Orphan, V. J.

2012-12-01

Although the subsurface biosphere is now recognized as an important reservoir of life on our planet, until recently the microbial community beneath open-ocean oligotrophic gyres (making up the majority of the seafloor) has just begun to be studied in detail. IODP Expedition 329 and the KNOX-022RR site survey cruise have taken some of the first steps at characterizing the microbial community beneath the South Pacific Gyre, a region with low organic carbon burial rates (10-8 and 10-10 moles C cm-1 yr-1), deep oxygen penetration (sediments are oxidized to the basement), and low prokaryotic cell counts (106 cells cm-3 to <103 cells cm-3). In these sediments, the dominant fraction of organic carbon may be aggregated or adsorbed to minerals, suggesting that microbes that are able to grow on the minerals may create potential "hotspots" of activity. In this study, we performed magnetic separation on oligotrophic sediment samples and examined the bacterial and archaeal communities using 16S rRNA tag sequencing. To determine if the mineral-associated cells were autotrophic and/or utilizing nitrate, we performed long-term (20 month) incubations with 13CO2 and 15NO3- from sediment taken at depths ~2-70 mbsf beneath the oligotrophic gyre and outside of the oligotrophic gyre (IODP Exp. 329 stations U1368-U1371). Subsequently we used the DNA stain SYBR Green I, and CARD-FISH-NanoSIMS to identify cells which were actively taking up the isotopic label. We then used SEM-EDS to identify the mineral particle composition. Preliminary results found the magnetic fraction in oligotrophic sediment (KNOX-022RR station SPG-5) from 1.2-2.6 mbsf showed a greater diversity of both bacteria and archaea. OTUs from Chloroflexi groups SO85 and SAR202 were dominant in the magnetic fraction. Firmicutes, Bacteroidetes, δ-Proteobacteria, Verrucomicrobia, Deferribacteres, WS3, OP10, and OP1 OTUs were found only in the magnetic fraction. Crenarchaeal OTUs from Marine Benthic Group B and Marine Group I

Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria.

PubMed

Sauder, Laura A; Ross, Ashley A; Neufeld, Josh D

2016-04-01

Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested onNitrosopumilus maritimus, two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representative Nitrosomonas europaea All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Diversity and enzyme-producing activity of culturable halophilic bacteria in Daishan Saltern of East China].

PubMed

Yang, Dan-Dan; Li, Qian; Huang, Jing-Jing; Chen, Min

2012-11-01

Soil and saline water samples were collected from the Daishan Saltern of East China, and the halophilic bacteria were isolated and cultured by using selective media, aimed to investigate the diversity and enzyme-producing activity of culturable halophilic bacteria in saltern environment. A total of 181 strains were isolated by culture-dependent method. Specific primers were used to amplify the 16S rRNA gene of bacteria and archaea. The operation taxonomy units (OTUs) were determined by ARDRA method, and the representative strain of each OTU was sequenced. The phylogenetic position of all the isolated strains was determined by 16S rRNA sequencing. The results showed that the isolated 181 strains displayed 21 operational taxonomic units (OTUs), of which, 12 OTUs belonged to halophilic bacteria, and the others belonged to halophilic archaea. Phylogenetic analysis indicated that there were 7 genera presented among the halophilic bacteria group, and 4 genera presented among the halophilic archaea group. The dominant halophilic strains were of Halomonas and Haloarcula, with 46.8% in halophilic bacteria and 49.1% in halophilic archaea group, respectively. Enzyme-producing analysis indicated that most strains displayed enzyme-producing activity, including the activities of producing amylase, proteinase and lipase, and the dominant strains capable of enzyme-producing were of Haloarcula. Our results showed that in the environment of Daishan Saltern, there existed a higher diversity of halophilic bacteria, being a source sink for screening enzyme-producing bacterial strains.

The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses

PubMed Central

Michel, Christian J.

2017-01-01

In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses. The method was based on the preferential occurrence of trinucleotides among the three frames at the gene population level. We extend here this definition at the gene level. This new statistical approach considers all the genes, i.e., of large and small lengths, with the same weight for searching the circular code X. As a consequence, the concept of circular code, in particular the reading frame retrieval, is directly associated to each gene. At the gene level, the circular code X is strengthened in the genes of bacteria, eukaryotes, plasmids, and viruses, and is now also identified in the genes of archaea. The genes of mitochondria and chloroplasts contain a subset of the circular code X. Finally, by studying viral genes, the circular code X was found in DNA genomes, RNA genomes, double-stranded genomes, and single-stranded genomes. PMID:28420220

Metabolism of halophilic archaea

PubMed Central

Falb, Michaela; Müller, Kerstin; Königsmaier, Lisa; Oberwinkler, Tanja; Horn, Patrick; von Gronau, Susanne; Gonzalez, Orland; Pfeiffer, Friedhelm; Bornberg-Bauer, Erich

2008-01-01

In spite of their common hypersaline environment, halophilic archaea are surprisingly different in their nutritional demands and metabolic pathways. The metabolic diversity of halophilic archaea was investigated at the genomic level through systematic metabolic reconstruction and comparative analysis of four completely sequenced species: Halobacterium salinarum, Haloarcula marismortui, Haloquadratum walsbyi, and the haloalkaliphile Natronomonas pharaonis. The comparative study reveals different sets of enzyme genes amongst halophilic archaea, e.g. in glycerol degradation, pentose metabolism, and folate synthesis. The carefully assessed metabolic data represent a reliable resource for future system biology approaches as it also links to current experimental data on (halo)archaea from the literature. Electronic supplementary material The online version of this article (doi:10.1007/s00792-008-0138-x) contains supplementary material, which is available to authorized users. PMID:18278431

Improvement of the soil nitrogen content and maize growth by earthworms and arbuscular mycorrhizal fungi in soils polluted by oxytetracycline.

PubMed

Cao, Jia; Wang, Chong; Ji, Dingge

2016-11-15

Interactions between earthworms (Eisenia fetida) and arbuscular mycorrhizal fungi (Rhizophagus intraradices, AM fungi) have been suggested to improve the maize nitrogen (N) content and biomass and were studied in soils polluted by oxytetracycline (OTC). Maize was planted and amended with AMF and/or earthworms (E) in the soil with low (1mgkg(-1) soil DM) or high (100mgkg(-1) soil DM) amounts of OTC pollution in comparison to soil without OTC. The root colonization, shoot and root biomass, shoot and root N contents, soil nitrogen forms, ammonia-oxidizing bacteria (AOB) and archaea (AOA) were measured at harvest. The results indicated that OTC decreased maize shoot and root biomass (p<0.05) by mediating the soil urease activity and AOB and AOA abundance, which resulted in a lower N availability for maize roots and shoots. There was a significant interaction between earthworms and AM fungi on the urease activity in soil polluted by OTC (p<0.05). Adding earthworms or AM fungi could increase the maize biomass and N content (p<0.05) in OTC polluted soil by increasing the urease activity and relieving the stress from OTC on the soil N cycle. AM fungi and earthworms interactively increased maize shoot and root biomass (p<0.05) in the OTC polluted soils through their regulation of the urease activity and the abundance of ammonia oxidizers, resulting in different soil NH4(+)-N and NO3(-)-N contents, which may contribute to the N content of maize shoots and roots. Earthworms and AM fungi could be used as an efficient method to relieve the OTC stress in agro-ecosystems. Copyright © 2016 Elsevier B.V. All rights reserved.

Mysterious Mycorrhizae? A Field Trip & Classroom Experiment to Demystify the Symbioses Formed between Plants & Fungi

ERIC Educational Resources Information Center

Johnson, Nancy C.; Chaudhary, V. Bala; Hoeksema, Jason D.; Moore, John C.; Pringle, Anne; Umbanhowar, James A.; Wilson, Gail W. T.

2009-01-01

Biology curricula cover fungi in units on bacteria, protists, and primitive plants, but fungi are more closely related to animals than to bacteria or plants. Like animals, fungi are heterotrophs and cannot create their own food; but, like plants, fungi have cell walls, and are for the most part immobile. Most species of fungi have a filamentous…

Effect of inorganic nutrients on relative contributions of fungi and bacteria to carbon flow from submerged decomposing leaf litter

Treesearch

Vladislav Gulis; Keller Suberkropp

2003-01-01

The relative contributions of fungi and bacteria to carbon flow from submerged decaying plant litter at different levels of inorganic nutrients (N and P) were studied. We estimated leaf mass loss, fungal and bacterial biomass and production, and microbial respiration and constructed partial carbon budgets for red maple leaf disks precolonized in a stream and then...

Nonspecific Adherence by Actinobacillus actinomycetemcomitans Requires Genes Widespread in Bacteria and Archaea

PubMed Central

Kachlany, Scott C.; Planet, Paul J.; Bhattacharjee, Mrinal K.; Kollia, Evyenia; DeSalle, Rob; Fine, Daniel H.; Figurski, David H.

2000-01-01

The gram-negative coccobacillus, Actinobacillus actinomycetemcomitans, is the putative agent for localized juvenile periodontitis, a particularly destructive form of periodontal disease in adolescents. This bacterium has also been isolated from a variety of other infections, notably endocarditis. Fresh clinical isolates of A. actinomycetemcomitans form tenacious biofilms, a property likely to be critical for colonization of teeth and other surfaces. Here we report the identification of a locus of seven genes required for nonspecific adherence of A. actinomycetemcomitans to surfaces. The recently developed transposon IS903φkan was used to isolate mutants of the rough clinical isolate CU1000 that are defective in tight adherence to surfaces (Tad−). Unlike wild-type cells, Tad− mutant cells adhere poorly to surfaces, fail to form large autoaggregates, and lack long, bundled fibrils. Nucleotide sequencing and genetic complementation analysis revealed a 6.7-kb region of the genome with seven adjacent genes (tadABCDEFG) required for tight adherence. The predicted TadA polypeptide is similar to VirB11, an ATPase involved in macromolecular transport. The predicted amino acid sequences of the other Tad polypeptides indicate membrane localization but no obvious functions. We suggest that the tad genes are involved in secretion of factors required for tight adherence of A. actinomycetemcomitans. Remarkably, complete and highly conserved tad gene clusters are present in the genomes of the bubonic plague bacillus Yersinia pestis and the human and animal pathogen Pasteurella multocida. Partial tad loci also occur in strikingly diverse Bacteria and Archaea. Our results show that the tad genes are required for tight adherence of A. actinomycetemcomitans to surfaces and are therefore likely to be essential for colonization and pathogenesis. The occurrence of similar genes in a wide array of microorganisms indicates that they have important functions. We propose that tad

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

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

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

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

Molecular Tools for the Detection of Nitrogen Cycling Archaea

PubMed Central

Rusch, Antje

2013-01-01

Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic capacities, which sets them up for potentially major roles in the biogeochemistry of their ecosystems. The detection, characterization, and quantification of archaeal functions in mixed communities require Archaea-specific primers or probes for the corresponding metabolic genes. Five pairs of degenerate primers were designed to target archaeal genes encoding key enzymes of nitrogen cycling: nitrite reductases NirA and NirB, nitrous oxide reductase (NosZ), nitrogenase reductase (NifH), and nitrate reductases NapA/NarG. Sensitivity towards their archaeal target gene, phylogenetic specificity, and gene specificity were evaluated in silico and in vitro. Owing to their moderate sensitivity/coverage, the novel nirB-targeted primers are suitable for pure culture studies only. The nirA-targeted primers showed sufficient sensitivity and phylogenetic specificity, but poor gene specificity. The primers designed for amplification of archaeal nosZ performed well in all 3 criteria; their discrimination against bacterial homologs appears to be weakened when Archaea are strongly outnumbered by bacteria in a mixed community. The novel nifH-targeted primers showed high sensitivity and gene specificity, but failed to discriminate against bacterial homologs. Despite limitations, 4 of the new primer pairs are suitable tools in several molecular methods applied in archaeal ecology. PMID:23365509

Gibberellin biosynthesis and metabolism: A convergent route for plants, fungi and bacteria.

PubMed

Salazar-Cerezo, Sonia; Martínez-Montiel, Nancy; García-Sánchez, Jenny; Pérez-Y-Terrón, Rocío; Martínez-Contreras, Rebeca D

2018-03-01

Gibberellins (GAs) are natural complex biomolecules initially identified as secondary metabolites in the fungus Gibberella fujikuroi with strong implications in plant physiology. GAs have been identified in different fungal and bacterial species, in some cases related to virulence, but the full understanding of the role of these metabolites in the different organisms would need additional investigation. In this review, we summarize the current evidence regarding a common pathway for GA synthesis in fungi, bacteria and plant from the genes depicted as part of the GA production cluster to the enzymes responsible for the catalytic transformations and the biosynthetical routes involved. Moreover, we present the relationship between these observations and the biotechnological applications of GAs in plants, which has shown an enormous commercial impact. Copyright © 2018 Elsevier GmbH. All rights reserved.

Biotransformation of chlorpyrifos and endosulfan by bacteria and fungi.

PubMed

Supreeth, M; Raju, N S

2017-08-01

Large quantities of pesticides are applied on crops to protect them from pests in modern agricultural practices around the globe. The two insecticides, chlorpyrifos, belonging to the organophosphorous group and endosulfan, belonging to the organochlorine group, are vastly used insecticides on agricultural crops in the last three decades. Hence, both these insecticides are ubiquitous in the environment. Once applied, these two insecticides undergo transformation in the environment either biologically or non-biologically. Microbial degradation has been considered a safe and cost-effective method for removing contaminants from the environment. Both the insecticides have been subjected to biodegradation studies using various bacteria and fungi by the researchers. Here, in this review, we report on biotransformed products formed during the course of biodegradation of these two insecticides and also discuss about the aftereffects of their transformed metabolites. This is important, because the primary biotransformed metabolites 3,5,6, trichloro-2-pyridinol of chlorpyrifos and endosulfan sulfate of endosulfan are toxic as their parent compounds and are noxious to variety of organisms. In conclusion, it is recommended to obtain microbial cultures capable of mineralizing pesticides completely without formation of any such toxic by-product before adopting bioremediation or bioaugmentation technology.

Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil.

PubMed

Sher, Yonatan; Ronen, Zeev; Nejidat, Ali

2016-08-01

Ammonia-oxidizing archaea and bacteria (AOA, AOB) catalyze the first and rate-limiting step of nitrification. To examine their differential responses to the wetting of dry and salty arid soil, AOA and AOB amoA genes (encoding subunit A of the ammonia monooxygenase) and transcripts were enumerated in dry (summer) and wet (after the first rainfall) soil under the canopy of halophytic shrubs and between the shrubs. AOA and AOB were more abundant under shrub canopies than between shrubs in both the dry and wetted soil. Soil wetting caused a significant decrease in AOB abundance under the canopy and an increase of AOA between the shrubs. The abundance of the archaeal amoA gene transcript was similar for both the wet and dry soil, and the transcript-to-gene ratios were < 1 independent of niche or water content. In contrast, the bacterial amoA transcript-to-gene ratios were between 78 and 514. The lowest ratio was in dry soil under the canopy and the highest in the soil between the shrubs. The results suggest that the AOA are more resilient to stress conditions and maintain a basic activity in arid ecosystems, while the AOB are more responsive to changes in the biotic and abiotic conditions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Archaea--timeline of the third domain.

PubMed

Cavicchioli, Ricardo

2011-01-01

The Archaea evolved as one of the three primary lineages several billion years ago, but the first archaea to be discovered were described in the scientific literature about 130 years ago. Moreover, the Archaea were formally proposed as the third domain of life only 20 years ago. Over this very short period of investigative history, the scientific community has learned many remarkable things about the Archaea--their unique cellular components and pathways, their abundance and critical function in diverse natural environments, and their quintessential role in shaping the evolutionary path of life on Earth. This Review charts the 'archaea movement', from its genesis through to key findings that, when viewed together, illustrate just how strongly the field has built on new knowledge to advance our understanding not only of the Archaea, but of biology as a whole.

Vascular plants mediate the effects of aridity and soil properties on ammonia-oxidizing bacteria and archaea.

PubMed

Delgado-Baquerizo, Manuel; Gallardo, Antonio; Wallenstein, Matthew D; Maestre, Fernando T

2013-08-01

An integrated perspective of the most important factors driving the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in natural ecosystems is lacking, especially in drylands. We evaluated how different climatic, abiotic, and nutrient-related factors determine AOA and AOB abundance in bare and vegetated microsites from grasslands throughout the Mediterranean Basin. We found a strong negative relationship between the abundance of AOA genes and soil fertility (availability of C, N, and P). Aridity and other abiotic factors (pH, sand content, and electrical conductivity) were more important than soil fertility in modulating the AOA/AOB ratio. AOB were more abundant under vegetated microsites, while AOA, highly resistant to stressful conditions, were more abundant in bare ground areas. These results suggest that AOA may carry out nitrification in less fertile microsites, while AOB predominate under more fertile conditions. Our results indicate that the influence of aridity and pH on the relative dominance of AOA and AOB genes is ultimately determined by local-scale environmental changes promoted by perennial vegetation. Thus, in spatially heterogeneous ecosystems such as drylands, there is a mutual exclusion and niche division between these microorganisms, suggesting that they may be functionally complementary. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Altered Carbohydrates Allocation by Associated Bacteria-fungi Interactions in a Bark Beetle-microbe Symbiosis

PubMed Central

Zhou, Fangyuan; Lou, Qiaozhe; Wang, Bo; Xu, Letian; Cheng, Chihang; Lu, Min; Sun, Jianghua

2016-01-01

Insect-microbe interaction is a key area of research in multiplayer symbiosis, yet little is known about the role of microbe-microbe interactions in insect-microbe symbioses. The red turpentine beetle (RTB) has destroyed millions of healthy pines in China and forms context-dependent relationships with associated fungi. The adult-associated fungus Leptographium procerum have played key roles in RTB colonization. However, common fungal associates (L. procerum and Ophiostoma minus) with RTB larvae compete for carbohydrates. Here, we report that dominant bacteria associated with RTB larvae buffer the competition by inhibiting the growth and D-glucose consumption of O. minus. However, they didn’t inhibit the growth of L. procerum and forced this fungus to consume D-pinitol before consuming D-glucose, even though D-glucose was available and a better carbon source not only for L. procerum but also for RTB larvae and associated bacteria. This suggests the most frequently isolated bacteria associated with RTB larvae could affect fungal growth and the sequence of carbohydrate consumption. Thus, this regulates carbohydrate allocation in the RTB larva-microbe community, which may in turn benefit RTB larvae development. We also discuss the mechanism of carbohydrate allocation in the RTB larva-microbe community, and its potential contribution to the maintenance of a symbiotic community. PMID:26839264

Antagonistic and synergistic toxic effects of Pb and Cd in a simple food chain: nematodes feeding on bacteria and fungi

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

Doelman, P.; Nieboer, G.; Schrooten, J.

1984-06-01

Soil pollution with heavy metals may affect the functioning of the soil biota by inhibiting the decomposition of organic matter and may also influence food chains. This paper presents the results of an investigation on how the reproduction of soil nematodes can be influenced by feeding on bacteria or fungi contaminated with lead and cadmium.

Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii.

PubMed

Taha; Siddiqui, K S; Campanaro, S; Najnin, T; Deshpande, N; Williams, T J; Aldrich-Wright, J; Wilkins, M; Curmi, P M G; Cavicchioli, R

2016-09-01

TRAM domain proteins present in Archaea and Bacteria have a β-barrel shape with anti-parallel β-sheets that form a nucleic acid binding surface; a structure also present in cold shock proteins (Csps). Aside from protein structures, experimental data defining the function of TRAM domains is lacking. Here, we explore the possible functional properties of a single TRAM domain protein, Ctr3 (cold-responsive TRAM domain protein 3) from the Antarctic archaeon Methanococcoides burtonii that has increased abundance during low temperature growth. Ribonucleic acid (RNA) bound by Ctr3 in vitro was determined using RNA-seq. Ctr3-bound M. burtonii RNA with a preference for transfer (t)RNA and 5S ribosomal RNA, and a potential binding motif was identified. In tRNA, the motif represented the C loop; a region that is conserved in tRNA from all domains of life and appears to be solvent exposed, potentially providing access for Ctr3 to bind. Ctr3 and Csps are structurally similar and are both inferred to function in low temperature translation. The broad representation of single TRAM domain proteins within Archaea compared with their apparent absence in Bacteria, and scarcity of Csps in Archaea but prevalence in Bacteria, suggests they represent distinct evolutionary lineages of functionally equivalent RNA-binding proteins. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Biological Control of Aquatic Plants with Pathogenic Fungi

DTIC Science & Technology

1981-01-01

reverse side II necoosary and Ident•l•y by block number) Aquatic plant control Fungi Aquatic plants Pathogenic fungi Biological control Waterhyacinths...BACTERIA ............. ................. D1 2 1 BIOTIGICAL CONTROL OF AQUATIC PLANTS WITH PATHOGENIC FUNGI PART I: INTRODUCTION 1. Plant pathogens have...first noted in Florida. 13. In December of 1973, Dr. K. E. Ctnway isolated a Cercospora species, along with many other fungi , from declining

Extremely Halophilic Bacteria in Crystallizer Ponds from Solar Salterns

PubMed Central

Antón, Josefa; Rosselló-Mora, Ramón; Rodríguez-Valera, Francisco; Amann, Rudolf

2000-01-01

It is generally assumed that hypersaline environments with sodium chloride concentrations close to saturation are dominated by halophilic members of the domain Archaea, while Bacteria are not considered to be relevant in this kind of environment. Here, we report the high abundance and growth of a new group of hitherto-uncultured Bacteria in crystallizer ponds (salinity, from 30 to 37%) from multipond solar salterns. In the present study, these Bacteria constituted from 5 to 25% of the total prokaryotic community and were affiliated with the Cytophaga-Flavobacterium-Bacteroides phylum. Growth was demonstrated in saturated NaCl. A provisional classification of this new bacterial group as “Candidatus Salinibacter gen. nov.” is proposed. The perception that Archaea are the only ecologically relevant prokaryotes in hypersaline aquatic environments should be revised. PMID:10877805

Antibiotic management of lung infections in cystic fibrosis. II. Nontuberculous mycobacteria, anaerobic bacteria, and fungi.

PubMed

Chmiel, James F; Aksamit, Timothy R; Chotirmall, Sanjay H; Dasenbrook, Elliott C; Elborn, J Stuart; LiPuma, John J; Ranganathan, Sarath C; Waters, Valerie J; Ratjen, Felix A

2014-10-01

Airway infections are a key component of cystic fibrosis (CF) lung disease. Whereas the approach to common pathogens such as Pseudomonas aeruginosa is guided by a significant body of evidence, other infections often pose a considerable challenge to treating physicians. In Part I of this series on the antibiotic management of difficult lung infections, we discussed bacterial organisms including methicillin-resistant Staphylococcus aureus, gram-negative bacterial infections, and treatment of multiple bacterial pathogens. Here, we summarize the approach to infections with nontuberculous mycobacteria, anaerobic bacteria, and fungi. Nontuberculous mycobacteria can significantly impact the course of lung disease in patients with CF, but differentiation between colonization and infection is difficult clinically as coinfection with other micro-organisms is common. Treatment consists of different classes of antibiotics, varies in intensity, and is best guided by a team of specialized clinicians and microbiologists. The ability of anaerobic bacteria to contribute to CF lung disease is less clear, even though clinical relevance has been reported in individual patients. Anaerobes detected in CF sputum are often resistant to multiple drugs, and treatment has not yet been shown to positively affect patient outcome. Fungi have gained significant interest as potential CF pathogens. Although the role of Candida is largely unclear, there is mounting evidence that Scedosporium species and Aspergillus fumigatus, beyond the classical presentation of allergic bronchopulmonary aspergillosis, can be relevant in patients with CF and treatment should be considered. At present, however there remains limited information on how best to select patients who could benefit from antifungal therapy.

Antibiotic Management of Lung Infections in Cystic Fibrosis. II. Nontuberculous Mycobacteria, Anaerobic Bacteria, and Fungi

PubMed Central

Aksamit, Timothy R.; Chotirmall, Sanjay H.; Dasenbrook, Elliott C.; Elborn, J. Stuart; LiPuma, John J.; Ranganathan, Sarath C.; Waters, Valerie J.; Ratjen, Felix A.

2014-01-01

Airway infections are a key component of cystic fibrosis (CF) lung disease. Whereas the approach to common pathogens such as Pseudomonas aeruginosa is guided by a significant body of evidence, other infections often pose a considerable challenge to treating physicians. In Part I of this series on the antibiotic management of difficult lung infections, we discussed bacterial organisms including methicillin-resistant Staphylococcus aureus, gram-negative bacterial infections, and treatment of multiple bacterial pathogens. Here, we summarize the approach to infections with nontuberculous mycobacteria, anaerobic bacteria, and fungi. Nontuberculous mycobacteria can significantly impact the course of lung disease in patients with CF, but differentiation between colonization and infection is difficult clinically as coinfection with other micro-organisms is common. Treatment consists of different classes of antibiotics, varies in intensity, and is best guided by a team of specialized clinicians and microbiologists. The ability of anaerobic bacteria to contribute to CF lung disease is less clear, even though clinical relevance has been reported in individual patients. Anaerobes detected in CF sputum are often resistant to multiple drugs, and treatment has not yet been shown to positively affect patient outcome. Fungi have gained significant interest as potential CF pathogens. Although the role of Candida is largely unclear, there is mounting evidence that Scedosporium species and Aspergillus fumigatus, beyond the classical presentation of allergic bronchopulmonary aspergillosis, can be relevant in patients with CF and treatment should be considered. At present, however there remains limited information on how best to select patients who could benefit from antifungal therapy. PMID:25167882

Archaea were widespread in sediments of the Messinian Salinity Crisis

NASA Astrophysics Data System (ADS)

Birgel, Daniel; Peckmann, Jörn

2015-04-01

sulfate reduction. One of the important processes fuelling authigenesis was microbial oxidation of methane. Lipid biomarker patterns reveal that a consortium of methanotrophic archaea and sulfate-reducing bacteria consumed methane in anoxic and hypersaline environments. Halophilic archaea other than those archaea involved in methane oxidation have been present in the depositional environment as well. This as to yet still somewhat random selection of examples provides evidence for the great diversity of environmental settings created during the MSC and the abundance of archaea in these environments, calling for more work on the geomicrobiology of the unrivaled archive of dramatic paleooceanographic change during the MSC.

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology.

PubMed

Adam, Panagiotis S; Borrel, Guillaume; Brochier-Armanet, Céline; Gribaldo, Simonetta

2017-11-01

The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.

Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island.

PubMed

Antranikian, Garabed; Suleiman, Marcel; Schäfers, Christian; Adams, Michael W W; Bartolucci, Simonetta; Blamey, Jenny M; Birkeland, Nils-Kåre; Bonch-Osmolovskaya, Elizaveta; da Costa, Milton S; Cowan, Don; Danson, Michael; Forterre, Patrick; Kelly, Robert; Ishino, Yoshizumi; Littlechild, Jennifer; Moracci, Marco; Noll, Kenneth; Oshima, Tairo; Robb, Frank; Rossi, Mosè; Santos, Helena; Schönheit, Peter; Sterner, Reinhard; Thauer, Rudolf; Thomm, Michael; Wiegel, Jürgen; Stetter, Karl Otto

2017-07-01

To obtain new insights into community compositions of hyperthermophilic microorganisms, defined as having optimal growth temperatures of 80 °C and above, sediment and water samples were taken from two shallow marine hydrothermal vents (I and II) with temperatures of 100 °C at Vulcano Island, Italy. A combinatorial approach of denaturant gradient gel electrophoresis (DGGE) and metagenomic sequencing was used for microbial community analyses of the samples. In addition, enrichment cultures, growing anaerobically on selected polysaccharides such as starch and cellulose, were also analyzed by the combinatorial approach. Our results showed a high abundance of hyperthermophilic archaea, especially in sample II, and a comparable diverse archaeal community composition in both samples. In particular, the strains of the hyperthermophilic anaerobic genera Staphylothermus and Thermococcus, and strains of the aerobic hyperthermophilic genus Aeropyrum, were abundant. Regarding the bacterial community, ε-Proteobacteria, especially the genera Sulfurimonas and Sulfurovum, were highly abundant. The microbial diversity of the enrichment cultures changed significantly by showing a high dominance of archaea, particularly the genera Thermococcus and Palaeococcus, depending on the carbon source and the selected temperature.

Impacts of flood damage on airborne bacteria and fungi in homes after the 2013 Colorado Front Range flood.

PubMed

Emerson, Joanne B; Keady, Patricia B; Brewer, Tess E; Clements, Nicholas; Morgan, Emily E; Awerbuch, Jonathan; Miller, Shelly L; Fierer, Noah

2015-03-03

Flood-damaged homes typically have elevated microbial loads, and their occupants have an increased incidence of allergies, asthma, and other respiratory ailments, yet the microbial communities in these homes remain under-studied. Using culture-independent approaches, we characterized bacterial and fungal communities in homes in Boulder, CO, USA 2-3 months after the historic September, 2013 flooding event. We collected passive air samples from basements in 50 homes (36 flood-damaged, 14 non-flooded), and we sequenced the bacterial 16S rRNA gene (V4-V5 region) and the fungal ITS1 region from these samples for community analyses. Quantitative PCR was used to estimate the abundances of bacteria and fungi in the passive air samples. Results indicate significant differences in bacterial and fungal community composition between flooded and non-flooded homes. Fungal abundances were estimated to be three times higher in flooded, relative to non-flooded homes, but there were no significant differences in bacterial abundances. Penicillium (fungi) and Pseudomonadaceae and Enterobacteriaceae (bacteria) were among the most abundant taxa in flooded homes. Our results suggest that bacterial and fungal communities continue to be affected by flooding, even after relative humidity has returned to baseline levels and remediation has removed any visible evidence of flood damage.

Differences in the sensitivity of fungi and bacteria to season and invertebrates affect leaf litter decomposition in a Mediterranean stream.

PubMed

Mora-Gómez, Juanita; Elosegi, Arturo; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Romaní, Anna M

2016-08-01

Microorganisms are key drivers of leaf litter decomposition; however, the mechanisms underlying the dynamics of different microbial groups are poorly understood. We investigated the effects of seasonal variation and invertebrates on fungal and bacterial dynamics, and on leaf litter decomposition. We followed the decomposition of Populus nigra litter in a Mediterranean stream through an annual cycle, using fine and coarse mesh bags. Irrespective of the season, microbial decomposition followed two stages. Initially, bacterial contribution to total microbial biomass was higher compared to later stages, and it was related to disaccharide and lignin degradation; in a later stage, bacteria were less important and were associated with hemicellulose and cellulose degradation, while fungi were related to lignin decomposition. The relevance of microbial groups in decomposition differed among seasons: fungi were more important in spring, whereas in summer, water quality changes seemed to favour bacteria and slowed down lignin and hemicellulose degradation. Invertebrates influenced litter-associated microbial assemblages (especially bacteria), stimulated enzyme efficiencies and reduced fungal biomass. We conclude that bacterial and fungal assemblages play distinctive roles in microbial decomposition and differ in their sensitivity to environmental changes, ultimately affecting litter decomposition, which might be particularly relevant in highly seasonal ecosystems, such as intermittent streams. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Anaerobic Fungi: A Potential Source of Biological H2 in the Oceanic Crust

PubMed Central

Ivarsson, Magnus; Schnürer, Anna; Bengtson, Stefan; Neubeck, Anna

2016-01-01

The recent recognition of fungi in the oceanic igneous crust challenges the understanding of this environment as being exclusively prokaryotic and forces reconsiderations of the ecology of the deep biosphere. Anoxic provinces in the igneous crust are abundant and increase with age and depth of the crust. The presence of anaerobic fungi in deep-sea sediments and on the seafloor introduces a type of organism with attributes of geobiological significance not previously accounted for. Anaerobic fungi are best known from the rumen of herbivores where they produce molecular hydrogen, which in turn stimulates the growth of methanogens. The symbiotic cooperation between anaerobic fungi and methanogens in the rumen enhance the metabolic rate and growth of both. Methanogens and other hydrogen-consuming anaerobic archaea are known from subseafloor basalt; however, the abiotic production of hydrogen is questioned to be sufficient to support such communities. Alternatively, biologically produced hydrogen could serve as a continuous source. Here, we propose anaerobic fungi as a source of bioavailable hydrogen in the oceanic crust, and a close interplay between anaerobic fungi and hydrogen-driven prokaryotes. PMID:27433154

Emission of bacteria and fungi in the air from wastewater treatment plants - a review.

PubMed

Korzeniewska, Ewa

2011-01-01

An increase in global population, coupled with intensive development of industry and agriculture, has resulted in the generation and accumulation of large amounts of waste around the world. The spread of pathogenic microorganisms, endotoxins, odours and dust particles in the air is an inevitable consequence of waste production and waste management. Thus, the risk of infections associated with wastewater treatment plants (WWTPs) has become of a particular importance in recent decades. Sewage and unstable sludge contain various pathogens such as viruses, bacteria, and human and animal parasites. These microorganisms can be transmitted to the ambient air in wastewater droplets, which are generated during aeration or mechanical moving of the sewage. Bioaerosols generated during wastewater treatment may therefore pose a potential health hazard to workers of these plants or to habitants of their surroundings. The degree of human exposure to airborne bacteria, fungi, endotoxin and other allergens may vary significantly depending upon the type and the capacity of a plant, kind of the facilities, performed activities and meteorological conditions.

Evaluation of support materials for the immobilization of sulfate-reducing bacteria and methanogenic archaea.

PubMed

Silva, A J; Hirasawa, J S; Varesche, M B; Foresti, E; Zaiat, M

2006-04-01

This paper reports on the adhesion of sulfate-reducing bacteria (SRB) and methanogenic archaea on polyurethane foam (PU), vegetal carbon (VC), low-density polyethylene (PE) and alumina-based ceramics (CE). Anaerobic differential reactors fed with a sulfate-rich synthetic wastewater were used to evaluate the formation of a biofilm. The PU presented the highest specific biomass concentration throughout the experiment, achieving 872 mg TVS/g support, while 84 mg TVS/g support was the maximum value obtained for the other materials. FISH results showed that bacterial cells rather than archaeal cells were predominant on the biofilms. These cells, detected with EUB338 probe, accounted for 76.2% (+/-1.6%), 79.7% (+/-1.3%), 84.4% (+/-1.4%) and 60.2% (+/-1.0%) in PU, VC, PE and CE, respectively, of the 4'6-diamidino-2-phenylindole (DAPI)-stained cells. From these percentages, 44.8% (+/-2.1%), 55.4% (+/-1.2%), 32.7% (+/-1.4%) and 18.1% (+/-1.1%), respectively, represented the SRB group. Archaeal cells, detected with ARC915 probe, accounted for 33.1% (+/-1.6%), 25.4% (+/-1.3%), 22.6% (+/-1.1%) and 41.9% (+/-1.0%) in PU, VC, PE and CE, respectively, of the DAPI-stained cells. Sulfate reduction efficiencies of 39% and 45% and mean chemical oxygen demand (COD) removal efficiencies of 86% and 90% were achieved for PU and VC, respectively. The other two supports, PE and CE, provided mean COD removal efficiencies of 84% and 86%, respectively. However, no sulfate reduction was observed with these supports.

Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials

PubMed Central

Taylor, Anne E; Zeglin, Lydia H; Wanzek, Thomas A; Myrold, David D; Bottomley, Peter J

2012-01-01

It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a 2-year wheat/fallow cycle, and adjacent uncultivated long-term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (P⩽0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomena: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH4+-availability that exist in the field. PMID:22695861

Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials.

PubMed

Taylor, Anne E; Zeglin, Lydia H; Wanzek, Thomas A; Myrold, David D; Bottomley, Peter J

2012-11-01

It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a 2-year wheat/fallow cycle, and adjacent uncultivated long-term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (P0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomena: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH(4)(+)-availability that exist in the field.

[Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].

PubMed

Zhang, Fan; Zhang, Bing; Xiang, Hua; Hu, Songnian

2009-11-01

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time. We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes. We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.

Growth, Survival, and Death of Bacteria and Fungi Following Wet-up of Seasonally Dried Soil Revealed by Heavy Water Stable Isotope Probing

NASA Astrophysics Data System (ADS)

Blazewicz, S.; Nuccio, E. E.; Lim, H.; Schwartz, E.; Brodie, E.; Firestone, M.

2013-12-01

The rapid increase in microbial activity that occurs when a dry soil is rewetted has been well documented and is of great interest due to implications of changing precipitation patterns on soil C dynamics. Several studies have shown minor net changes in microbial population diversity or abundance following wet-up, but the gross population dynamics of bacteria and fungi resulting from soil wet-up are virtually unknown due to the technical difficulties associated with such measurements. Here we applied DNA stable isotope probing with H218O coupled with quantitative PCR and high throughput sequencing of bacterial 16S rRNA genes to characterize taxonomic composition of bacteria and to describe new growth, survival, and mortality of bacteria and fungi following the rewetting of a seasonally dried California annual grassland soil. Total microbial abundance revealed little change throughout the 7-day post-wet incubation, but there was substantial turnover of both bacterial and fungal populations (49 and 52% respectively). New growth was linear between 24 and 168 hours for both bacteria and fungi with average growth rates of 2.3 x 108 bacterial 16S rRNA gene copies gdw-1 h-1 and 4.3 x 107 fungal ITS copies gdw-1 h-1. While bacteria and fungi differed in their mortality and survival characteristics during the 7-day incubation, mortality that occurred within the first 3 hours was similar with 25 and 27% of bacterial and fungal gene copies disappearing from the pre-wet community, respectively. The rapid disappearance of gene copies indicates that cell death, occurring either during the extreme dry down period (preceding 5 months) or during the rapid change in water-potential due to wet-up, generates a significant pool of available C that likely contributes to the large pulse in CO2 associated with wet-up. Sequential bacterial growth patterns observed at the phylum and order levels suggest that an ecologically coherent response was observable at coarse taxonomic levels with

Comparative genomics of defense systems in archaea and bacteria

PubMed Central

Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.

2013-01-01

Our knowledge of prokaryotic defense systems has vastly expanded as the result of comparative genomic analysis, followed by experimental validation. This expansion is both quantitative, including the discovery of diverse new examples of known types of defense systems, such as restriction-modification or toxin-antitoxin systems, and qualitative, including the discovery of fundamentally new defense mechanisms, such as the CRISPR-Cas immunity system. Large-scale statistical analysis reveals that the distribution of different defense systems in bacterial and archaeal taxa is non-uniform, with four groups of organisms distinguishable with respect to the overall abundance and the balance between specific types of defense systems. The genes encoding defense system components in bacterial and archaea typically cluster in defense islands. In addition to genes encoding known defense systems, these islands contain numerous uncharacterized genes, which are candidates for new types of defense systems. The tight association of the genes encoding immunity systems and dormancy- or cell death-inducing defense systems in prokaryotic genomes suggests that these two major types of defense are functionally coupled, providing for effective protection at the population level. PMID:23470997

Tropical Aquatic Archaea Show Environment-Specific Community Composition

PubMed Central

Silveira, Cynthia B.; Cardoso, Alexander M.; Coutinho, Felipe H.; Lima, Joyce L.; Pinto, Leonardo H.; Albano, Rodolpho M.; Clementino, Maysa M.; Martins, Orlando B.; Vieira, Ricardo P.

2013-01-01

The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota , a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria. PMID:24086729

Contribution of arbuscular mycorrhizal fungi and/or bacteria to enhancing plant drought tolerance under natural soil conditions: effectiveness of autochthonous or allochthonous strains.

PubMed

Ortiz, N; Armada, E; Duque, E; Roldán, A; Azcón, R

2015-02-01

Autochthonous microorganisms [a consortium of arbuscular-mycorrhizal (AM) fungi and Bacillus thuringiensis (Bt)] were assayed and compared to Rhizophagus intraradices (Ri), Bacillus megaterium (Bm) or Pseudomonas putida (Psp) and non-inoculation on Trifolium repens in a natural arid soil under drought conditions. The autochthonous bacteria Bt and the allochthonous bacteria Psp increased nutrients and the relative water content and decreased stomatal conductance, electrolyte leakage, proline and APX activity, indicating their abilities to alleviate the drought stress. Mycorrhizal inoculation significantly enhanced plant growth, nutrient uptake and the relative water content, particularly when associated with specific bacteria minimizing drought stress-imposed effects. Specific combinations of autochthonous or allochthonous inoculants also contributed to plant drought tolerance by changing proline and antioxidative activities. However, non-inoculated plants had low relative water and nutrients contents, shoot proline accumulation and glutathione reductase activity, but the highest superoxide dismutase activity, stomatal conductance and electrolyte leakage. Microbial activities irrespective of the microbial origin seem to be coordinately functioning in the plant as an adaptive response to modulated water stress tolerance and minimizing the stress damage. The autochthonous AM fungi with Bt or Psp and those allochthonous Ri with Bm or Psp inoculants increased water stress alleviation. The autochthonous Bt showed the greatest ability to survive under high osmotic stress compared to the allochthonous strains, but when single inoculated or associated with Ri or AM fungi were similarly efficient in terms of physiological and nutritional status and in increasing plant drought tolerance, attenuating and compensating for the detrimental effect of water limitation. Copyright © 2014 Elsevier GmbH. All rights reserved.

Effect of Various Organic Matter stimulates Bacteria and Arbuscular Mycorrhizal Fungi Plantations on Eroded Slopes in Nepal

NASA Astrophysics Data System (ADS)

Shrestha Vaidya, G.; Shrestha, K.; Wallander, H.

2009-04-01

Erosion resulting from landslides is a serious problem in mountainous countries such as Nepal. To restore such sites it is essential to establish plant cover that protects the soil and reduces erosion. Trees and shrubs on the lower hillsides in Nepal form symbiosis with arbuscular mycorrhizal (AM) fungi and these fungi are important for the uptake of mineral nutrients from the soil. In addition, the mycelia formed by these fungi have an important function in stabilizing the soil. The success of plantations of these eroded slopes is therefore highly dependent on the extent of mycorrhizal colonization of the plants. Mycorrhizal fungi growing in symbiosis with plants are essential in this respect because they improve both plant and nutrient uptake and soil structure. We investigated the influence of organic matter and P amendment on recently produced biomass of bacteria and arbuscular mycorrhizal (AM) fungi in eroded slopes in Nepal. Eroded soil mixed with different types of organic matter was placed in mesh bags which were buried around the trees of Bauhinia purpurea and Leucaena diversifolia .This experiment were done in two seasons ( (the wet and the dry season). Signature fatty acids were used to determine bacterial and AM fungal biomass after the six month intervals. The amount and composition of AM fungal spores were analyzed in the mesh bags from the wet and dry seasons. More microbial biomass was produced during wet season than during dry season. Further more, organic matter addition enhanced the production of AM fungal and bacterial biomass during both seasons. The positive influence of organic matter addition on AM fungi could be an important contribution to plant survival, growth and nutrient composition in the soil in plantations on eroded slopes. Different AM spore communities and bacterial profiles were obtained with different organic amendments and this suggests a possible way of selecting for specific microbial communities in the management of eroded

Variation of airborne bacteria and fungi at Emperor Qin's Terra-Cotta Museum, Xi'an, China, during the "Oct. 1" gold week period of 2006.

PubMed

Chen, Yi-Ping; Cui, Ying; Dong, Jun-Gang

2010-02-01

To stimulate the national economy, a so-called "gold week" comprising May Day and National Day has been put in force by the government, and the first golden-week holiday began on October 1, 1999. Statistical data show that about 15,000 visitors were received each day by Emperor Qin's Terra-Cotta Museum during just such a gold week period. To evaluate the effects of tourism on indoor air, airborne samples were collected by the sedimentation plate method for 5 min during the "Oct. 1" gold week period of 2006, and both composition and changes of airborne bacteria and fungi in indoor/outdoor air in the museums were investigated. Airborne microbes were simultaneously collected by means of gravitational sedimentation on open Petri dishes. Three parallel samples were collected at the same time each day, and samples were subsequently incubated in the lab. Microbiology media were prepared before each experiment by a professional laboratory. Concentrations were calculated and presented as average data of colony-forming units per cubic meter of air (CFU/m(3)). The results show that (1) 13 bacterial genera and eight genera of fungi were identified from indoor and outdoor air at Emperor Qin's Terra-Cotta Museum during "Oct. 1" gold week in 2006. The bacterial groups occupied 61%, the fungi groups occupied 36%, and others occupied 3% of the total number of isolated microorganism genera. (2) As for the comparison of indoor and outdoor samples, the average concentrations of fungi were higher during the afternoon (13:00) than for the morning (09:00). The average concentrations of bacteria in indoor air were higher during the afternoon (13:00) than for the morning (9:00), and in outdoor air, they were lower during the afternoon (13:00) than for the morning (9:00). (3) The average concentrations of five dominant groups of bacteria and three dominant groups of fungi were higher during the afternoon (13:00) than for the morning (9:00) in the indoor air, but the average concentrations

Growth of ammonia-oxidizing archaea and bacteria in cattle manure compost under various temperatures and ammonia concentrations.

PubMed

Oishi, Ryu; Tada, Chika; Asano, Ryoki; Yamamoto, Nozomi; Suyama, Yoshihisa; Nakai, Yutaka

2012-05-01

A recent study showed that ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) coexist in the process of cattle manure composting. To investigate their physiological characteristics, liquid cultures seeded with fermenting cattle manure compost were incubated at various temperatures (37°C, 46°C, or 60°C) and ammonium concentrations (0.5, 1, 4, or 10 mM NH (4) (+) -N). The growth rates of the AOB and AOA were monitored using real-time polymerase chain reaction analysis targeting the bacterial and archaeal ammonia monooxygenase subunit A genes. AOB grew at 37°C and 4 or 10 mM NH (4) (+) -N, whereas AOA grew at 46°C and 10 mM NH (4) (+) -N. Incubation with allylthiourea indicated that the AOB and AOA grew by oxidizing ammonia. Denaturing gradient gel electrophoresis and subsequent sequencing analyses revealed that a bacterium related to Nitrosomonas halophila and an archaeon related to Candidatus Nitrososphaera gargensis were the predominant AOB and AOA, respectively, in the seed compost and in cultures after incubation. This is the first report to demonstrate that the predominant AOA in cattle manure compost can grow and can probably oxidize ammonia under moderately thermophilic conditions.

Community structure of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in soil treated with the insecticide imidacloprid.

PubMed

Cycoń, Mariusz; Piotrowska-Seget, Zofia

2015-01-01

The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S) and the Shannon-Wiener index (H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the 10∗FR dosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4 (+), known as the most important factor which determines the contribution of these microorganisms to soil nitrification.

Response of ammonia oxidizing bacteria and archaea to acute zinc stress and different moisture regimes in soil.

PubMed

Vasileiadis, Sotirios; Coppolecchia, Damiano; Puglisi, Edoardo; Balloi, Annalisa; Mapelli, Francesca; Hamon, Rebecca E; Daffonchio, Daniele; Trevisan, Marco

2012-11-01

Ammonia oxidation has been intensively studied for its sensitivity to environmental shifts and stresses. However, acute stress effects on the occurrence and composition of ammonia oxidizing bacteria (AOB) and archaea (AOA) based on expression of related molecular markers in complex soil environments have been to an extent overlooked, particularly concerning transient but commonly occurring environmental changes like soil moisture shifts. The present study investigates the responses of AOB and AOA to moisture shifts and high Zn soil content. AmoA gene copies and transcripts of AOB and AOA along with potential nitrification activity were measured in a soil microcosm approach for investigating the referred environmental shifts. Moisture change from 87 to 50 % of the water holding capacity caused a ~99 % reduction of AOB but not of AOA amoA transcripts that did not change significantly. Increasing applied zinc concentrations resulted in a reduction of potential nitrification rates and negatively affected studied gene expressions of both AOB and AOA, with AOB being more responsive. Both 16 S rRNA and amoA transcripts of AOB had an inverse relation to the applied zinc, indicating a gradual loss in total cell activity. Our results suggest the existence of pronounced differences between AOB and AOA concerning ammonia oxidation activity.

Community Structure of Ammonia-Oxidizing Archaea and Ammonia-Oxidizing Bacteria in Soil Treated with the Insecticide Imidacloprid

PubMed Central

Cycoń, Mariusz; Piotrowska-Seget, Zofia

2015-01-01

The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S) and the Shannon-Wiener index (H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the 10∗FR dosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4 +, known as the most important factor which determines the contribution of these microorganisms to soil nitrification. PMID:25705674

Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria.

PubMed

Meinhardt, Kelley A; Bertagnolli, Anthony; Pannu, Manmeet W; Strand, Stuart E; Brown, Sally L; Stahl, David A

2015-04-01

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) fill key roles in the nitrogen cycle. Thus, well-vetted methods for characterizing their distribution are essential for framing studies of their significance in natural and managed systems. Quantification of the gene coding for one subunit of the ammonia monooxygenase (amoA) by polymerase chain reaction is frequently employed to enumerate the two groups. However, variable amplification of sequence variants comprising this conserved genetic marker for ammonia oxidizers potentially compromises within- and between-system comparisons. We compared the performance of newly designed non-degenerate quantitative polymerase chain reaction primer sets to existing primer sets commonly used to quantify the amoA of AOA and AOB using a collection of plasmids and soil DNA samples. The new AOA primer set provided improved quantification of model mixtures of different amoA sequence variants and increased detection of amoA in DNA recovered from soils. Although both primer sets for the AOB provided similar results for many comparisons, the new primers demonstrated increased detection in environmental application. Thus, the new primer sets should provide a useful complement to primers now commonly used to characterize the environmental distribution of AOA and AOB. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Thermophilic Fungi: Their Physiology and Enzymes†

PubMed Central

Maheshwari, Ramesh; Bharadwaj, Girish; Bhat, Mahalingeshwara K.

2000-01-01

Thermophilic fungi are a small assemblage in mycota that have a minimum temperature of growth at or above 20°C and a maximum temperature of growth extending up to 60 to 62°C. As the only representatives of eukaryotic organisms that can grow at temperatures above 45°C, the thermophilic fungi are valuable experimental systems for investigations of mechanisms that allow growth at moderately high temperature yet limit their growth beyond 60 to 62°C. Although widespread in terrestrial habitats, they have remained underexplored compared to thermophilic species of eubacteria and archaea. However, thermophilic fungi are potential sources of enzymes with scientific and commercial interests. This review, for the first time, compiles information on the physiology and enzymes of thermophilic fungi. Thermophilic fungi can be grown in minimal media with metabolic rates and growth yields comparable to those of mesophilic fungi. Studies of their growth kinetics, respiration, mixed-substrate utilization, nutrient uptake, and protein breakdown rate have provided some basic information not only on thermophilic fungi but also on filamentous fungi in general. Some species have the ability to grow at ambient temperatures if cultures are initiated with germinated spores or mycelial inoculum or if a nutritionally rich medium is used. Thermophilic fungi have a powerful ability to degrade polysaccharide constituents of biomass. The properties of their enzymes show differences not only among species but also among strains of the same species. Their extracellular enzymes display temperature optima for activity that are close to or above the optimum temperature for the growth of organism and, in general, are more heat stable than those of the mesophilic fungi. Some extracellular enzymes from thermophilic fungi are being produced commercially, and a few others have commercial prospects. Genes of thermophilic fungi encoding lipase, protease, xylanase, and cellulase have been cloned and

Osmoadaptation and osmoregulation in archaea: update 2004.

PubMed

Roberts, Mary F

2004-09-01

The response of archaea to changes in external NaCl is reviewed and compared to what is known about osmoadaptation and osmoregulation in bacteria and eukaryotes. Cells placed in altered external NaCl exhibit short term and long term responses. The earliest events are likely to be water movement through aquaporin-like channels (efflux if external NaCl has been increased, influx into the cell if the external NaCl has been decreased) and ion movement (e.g., K+ moving in the direction opposite to water flow) through channels sensitive to osmotic pressure. A brief discussion of recent structures of homologues of these membrane proteins is presented. Accumulation of organic solutes, either by uptake from the medium or de novo synthesis, is triggered after these initial changes. Archaea have some unique organic solutes (osmolytes) that are not used by other organisms. These as well as other more common solutes have a role in stabilizing macromolecules from denaturation. Many osmolytes are distinguished by their stability in the cell and their lack of strong interactions with cellular components. A cell may respond by accumulating one or more temporary osmolytes, then over time readjust the intracellular solute distribution to what is optimal for cell growth under the new conditions. Coupled with the movement and accumulation of solutes is the induction of stress proteins (e.g., chaperonins) and, in some cases, transcriptional regulation of key enzymes. The response to NaCl stress of Methanococcus thermolithotrophicus is presented as an example of how one particular archaeon responds and adapts to altered osmotic pressure. The detailed response of many other archaea to osmotic stress will be needed in order to identify features (aside from some of the organic osmolytes) unique to the organisms in this kingdom.

IMPACT OF SOIL MANAGEMENT ON COTTON RHIZOSPHERE BACTERIA

USDA-ARS?s Scientific Manuscript database

Soil dwelling bacteria and fungi are responsible for a number of ecosystem services critical to agriculture. In particular, bacteria living in the rhizosphere (portion of soil directly influenced by plant roots) and arbuscular mycorrhizal fungi have been shown to improve nutrient and water uptake an...

Population ecology of nitrifying archaea and bacteria in the Southern California Bight.

PubMed

Beman, J Michael; Sachdeva, Rohan; Fuhrman, Jed A

2010-05-01

Marine Crenarchaeota are among the most abundant microbial groups in the ocean, and although relatively little is currently known about their biogeochemical roles in marine ecosystems, recognition that Crenarchaeota posses ammonia monooxygenase (amoA) genes and may act as ammonia-oxidizing archaea (AOA) offers another means of probing the ecology of these microorganisms. Here we use a time series approach combining quantification of archaeal and bacterial ammonia oxidizers with bacterial community fingerprints and biogeochemistry, to explore the population and community ecology of nitrification. At multiple depths (150, 500 and 890 m) in the Southern California Bight sampled monthly from 2003 to 2006, AOA were enumerated via quantitative PCR of archaeal amoA and marine group 1 Crenarchaeota 16S rRNA genes. Based on amoA genes, AOA were highly variable in time - a consistent feature of marine Crenarchaeota- however, average values were similar at different depths and ranged from 2.20 to 2.76 x 10(4) amoA copies ml(-1). Archaeal amoA genes were correlated with Crenarchaeota 16S rRNA genes (r(2) = 0.79) and the slope of this relationship was 1.02, demonstrating that the majority of marine group 1 Crenarchaeota present over the dates and depths sampled possessed amoA. Two AOA clades were specifically quantified and compared with betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) amoA genes at 150 m; these AOA groups were found to strongly co-vary in time (r(2) = 0.70, P < 0.001) whereas AOA : beta-AOB ratios ranged from 13 to 5630. Increases in the AOA : beta-AOB ratio correlated with the accumulation of nitrite (r(2) = 0.87, P < 0.001), and may be indicative of differences in substrate affinities and activities leading to periodic decoupling between ammonia and nitrite oxidation. These data capture a dynamic nitrogen cycle in which multiple microbial groups appear to be active participants.

Testing the Role of Microbial Ecology, Redox-Mediated Deep Water Production and Hypersalinity on TEX86: Lipids and 16s Sequences from Archaea and Bacteria in the Water Column and Sediments of Orca Basin

NASA Astrophysics Data System (ADS)

Warren, C.; Romero, I.; Ellis, G.; Goddard, E.; Krishnan, S.; Nigro, L. M.; Super, J. R.; Zhang, Y.; Zhuang, G.; Hollander, D. J.; Pagani, M.

2014-12-01

Mesophilic marine archaea and bacteria are known to substantially contribute to the oceanic microbial biomass and play critical roles in global carbon, nitrogen and nutrient cycles. The Orca Basin, a 2400 meter deep bathymetric depression on the continental slope of the north-central Gulf of Mexico, is an ideal environment to examine how redox-dependent biochemical processes control the input and cycling of bacterial and archaea-derived lipid compounds from formation in near-surface water, through secondary recycling processes operating at the redox-transition in the water column, to sedimentary diagenetic processes operating in oxic to anoxic zones within the basin. The lowermost 180 meters of the Orca Basin is characterized by an anoxic, hypersaline brine that is separated from the overlying oxic seawater by a well-defined redox sequence associated with a systematic increasing in salinity from 35 - 250‰. While surface water conditions are viewed as normal marine with a seasonally productive water column, the sub-oxic to anoxic transition zones within the deep-water column and the sediment spans over 200 m allowing the unique opportunity for discrete sampling of resident organisms and lipids. Here we present 16s rRNA sequence data of Bacteria and Archaea collected parallel to GDGT lipid profiles and in situ environmental measurements from the sediment and overlying water column in the intermediate zone of the basin, where movements of chemical transition zones are preserved. We evaluated GDGTs and corresponding taxa across the surface water, chlorophyll maximum, thermocline, and the deep redox boundary, including oxygenation, denitrification, manganese, iron and sulfate reduction zones, to determine if GDGTs are being produced under these conditions and how surface-derived GDGT lipids and the TEX86 signal may be altered. The results have implications for the application of the TEX86 paleotemperature proxy.

Compost biodegradation of recalcitrant hoof keratin by bacteria and fungi.

PubMed

Reuter, T; Gilroyed, B H; Xu, W; McAllister, T A; Stanford, K

2015-08-01

Compost activities efficiently break down a wide range of organic substances over time. In this study, bovine hoof was used as recalcitrant protein model to gain so far cryptic information on biodegradation during livestock mortalities composting. Bovine hooves (black and white), containing different amounts of melanin, placed into nylon bags were monitored during composting of cattle mortalities for up to 230 days. Besides physiochemical analysis, bacterial 16S and fungal 18S DNA fragments were amplified by PCR and profiles were separated by DGGE. Sequence analysis of separated fragments revealed various bacterial and fungal identities during composting. The microbial diversity was affected by a time-temperature interaction and by the hoof colour. Our molecular data, supported by electron microscopy, suggest hoof colonization by shifting bacteria and fungi communities. During composting, microbial communities work collaboratively in the degradation of recalcitrant organic matter such as keratin over time. A number of biomolecules including recalcitrant proteins may persist in environmental reservoirs, but breakdown can occur during composting. A combination of bioactivity and physiochemical conditions appear to be decisive for the fate of persistent biomolecules. © 2015 The Society for Applied Microbiology.

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

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

Chai, Juanjuan; Kora, Guruprasad; Ahn, Tae-Hyuk

2014-10-09

To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accuratemore » comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. In conclusion, our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.« less

Possible roles of uncultured archaea in carbon cycling in methane-seep sediments

NASA Astrophysics Data System (ADS)

Yoshinaga, Marcos Y.; Lazar, Cassandre S.; Elvert, Marcus; Lin, Yu-Shih; Zhu, Chun; Heuer, Verena B.; Teske, Andreas; Hinrichs, Kai-Uwe

2015-09-01

Studies on microbial carbon cycling uniformly confirm that anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria represent the dominant and most active fraction of the sedimentary microbial community in methane-seep sediments. However, little is known about other frequently observed and abundant microbial taxa, their role in carbon cycling and association with the anaerobic oxidation of methane (AOM). Here, we provide a comprehensive characterization of stable carbon isotopes (δ13C) from several intact polar lipid (IPL) classes and metabolite pools in a downcore profile at a cold seep within the oxygen minimum zone off Pakistan. We aimed to evaluate microbial carbon metabolism using IPLs in relation to redox conditions, metabolites and 16S rRNA gene libraries. The 13C-depleted signature of carbon pools and microbial metabolites in pore waters (e.g., dissolved inorganic carbon, lactate and acetate) demonstrated high accumulation of AOM-associated biomass and subsequent turnover thereof. ANMEs accounted for a small fraction of the archaeal 16S rRNA gene survey, whereas sequences of other uncultured benthic archaea dominated the clone libraries, particularly the Marine Benthic Group D. On the basis of lipid diversity and carbon isotope information, we suggest that structurally diverse phospho- and glycolipids, including the recently identified unsaturated tetraethers that are particularly abundant in this setting, are likely derived from archaea other than ANMEs. Through the evaluation of δ13C values of individual IPL, our results indicate heterotrophy as a possible metabolic pathway of archaea in these AOM-dominated sediments.

Gut Colonization by Methanogenic Archaea Is Associated with Organic Dairy Consumption in Children

PubMed Central

van de Pol, Jeroen A. A.; van Best, Niels; Mbakwa, Catherine A.; Thijs, Carel; Savelkoul, Paul H.; Arts, Ilja C. W.; Hornef, Mathias W.; Mommers, Monique; Penders, John

2017-01-01

The gut microbiota represents a complex and diverse ecosystem with a profound impact on human health, promoting immune maturation, and host metabolism as well as colonization resistance. Important members that have often been disregarded are the methanogenic archaea. Methanogenic archaea reduce hydrogen levels via the production of methane, thereby stimulating food fermentation by saccharolytic bacteria. On the other hand, colonization by archaea has been suggested to promote a number of gastrointestinal and metabolic diseases such as colorectal cancer, inflammatory bowel disease, and obesity. Archaea have been shown to be absent during infancy while omnipresent in school-aged children, suggesting that colonization may result from environmental exposure during childhood. The factors that determine the acquisition of methanogenic archaea, however, have remained undefined. Therefore, we aimed to explore determinants associated with the acquisition of the two main gastrointestinal archaeal species, Methanobrevibacter smithii and Methanosphaera stadtmanae, in children. Within the context of the KOALA Birth Cohort Study, fecal samples from 472 children aged 6–10 years were analyzed for the abundance of M. smithii and M. stadtmanae using qPCR. Environmental factors such as diet, lifestyle, hygiene, child rearing, and medication were recorded by repeated questionnaires. The relationship between these determinants and the presence and abundance of archaea was analyzed by logistic and linear regression respectively. Three hundred and sixty-nine out of the 472 children (78.2%) were colonized by M. smithii, and 39 out of the 472 children (8.3%) by M. stadtmanae. The consumption of organic yogurt (odds ratio: 4.25, CI95: 1.51; 11.95) and the consumption of organic milk (odds ratio: 5.58, CI95: 1.83; 17.01) were positively associated with the presence of M. smithii. We subsequently screened raw milk, processed milk, and yogurt samples for methanogens. We identified milk

Aliphatic hydrocarbons of the fungi.

NASA Technical Reports Server (NTRS)

Weete, J. D.

1972-01-01

Review of studies of aliphatic hydrocarbons which have been recently detected in the spores of phytopathogenic fungi, and are found to be structurally very similar to the alkanes of higher plants. It appears that the hydrocarbon components of the few mycelial and yeast forms reported resemble the distribution found in bacteria. The occurence and distribution of these compounds in the fungi is discussed. Suggested functional roles of fungal spore alkanes are presented.

Gut Microbial Diversity Assessment of Indian Type-2-Diabetics Reveals Alterations in Eubacteria, Archaea, and Eukaryotes.

PubMed

Bhute, Shrikant S; Suryavanshi, Mangesh V; Joshi, Suyog M; Yajnik, Chittaranjan S; Shouche, Yogesh S; Ghaskadbi, Saroj S

2017-01-01

Diabetes in India has distinct genetic, nutritional, developmental and socio-economic aspects; owing to the fact that changes in gut microbiota are associated with diabetes, we employed semiconductor-based sequencing to characterize gut microbiota of diabetic subjects from this region. We suggest consolidated dysbiosis of eubacterial, archaeal and eukaryotic components in the gut microbiota of newly diagnosed (New-DMs) and long-standing diabetic subjects (Known-DMs) compared to healthy subjects (NGTs). Increased abundance of phylum Firmicutes ( p = 0.010) and Operational Taxonomic Units (OTUs) of Lactobacillus ( p < 0.01) were observed in Known-DMs subjects along with the concomitant graded decrease in butyrate-producing bacterial families like Ruminococcaceae and Lachnospiraceae. Eukaryotes and fungi were the least affected components in these subjects but archaea, except Methanobrevibacter were significantly decreased in them. The two dominant archaea viz. Methanobrevibacater and Methanosphaera followed opposite trends in abundance from NGTs to Known-DMs subjects. There was a substantial reduction in eubacteria, with a noticeable decrease in Bacteroidetes phylum ( p = 0.098) and an increased abundance of fungi in New-DMs subjects. Likewise, opportunistic fungal pathogens such as Aspergillus, Candida were found to be enriched in New-DMs subjects. Analysis of eubacterial interaction network revealed disease-state specific patterns of ecological interactions, suggesting the distinct behavior of individual components of eubacteria in response to the disease. PERMANOVA test indicated that the eubacterial component was associated with diabetes-related risk factors like high triglyceride ( p = 0.05), low HDL ( p = 0.03), and waist-to-hip ratio ( p = 0.02). Metagenomic imputation of eubacteria depict deficiencies of various essential functions such as carbohydrate metabolism, amino acid metabolism etc. in New-DMs subjects. Results presented here shows that in diabetes

Gut Microbial Diversity Assessment of Indian Type-2-Diabetics Reveals Alterations in Eubacteria, Archaea, and Eukaryotes

PubMed Central

Bhute, Shrikant S.; Suryavanshi, Mangesh V.; Joshi, Suyog M.; Yajnik, Chittaranjan S.; Shouche, Yogesh S.; Ghaskadbi, Saroj S.

2017-01-01

Diabetes in India has distinct genetic, nutritional, developmental and socio-economic aspects; owing to the fact that changes in gut microbiota are associated with diabetes, we employed semiconductor-based sequencing to characterize gut microbiota of diabetic subjects from this region. We suggest consolidated dysbiosis of eubacterial, archaeal and eukaryotic components in the gut microbiota of newly diagnosed (New-DMs) and long-standing diabetic subjects (Known-DMs) compared to healthy subjects (NGTs). Increased abundance of phylum Firmicutes (p = 0.010) and Operational Taxonomic Units (OTUs) of Lactobacillus (p < 0.01) were observed in Known-DMs subjects along with the concomitant graded decrease in butyrate-producing bacterial families like Ruminococcaceae and Lachnospiraceae. Eukaryotes and fungi were the least affected components in these subjects but archaea, except Methanobrevibacter were significantly decreased in them. The two dominant archaea viz. Methanobrevibacater and Methanosphaera followed opposite trends in abundance from NGTs to Known-DMs subjects. There was a substantial reduction in eubacteria, with a noticeable decrease in Bacteroidetes phylum (p = 0.098) and an increased abundance of fungi in New-DMs subjects. Likewise, opportunistic fungal pathogens such as Aspergillus, Candida were found to be enriched in New-DMs subjects. Analysis of eubacterial interaction network revealed disease-state specific patterns of ecological interactions, suggesting the distinct behavior of individual components of eubacteria in response to the disease. PERMANOVA test indicated that the eubacterial component was associated with diabetes-related risk factors like high triglyceride (p = 0.05), low HDL (p = 0.03), and waist-to-hip ratio (p = 0.02). Metagenomic imputation of eubacteria depict deficiencies of various essential functions such as carbohydrate metabolism, amino acid metabolism etc. in New-DMs subjects. Results presented here shows that in diabetes

Driving Apart and Segregating Genomes in Archaea.

PubMed

Barillà, Daniela

2016-12-01

Genome segregation is a fundamental biological process in organisms from all domains of life. How this stage of the cell cycle unfolds in Eukarya has been clearly defined and considerable progress has been made to unravel chromosome partition in Bacteria. The picture is still elusive in Archaea. The lineages of this domain exhibit different cell-cycle lifestyles and wide-ranging chromosome copy numbers, fluctuating from 1 up to 55. This plurality of patterns suggests that a variety of mechanisms might underpin disentangling and delivery of DNA molecules to daughter cells. Here I describe recent developments in archaeal genome maintenance, including investigations of novel genome segregation machines that point to unforeseen bacterial and eukaryotic connections. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

Influence of land use intensity on the diversity of ammonia oxidizing bacteria and archaea in soils from grassland ecosystems.

PubMed

Meyer, Annabel; Focks, Andreas; Radl, Viviane; Welzl, Gerhard; Schöning, Ingo; Schloter, Michael

2014-01-01

In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates.

Detection of bacteria and fungi in blood of patients with febrile neutropenia by real-time PCR with universal primers and probes.

PubMed

Teranishi, Hideto; Ohzono, Nanae; Inamura, Norikazu; Kato, Atsushi; Wakabayashi, Tokio; Akaike, Hiroto; Terada, Kihei; Ouchi, Kazunobu

2015-03-01

Febrile neutropenia is the main treatment-related cause of mortality in cancer patients. During June 2012 to April 2014, 97 blood culture samples were collected from patients receiving chemotherapy for hematological malignancy and cancer with febrile neutropenia episodes (FNEs). The samples were examined for the presence of bacteria and fungi using real-time PCR amplification and sequencing of 16S and 18S rRNA genes. Bacteria were identified in 20 of 97 samples (20.6%) by the real-time PCR assay and in 10 of 97 (10.3%) samples by blood culture. In 6 blood culture-positive samples, the real-time PCR assay detected the same type of bacteria. No fungi were detected by the real-time PCR assay or blood culture. During antibiotic therapy, all samples were negative by blood culture, but the real-time PCR assay yielded a positive result in 2 cases of 2 (100%). The bacterial DNA copy number was not well correlated with the serum C-reactive protein titer of patients with FNEs. We conclude that a real-time PCR assay could provide better detection of causative microbes' in a shorter time, and with a smaller blood sample than blood culture. Using a real-time PCR assay in combination with blood culture could improve microbiological documentation of FNEs. Copyright © 2014 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests.

PubMed

McKernan, Kevin; Spangler, Jessica; Helbert, Yvonne; Lynch, Ryan C; Devitt-Lee, Adrian; Zhang, Lei; Orphe, Wendell; Warner, Jason; Foss, Theodore; Hudalla, Christopher J; Silva, Matthew; Smith, Douglas R

2016-01-01

Background : The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods : A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA. All samples were then subjected to next-generation sequencing and metagenomics analysis to enumerate the bacteria and fungi present before and after growth on culture-based media. Results : Several pathogenic or toxigenic bacterial and fungal species were identified in proportions of >5% of classified reads on the samples, including Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, Ralstonia pickettii, Salmonella enterica, Stenotrophomonas maltophilia, Aspergillus ostianus, Aspergillus sydowii, Penicillium citrinum and Penicillium steckii. Samples subjected to culture showed substantial shifts in the number and diversity of species present, including the failure of Aspergillus species to grow well on either platform. Substantial growth of Clostridium botulinum and other bacteria were frequently observed on one or both of the culture-based TYM platforms. The presence of plant growth promoting (beneficial) fungal species further influenced the differential growth of species in the microbiome of each sample. Conclusions : These findings have important implications for the Cannabis and food safety testing industries.

Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India.

PubMed

Rao, Subramanya; Chan, Yuki; Bugler-Lacap, Donnabella C; Bhatnagar, Ashish; Bhatnagar, Monica; Pointing, Stephen B

2016-03-01

A culture-independent diversity assessment of archaea, bacteria and fungi in the Thar Desert in India was made. Six locations in Ajmer, Jaisalmer, Jaipur and Jodhupur included semi-arid soils, arid soils, arid sand dunes, plus arid cryptoendolithic substrates. A real-time quantitative PCR approach revealed that bacteria dominated soils and cryptoendoliths, whilst fungi dominated sand dunes. The archaea formed a minor component of all communities. Comparison of rRNA-defined community structure revealed that substrate and climate rather than location were the most parsimonious predictors. Sequence-based identification of 1240 phylotypes revealed that most taxa were common desert microorganisms. Semi-arid soils were dominated by actinobacteria and alpha proteobacteria, arid soils by chloroflexi and alpha proteobacteria, sand dunes by ascomycete fungi and cryptoendoliths by cyanobacteria. Climatic variables that best explained this distribution were mean annual rainfall and maximum annual temperature. Substrate variables that contributed most to observed diversity patterns were conductivity, soluble salts, Ca(2+) and pH. This represents an important addition to the inventory of desert microbiota, novel insight into the abiotic drivers of community assembly, and the first report of biodiversity in a monsoon desert system.

Isolation of marine fungi Aspergillus sp. and its in vitro antifouling activity against marine bacteria.

PubMed

Thiyagarajan, Santhananmari; Bavya, Manoharan; Jamal, Alruwaili

2016-09-01

Biofouling is considered as a main issue of concern in aquatic environment causing severe economic loss and pollution. The aim of the present study was to isolate marine fungus antagonistic to biofouling bacteria and to define antifouling compounds present in it. Using standard plate method five predominant biofouling bacteria viz., Methylococcus sp., Flavobacterium sp., Marinococcus sp., Serratia sp. and Pseudomonas sp. were isolated from marine solid substances on Zobell's agar. Tolerance range of these bacteria to NaCl was 2-10%. Isolation of fungi from mangrove and estuarine sediments and their screening identified Aspergillus sp. EF4 as a potential isolate. This isolate caused inhibition of all the five test bacterial cultures measuring zone diameters respectively of 11, 16, 12, 13 and 11mm.? Subsequent to submerged fermentation using shaking flask method this fungus produced bioactive compounds within 5 days. The culture parameters optimized were raffinose as carbon source, yeast extract as lone nitrogen source, pH up to 9.0 and temperature up to 40?C. Antifouling compounds of culture filtrate were separated and detected by a three-step procedure involving thin layer chromatography, bioautography and preparative TLC. The in vitro assay involving glass slide-wooden stick-biofilm method revealed that these compounds could cause inhibition and destruction of bacteria to an extent of 2.16 x 104 CFU ml-1 and 2.46 x 104 CFU ml-1 respectively while growth of bacteria in control beaker was enumerated to be 4.41 x 104 CFU ml-1. High performance liquid chromatography of culture filtrate indicated probable principal antifouling compound as Fumonisin B2. Isolation of antagonistic marine fungus from Indian coast and detection of its antifouling compound would help in planning effective strategies for controlling biofouling in marine environment.

Archaea produce lower yields of N2 O than bacteria during aerobic ammonia oxidation in soil.

PubMed

Hink, Linda; Nicol, Graeme W; Prosser, James I

2017-12-01

Nitrogen fertilisation of agricultural soil contributes significantly to emissions of the potent greenhouse gas nitrous oxide (N 2 O), which is generated during denitrification and, in oxic soils, mainly by ammonia oxidisers. Although laboratory cultures of ammonia oxidising bacteria (AOB) and archaea (AOA) produce N 2 O, their relative activities in soil are unknown. This work tested the hypothesis that AOB dominate ammonia oxidation and N 2 O production under conditions of high inorganic ammonia (NH 3 ) input, but result mainly from the activity of AOA when NH 3 is derived from mineralisation. 1-octyne, a recently discovered inhibitor of AOB, was used to distinguish N 2 O production resulting from archaeal and bacterial ammonia oxidation in soil microcosms, and specifically inhibited AOB growth, activity and N 2 O production. In unamended soils, ammonia oxidation and N 2 O production were lower and resulted mainly from ammonia oxidation by AOA. The AOA N 2 O yield relative to nitrite produced was half that of AOB, likely due to additional enzymatic mechanisms in the latter, but ammonia oxidation and N 2 O production were directly linked in all treatments. Relative contributions of AOA and AOB to N 2 O production, therefore, reflect their respective contributions to ammonia oxidation. These results suggest potential mitigation strategies for N 2 O emissions from fertilised agricultural soils. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Quantitative analyses of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in fields with different soil types.

PubMed

Morimoto, Sho; Hayatsu, Masahito; Takada Hoshino, Yuko; Nagaoka, Kazunari; Yamazaki, Masatsugu; Karasawa, Toshihiko; Takenaka, Makoto; Akiyama, Hiroko

2011-01-01

Soil type is one of the key factors affecting soil microbial communities. With regard to ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), however, it has not been determined how soil type affects their community size and soil nitrification activity. Here we quantitatively analyzed the ammonia monooxygenase genes (amoA) of these ammonia oxidizers in fields with three different soil types (Low-humic Andosol [LHA], Gray Lowland Soil [GLS], and Yellow Soil [YS]) under common cropping conditions, and assessed the relationships between soil nitrification activity and the abundance of each amoA. Nitrification activity of LHA was highest, followed by that of GLS and YS; this order was consistent with that for the abundance of AOB amoA. Abundance of AOB amoA showed temporal variation, which was similar to that observed in nitrification activity, and a strong relationship (adjusted R(2)=0.742) was observed between the abundance of AOB amoA and nitrification activity. Abundance of AOA amoA also exhibited a significant relationship (adjusted R(2)=0.228) with nitrification activity, although this relationship was much weaker. Our results indicate that soil type affects the community size of AOA and AOB and the resulting nitrification activity, and that AOB are major contributors to nitrification in soils, while AOA are partially responsible.

[Distribution and Diversity of Ammonium-oxidizing Archaea and Ammonium-oxidizing Bacteria in Surface Sediments of Oujiang River].

PubMed

Li, Hu; Huang, Fu-yi; Su, Jian-qiang; Hong, You-wei; Yu, Shen

2015-12-01

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play important roles in the biogeochemical nitrogen cycle. Rivers are important ecosystems containing a large number of functional microbes in nitrogen cycle. In this study, denaturing gradient gel electrophoresis (DGGE ) and real-time quantitative PCR (qPCR) technology were used to analyze the distribution and diversity of AOA and AOB in sediments from Oujiang. The results showed that the AOA community structure was similar among various sites, while the AOB community structure was significantly different, in which all detected AOB sequences were classified into Nitrosospira and Nitrosomonas, and 90% affiliated to Nitrosospira. The community composition of AOA was influenced by NH₄⁺ and TS, in addition, the AOB composition was affected by NH₄⁺, EC, pH, NO₃⁻, TC and TN. Total sulfur (TS) and electrical conductivity (EC) were the major factors influencing the diversity of AOA and AOB, respectively. AOA abundance was significantly higher than that of AOB. EC, NH₄⁺-N and NO₃⁻-N were the main environmental factors affecting the abundance of AOA and AOB. This study indicated that the community composition and diversity of AOA and AOB were significantly influenced by environmental factors, and AOA might be dominant drivers in the ammonia oxidation process in Oujiang surface sediment.

A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins

PubMed Central

2008-01-01

Background Hemerythrins, are the non-heme, diiron binding respiratory proteins of brachiopods, priapulids and sipunculans; they are also found in annelids and bacteria, where their functions have not been fully elucidated. Results A search for putative Hrs in the genomes of 43 archaea, 444 bacteria and 135 eukaryotes, revealed their presence in 3 archaea, 118 bacteria, several fungi, one apicomplexan, a heterolobosan, a cnidarian and several annelids. About a fourth of the Hr sequences were identified as N- or C-terminal domains of chimeric, chemotactic gene regulators. The function of the remaining single domain bacterial Hrs remains to be determined. In addition to oxygen transport, the possible functions in annelids have been proposed to include cadmium-binding, antibacterial action and immunoprotection. A Bayesian phylogenetic tree revealed a split into two clades, one encompassing archaea, bacteria and fungi, and the other comprising the remaining eukaryotes. The annelid and sipunculan Hrs share the same intron-exon structure, different from that of the cnidarian Hr. Conclusion The phylogenomic profile of Hrs demonstrated a limited occurrence in bacteria and archaea and a marked absence in the vast majority of multicellular organisms. Among the metazoa, Hrs have survived in a cnidarian and in a few protostome groups; hence, it appears that in metazoans the Hr gene was lost in deuterostome ancestor(s) after the radiata/bilateria split. Signal peptide sequences in several Hirudinea Hrs suggest for the first time, the possibility of extracellular localization. Since the α-helical bundle is likely to have been among the earliest protein folds, Hrs represent an ancient family of iron-binding proteins, whose primary function in bacteria may have been that of an oxygen sensor, enabling aerophilic or aerophobic responses. Although Hrs evolved to function as O2 transporters in brachiopods, priapulids and sipunculans, their function in annelids remains to be elucidated

Recent developments in the taxonomic affiliation and phylogenetic positioning of fungi: impact in applied microbiology and environmental biotechnology.

PubMed

Voigt, Kerstin; Kirk, Paul M

2011-04-01

The goal of modern taxonomy is to understand the relationships of living organisms in terms of evolutionary descent. Thereby, the relationships between living organisms are understood in terms of nested clades--every time a speciation event takes place, two new clades are produced. Life comprises three domains of living organisms, these are the Bacteria, the Archaea and the Eukaryota. Within the eukaryotic domain, the fungi form a monophyletic group of the eukaryotic crown group and are thus high up in the evolutionary hierarchy of life. Fungus-like organisms possess certain morphological features of fungi, such as the hyphal organization of the Oomycota or the spores and reproductive structures inside a fructification of plasmodiophorids (Plasmodiophoromycota) and slime moulds (Mycetozoa). The first group are algae which secondarily lost their plastids during evolution and contain cellulose in their cell walls. Both osmotrophic phyla, the Oomycota and the Plasmidiophoromycota belong to the Chromista and Rhizaria, respectively, whereas the last group, the cellular and plasmodial slime moulds (Mycetozoa) are phagotrophic amoeboid protists belonging to the Amoebozoa. These fungus-like organisms are not considered further in this review. The Fungi sensu stricto comprise a heterogenous, often inconspicuous group of microorganisms which (1) are primarily heterotrophic with an (2) osmotrophic style of nutrition containing (3) chitin and its derivatives in the cell wall. This review discusses species concepts and current strategies in fungal taxonomy, phylogenetic affiliations of miscellaneous fungus-like groups like the microsporidia, perspectives of fungal nomenclature, and their impact on natural product research.

Archaea Signal Recognition Particle Shows the Way

PubMed Central

Zwieb, Christian; Bhuiyan, Shakhawat

2010-01-01

Archaea SRP is composed of an SRP RNA molecule and two bound proteins named SRP19 and SRP54. Regulated by the binding and hydrolysis of guanosine triphosphates, the RNA-bound SRP54 protein transiently associates not only with the hydrophobic signal sequence as it emerges from the ribosomal exit tunnel, but also interacts with the membrane-associated SRP receptor (FtsY). Comparative analyses of the archaea genomes and their SRP component sequences, combined with structural and biochemical data, support a prominent role of the SRP RNA in the assembly and function of the archaea SRP. The 5e motif, which in eukaryotes binds a 72 kilodalton protein, is preserved in most archaea SRP RNAs despite the lack of an archaea SRP72 homolog. The primary function of the 5e region may be to serve as a hinge, strategically positioned between the small and large SRP domain, allowing the elongated SRP to bind simultaneously to distant ribosomal sites. SRP19, required in eukaryotes for initiating SRP assembly, appears to play a subordinate role in the archaea SRP or may be defunct. The N-terminal A region and a novel C-terminal R region of the archaea SRP receptor (FtsY) are strikingly diverse or absent even among the members of a taxonomic subgroup. PMID:20672053

pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China.

PubMed

Li, Hu; Weng, Bo-Sen; Huang, Fu-Yi; Su, Jian-Qiang; Yang, Xiao-Ru

2015-07-01

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity.

Microbial diversity in sugarcane ethanol production in a Brazilian distillery using a culture-independent method.

PubMed

Costa, Ohana Yonara Assis; Souto, Betulia Morais; Tupinambá, Daiva Domenech; Bergmann, Jessica Carvalho; Kyaw, Cynthia Maria; Kruger, Ricardo Henrique; Barreto, Cristine Chaves; Quirino, Betania Ferraz

2015-01-01

Sugarcane ethanol production occurs in non-sterile conditions, and microbial contamination can decrease productivity. In this study, we assessed the microbial diversity of contaminants of ethanol production in an industrial facility in Brazil. Samples obtained at different stages were analyzed by pyrosequencing-based profiling of bacterial and archaeal 16S rRNA genes and the fungal internal transcribed spacer region. A total of 355 bacterial groups, 22 archaeal groups, and 203 fungal groups were identified, and community changes were related to temperature changes at certain stages. After fermentation, Lactobacillus and unclassified Lactobacillaceae accounted for nearly 100 % of the bacterial sequences. Predominant Fungi groups were "unclassified Fungi," Meyerozyma, and Candida. The predominant Archaea group was unclassified Thaumarchaeota. This is the first work to assess the diversity of Bacteria, and Archaea and Fungi associated with the industrial process of sugarcane-ethanol production using culture-independent techniques.

Heteroresistance and fungi.

PubMed

Ferreira, Gabriella F; Santos, Daniel A

2017-09-01

The concept of heteroresistance refers to the heterogeneous susceptibility to an antimicrobial drug in a microorganism population, meaning that some clones may be resistant and others are susceptible. This phenomenon has been widely studied in bacteria, but little attention has been given to its expression in fungi. We review the available literature on heteroresistance in fungi and invite the reader to recognise this phenomenon as a fungal mechanism to adapt to environmental stress, which may interfere both in resistance and virulence. Finally, heteroresistance may explain the treatment failures to eradicate mycosis in some patients treated with a seemingly appropriate antifungal. © 2017 Blackwell Verlag GmbH.

Direct quantitation of fatty acids present in bacteria and fungi: stability of the cyclopropane ring to chlorotrimethylsilane.

PubMed

Eras, Jordi; Oró, Robert; Torres, Mercè; Canela, Ramon

2008-07-09

The stability of the cyclopropane ring and the fatty acid composition of microbial cells were determined using chlorotrimethylsilane as reagent with three different conditions 80 degrees C for 1 h, 60 degrees C for 1 h, and 60 degrees C for 2 h. Chlorotrimethylsilane permits a simultaneous extraction and derivatization of fatty acids. A basic method was used as reference. The bacteria, Escherichia coli, Burkholderia cepacia, and Lactobacillus brevis, and fungi Aspergillus niger and Gibberella fujikuroi were used. The stability of the cyclopropane ring on acidic conditions was tested using the cyclopropanecarboxylic acid and a commercial mixture of bacteria fatty acid methyl esters (BAME). Fisher's least significant difference test showed significant differences among the methods. The method using chlorotrimethylsilane and 1-pentanol for 1 h at 80 degrees C gave the best results in cyclopropane, hydroxyl, and total fatty acid recoveries. This procedure allows the fast and easy one-step direct extraction derivatization.

Impact of a high ammonia-ammonium-pH system on methane-producing archaea and sulfate-reducing bacteria in mesophilic anaerobic digestion.

PubMed

Dai, Xiaohu; Hu, Chongliang; Zhang, Dong; Dai, Lingling; Duan, Nina

2017-12-01

A novel strategy for acclimation to ammonia stress was implemented by stimulating a high ammonia-ammonium-pH environment in a high-solid anaerobic digestion (AD) system in this study. Three semi-continuously stirred anaerobic reactors performed well over the whole study period under mesophilic conditions, especially in experimental group (R-2) when accommodated from acclimation period which the maximum total ammonia nitrogen (TAN) and free ammonia nitrogen (FAN) increased to 4921 and 2996mg/L, respectively. Moreover, when it accommodated the high ammonia-ammonium-pH system, the daily biogas production and methane content were similar to those in R-1 (the blank control to R-2), but the hydrogen sulfide (H 2 S) content lower than the blank control. Moreover, mechanistic studies showed that high ammonia stress enhanced the activity of coenzyme F 420 . The results of real-time fluorescent quantitative polymerase chain reaction (PCR) showed that ammonia stress decreased the abundance of sulfate-reducing bacteria and increased the abundance of methane-producing archaea. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparative genomic analysis reveals 2-oxoacid dehydrogenase complex lipoylation correlation with aerobiosis in archaea.

PubMed

Borziak, Kirill; Posner, Mareike G; Upadhyay, Abhishek; Danson, Michael J; Bagby, Stefan; Dorus, Steve

2014-01-01

Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs), is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA), which in archaea is typically encoded by two genes (LplA-N and LplA-C), or by a lipoyl(octanoyl) transferase (LipB or LipM) plus a lipoic acid synthetase (LipA). Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL)-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across the archaea

A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea

PubMed Central

Yan, Zhen

2017-01-01

ABSTRACT Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO2-reducing methanogenic anaerobes (methanogens) from the domain Archaea. Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea. The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F420 (F420H2) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F420H2 and reduction of ferredoxin with the exergonic oxidation of F420H2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting. PMID:28174314

Molecular evidence of Late Archean archaea and the presence of a subsurface hydrothermal biosphere

PubMed Central

Ventura, Gregory T.; Kenig, Fabien; Reddy, Christopher M.; Schieber, Juergen; Frysinger, Glenn S.; Nelson, Robert K.; Dinel, Etienne; Gaines, Richard B.; Schaeffer, Philippe

2007-01-01

Highly cracked and isomerized archaeal lipids and bacterial lipids, structurally changed by thermal stress, are present in solvent extracts of 2,707- to 2,685-million-year-old (Ma) metasedimentary rocks from Timmins, ON, Canada. These lipids appear in conventional gas chromatograms as unresolved complex mixtures and include cyclic and acyclic biphytanes, C36–C39 derivatives of the biphytanes, and C31–C35 extended hopanes. Biphytane and extended hopanes are also found in high-pressure catalytic hydrogenation products released from solvent-extracted sediments, indicating that archaea and bacteria were present in Late Archean sedimentary environments. Postdepositional, hydrothermal gold mineralization and graphite precipitation occurred before metamorphism (≈2,665 Ma). Late Archean metamorphism significantly reduced the kerogen's adsorptive capacity and severely restricted sediment porosity, limiting the potential for post-Archean additions of organic matter to the samples. Argillites exposed to hydrothermal gold mineralization have disproportionately high concentrations of extractable archaeal and bacterial lipids relative to what is releasable from their respective high-pressure catalytic hydrogenation product and what is observed for argillites deposited away from these hydrothermal settings. The addition of these lipids to the sediments likely results from a Late Archean subsurface hydrothermal biosphere of archaea and bacteria. PMID:17726114

Anaerobic Ammonium-Oxidizing Bacteria: Unique Microorganisms with Exceptional Properties

PubMed Central

Jetten, Mike S. M.

2012-01-01

Summary: Anaerobic ammonium-oxidizing (anammox) bacteria defy many microbiological concepts and share numerous properties with both eukaryotes and archaea. Among their most intriguing characteristics are their compartmentalized cell plan and archaeon-like cell wall. Here we review our current knowledge about anammox cell biology. The anammox cell is divided into three separate compartments by bilayer membranes. The anammox cell consists of (from outside to inside) the cell wall, paryphoplasm, riboplasm, and anammoxosome. Not much is known about the composition or function of both the anammox cell wall and the paryphoplasm compartment. The cell wall is proposed to be proteinaceous and to lack both peptidoglycan and an outer membrane typical of Gram-negative bacteria. The function of the paryphoplasm is unknown, but it contains the cell division ring. The riboplasm resembles the standard cytoplasmic compartment of other bacteria; it contains ribosomes and the nucleoid. The anammoxosome occupies most of the cell volume and is a so-called “prokaryotic organelle” analogous to the eukaryotic mitochondrion. This is the site where the anammox reaction takes place, coupled over the curved anammoxosome membrane, possibly giving rise to a proton motive force and subsequent ATP synthesis. With these unique properties, anammox bacteria are food for thought concerning the early evolution of the domains Bacteria, Archaea, and Eukarya. PMID:22933561

Comparison of simple sequence repeats in 19 Archaea.

PubMed

Trivedi, S

2006-12-05

All organisms that have been studied until now have been found to have differential distribution of simple sequence repeats (SSRs), with more SSRs in intergenic than in coding sequences. SSR distribution was investigated in Archaea genomes where complete chromosome sequences of 19 Archaea were analyzed with the program SPUTNIK to find di- to penta-nucleotide repeats. The number of repeats was determined for the complete chromosome sequences and for the coding and non-coding sequences. Different from what has been found for other groups of organisms, there is an abundance of SSRs in coding regions of the genome of some Archaea. Dinucleotide repeats were rare and CG repeats were found in only two Archaea. In general, trinucleotide repeats are the most abundant SSR motifs; however, pentanucleotide repeats are abundant in some Archaea. Some of the tetranucleotide and pentanucleotide repeat motifs are organism specific. In general, repeats are short and CG-rich repeats are present in Archaea having a CG-rich genome. Among the 19 Archaea, SSR density was not correlated with genome size or with optimum growth temperature. Pentanucleotide density had an inverse correlation with the CG content of the genome.

First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat.

PubMed

Muller, Félix; Brissac, Terry; Le Bris, Nadine; Felbeck, Horst; Gros, Olivier

2010-08-01

Archaea may be involved in global energy cycles, and are known for their ability to interact with eukaryotic species (sponges, corals and ascidians) or as archaeal-bacterial consortia. The recently proposed phylum Thaumarchaeota may represent the deepest branching lineage in the archaeal phylogeny emerging before the divergence between Euryarchaeota and Crenarchaeota. Here we report the first characterization of two marine thaumarchaeal species from shallow waters that consist of multiple giant cells. One species is coated with sulfur-oxidizing γ-Proteobacteria. These new uncultured thaumarchaeal species are able to live in the sulfide-rich environments of a tropical mangrove swamp, either on living tissues such as roots or on various kinds of materials such as stones, sunken woods, etc. These archaea and archaea/bacteria associations have been studied using light microscopy, transmission electron microscopy and scanning electron microscopy. Species identification of archaeons and the putative bacterial symbiont have been assessed by 16S small subunit ribosomal RNA analysis. The sulfur-oxidizing ability of the bacteria has been assessed by genetic investigation on alpha-subunit of the adenosine-5'-phosphosulfate reductase/oxidase's (AprA). Species identifications have been confirmed by fluorescence in situ hybridization using specific probes designed in this study. In this article, we describe two new giant archaeal species that form the biggest archaeal filaments ever observed. One of these species is covered by a specific biofilm of sulfur-oxidizing γ-Proteobacteria. This study highlights an unexpected morphological and genetic diversity of the phylum Thaumarchaeota. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil

PubMed Central

Morawe, Mareen; Hoeke, Henrike; Wissenbach, Dirk K.; Lentendu, Guillaume; Wubet, Tesfaye; Kröber, Eileen; Kolb, Steffen

2017-01-01

Methanol is an abundant atmospheric volatile organic compound that is released from both living and decaying plant material. In forest and other aerated soils, methanol can be consumed by methanol-utilizing microorganisms that constitute a known terrestrial sink. However, the environmental factors that drive the biodiversity of such methanol-utilizers have been hardly resolved. Soil-derived isolates of methanol-utilizers can also often assimilate multicarbon compounds as alternative substrates. Here, we conducted a comparative DNA stable isotope probing experiment under methylotrophic (only [13C1]-methanol was supplemented) and combined substrate conditions ([12C1]-methanol and alternative multi-carbon [13Cu]-substrates were simultaneously supplemented) to (i) identify methanol-utilizing microorganisms of a deciduous forest soil (European beech dominated temperate forest in Germany), (ii) assess their substrate range in the soil environment, and (iii) evaluate their trophic links to other soil microorganisms. The applied multi-carbon substrates represented typical intermediates of organic matter degradation, such as acetate, plant-derived sugars (xylose and glucose), and a lignin-derived aromatic compound (vanillic acid). An experimentally induced pH shift was associated with substantial changes of the diversity of active methanol-utilizers suggesting that soil pH was a niche-defining factor of these microorganisms. The main bacterial methanol-utilizers were members of the Beijerinckiaceae (Bacteria) that played a central role in a detected methanol-based food web. A clear preference for methanol or multi-carbon substrates as carbon source of different Beijerinckiaceae-affiliated phylotypes was observed suggesting a restricted substrate range of the methylotrophic representatives. Apart from Bacteria, we also identified the yeasts Cryptococcus and Trichosporon as methanol-derived carbon-utilizing fungi suggesting that further research is needed to exclude or prove

[Diversity of soil archaea in Tibetan Mila Mountains].

PubMed

Meng, Xiangwei; Mao, Zhenchuan; Chen, Guohua; Yang, Yuhong; Xie, Bingyan

2009-08-01

In order to study the diversity of archaea and ammonia-oxidizing archaea (AOA) of the alp prairie soil in Mila Mountain of Tibet. Total microbial DNA was directly extracted from the alp prairie of Mila Mountain. The clone library of 16S rRNA genes and amoA genes were amplified by PCR with universal primer sets. The sequences of archaea and AOA were defined into operational taxonomic units (OTUs) according to the 97% similarity threshold for OTU assignment was performed using the software program DOTUR. Phylogenetic analysis revealed archaea in the soil of Mila Mountain including the Crenarchaeota (71.7%) and unclassified-Archaea (28.3%) phyla. All the Crenarchaeota belong to the Thermoprotei. Phylogenetic analysis revealed AOA in the alp prairie soil of Mila Mountain belonged to the kingdom Crenarchaeota. Archaea and AOA species composition from Mila Mountain included 64 OTUs and 75 OTUs. These findings show prolific archaeal diversity in the alp prairie soil of Mila Mountain, where they may be actively involved in nitrification.

Microbial mats: an ecological niche for fungi

PubMed Central

Cantrell, Sharon A.; Duval-Pérez, Lisabeth

2013-01-01

Fungi were documented in tropical hypersaline microbial mats and their role in the degradation of complex carbohydrates (exopolymeric substance – EPS) was explored. Fungal diversity is higher during the wet season with Acremonium, Aspergillus, Cladosporium, and Penicillium among the more common genera. Diversity is also higher in the oxic layer and in young and transient mats. Enrichments with xanthan (a model EPS) show that without antibiotics (full community) degradation is faster than enrichments with antibacterial (fungal community) and antifungal (bacterial community) agents, suggesting that degradation is performed by a consortium of organisms (bacteria and fungi). The combined evidence from all experiments indicates that bacteria carried out approximately two-third of the xanthan degradation. The pattern of degradation is similar between seasons and layers but degradation is faster in enrichments from the wet season. The research suggests that fungi thrive in these hypersaline consortia and may participate in the carbon cycle through the degradation of complex carbohydrates. PMID:23577004

Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests

PubMed Central

McKernan, Kevin; Spangler, Jessica; Helbert, Yvonne; Lynch, Ryan C.; Devitt-Lee, Adrian; Zhang, Lei; Orphe, Wendell; Warner, Jason; Foss, Theodore; Hudalla, Christopher J.; Silva, Matthew; Smith, Douglas R.

2016-01-01

Background: The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods: A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA. All samples were then subjected to next-generation sequencing and metagenomics analysis to enumerate the bacteria and fungi present before and after growth on culture-based media. Results: Several pathogenic or toxigenic bacterial and fungal species were identified in proportions of >5% of classified reads on the samples, including Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, Ralstonia pickettii, Salmonella enterica, Stenotrophomonas maltophilia, Aspergillus ostianus, Aspergillus sydowii, Penicillium citrinum and Penicillium steckii. Samples subjected to culture showed substantial shifts in the number and diversity of species present, including the failure of Aspergillus species to grow well on either platform. Substantial growth of Clostridium botulinum and other bacteria were frequently observed on one or both of the culture-based TYM platforms. The presence of plant growth promoting (beneficial) fungal species further influenced the differential growth of species in the microbiome of each sample. Conclusions: These findings have important implications for the Cannabis and food safety testing industries. PMID:27853518

Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China.

PubMed

Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Wen, Donghui

2015-05-01

Under the increasing pressure of human activities, Hangzhou Bay has become one of the most seriously polluted waters along China's coast. Considering the excessive inorganic nitrogen detected in the bay, in this study, the impact of an effluent from a coastal industrial park on ammonia-oxidizing microorganisms (AOMs) of the receiving area was interpreted for the first time by molecular technologies. Revealed by real-time PCR, the ratio of archaeal amoA/bacterial amoA ranged from 5.68 × 10(-6) to 4.79 × 10(-5) in the activated sludge from two wastewater treatment plants (WWTPs) and 0.54-3.44 in the sediments from the effluent receiving coastal area. Analyzed by clone and pyrosequencing libraries, genus Nitrosomonas was the predominant ammonia-oxidizing bacteria (AOB), but no ammonia-oxidizing archaea (AOA) was abundant enough for sequencing in the activated sludge from the WWTPs; genus Nitrosomonas and Nitrosopumilus were the dominant AOB and AOA, respectively, in the coastal sediments. The different abundance of AOA but similar structure of AOB between the WWTPs and nearby coastal area probably indicated an anthropogenic impact on the microbial ecology in Hangzhou Bay.

Intercontinental dispersal of bacteria and archaea by transpacific winds

USGS Publications Warehouse

D. Smith,; H. Timonen,; D. Jaffe,; Griffin, Dale W.; M. Birmele,; Perry, K.D.; Ward, P.D.; M. Roberts,

2013-01-01

Microorganisms are abundant in the upper atmosphere, particularly downwind of arid regions, where winds can mobilize large amounts of topsoil and dust. However, the challenge of collecting samples from the upper atmosphere and reliance upon culture-based characterization methods have prevented a comprehensive understanding of globally dispersed airborne microbes. In spring 2011 at the Mt. Bachelor Observatory in North America (2.8 km above sea level), we captured enough microbial biomass in two transpacific air plumes to permit a microarray analysis using 16S rRNA genes. Thousands of distinct bacterial taxa spanning a wide range of phyla and surface environments were detected before, during, and after each Asian long-range transport event. Interestingly, the transpacific plumes delivered higher concentrations of taxa already in the background air (particularly Proteobacteria, Actinobacteria, and Firmicutes). While some bacterial families and a few marine archaea appeared for the first and only time during the plumes, the microbial community compositions were similar, despite the unique transport histories of the air masses. It seems plausible, when coupled with atmospheric modeling and chemical analysis, that microbial biogeography can be used to pinpoint the source of intercontinental dust plumes. Given the degree of richness measured in our study, the overall contribution of Asian aerosols to microbial species in North American air warrants additional investigation.

Intercontinental Dispersal of Bacteria and Archaea by Transpacific Winds

PubMed Central

Timonen, Hilkka J.; Jaffe, Daniel A.; Griffin, Dale W.; Birmele, Michele N.; Perry, Kevin D.; Ward, Peter D.; Roberts, Michael S.

2013-01-01

Microorganisms are abundant in the upper atmosphere, particularly downwind of arid regions, where winds can mobilize large amounts of topsoil and dust. However, the challenge of collecting samples from the upper atmosphere and reliance upon culture-based characterization methods have prevented a comprehensive understanding of globally dispersed airborne microbes. In spring 2011 at the Mt. Bachelor Observatory in North America (2.8 km above sea level), we captured enough microbial biomass in two transpacific air plumes to permit a microarray analysis using 16S rRNA genes. Thousands of distinct bacterial taxa spanning a wide range of phyla and surface environments were detected before, during, and after each Asian long-range transport event. Interestingly, the transpacific plumes delivered higher concentrations of taxa already in the background air (particularly Proteobacteria, Actinobacteria, and Firmicutes). While some bacterial families and a few marine archaea appeared for the first and only time during the plumes, the microbial community compositions were similar, despite the unique transport histories of the air masses. It seems plausible, when coupled with atmospheric modeling and chemical analysis, that microbial biogeography can be used to pinpoint the source of intercontinental dust plumes. Given the degree of richness measured in our study, the overall contribution of Asian aerosols to microbial species in North American air warrants additional investigation. PMID:23220959

Induction of trap formation in nematode-trapping fungi by bacteria-released ammonia.

PubMed

Su, H N; Xu, Y Y; Wang, X; Zhang, K Q; Li, G H

2016-04-01

A total of 11 bacterial strains were assayed for bacteria-induced trap formation in the nematode-trapping fungus Arthrobotrys oligospora YMF1·01883 with two-compartmented Petri dish. These strains were identified on the basis of their 16S rRNA gene sequences. Volatile organic compounds (VOCs) of eight isolates were extracted using solid-phase micro-extraction (SPME) and their structures were identified based on gas chromatography-mass spectrometry (GC-MS). At the same time, all isolates were used for quantitative measurement of ammonia by the indophenol blue method. The effects of pure commercial compounds on inducement of trap formation in A. oligospora were tested. Taken together, results demonstrated that the predominant bacterial volatile compound inducing trap formation was ammonia. Meanwhile, ammonia also played a role in other nematode-trapping fungi, including Arthrobotrys guizhouensis YMF1·00014, producing adhesive nets; Dactylellina phymatopaga YMF1·01474, producing adhesive knobs; Dactylellina cionopaga YMF1·01472, producing adhesive columns and Drechslerella brochopaga YMF1·01829, producing constricting rings. © 2016 The Society for Applied Microbiology.

Predominant MIC Mechanisms in the Oil and Gas Industry

DTIC Science & Technology

literature, terms such as microbial corrosion, biocorrosion, microbially influenced/induced corrosion, and biodegradation are often applied. All descriptions...express that microorganisms (bacteria, archaea, and fungi) influence the corrosion process of a given material. In this chapter, an overview of the common MIC mechanisms encountered in the oil and gas industry is presented.

Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.

PubMed

Tago, Kanako; Okubo, Takashi; Shimomura, Yumi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Nagayama, Atsushi; Hayatsu, Masahito

2015-01-01

The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers' fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers' sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 10(5)-9.2 × 10(6) and 1.7 × 10(6)-5.3 × 10(7) gene copies g dry soil(-1), respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.

Environmental Factors Shaping the Community Structure of Ammonia-Oxidizing Bacteria and Archaea in Sugarcane Field Soil

PubMed Central

Tago, Kanako; Okubo, Takashi; Shimomura, Yumi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Nagayama, Atsushi; Hayatsu, Masahito

2015-01-01

The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers’ fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers’ sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 105–9.2 × 106 and 1.7 × 106–5.3 × 107 gene copies g dry soil−1, respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields. PMID:25736866

Distinct responses in ammonia-oxidizing archaea and bacteria after addition of biosolids to an agricultural soil.

PubMed

Kelly, John J; Policht, Katherine; Grancharova, Tanya; Hundal, Lakhwinder S

2011-09-01

The recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare(-1) year(-1)) and double the agronomic rate (54 Mg hectare(-1) year(-1)), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare(-1) year(-1)). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterial amoA genes. In addition, only archaeal amoA gene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaeal amoA genes were significantly higher than copy numbers of bacterial amoA genes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches.

Effect of vegetation types on soil arbuscular mycorrhizal fungi and nitrogen-fixing bacterial communities in a karst region.

PubMed

Liang, Yueming; Pan, Fujing; He, Xunyang; Chen, Xiangbi; Su, Yirong

2016-09-01

Arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria play important roles in plant growth and recovery in degraded ecosystems. The desertification in karst regions has become more severe in recent decades. Evaluation of the fungal and bacterial diversity of such regions during vegetation restoration is required for effective protection and restoration in these regions. Therefore, we analyzed relationships among AM fungi and nitrogen-fixing bacteria abundances, plant species diversity, and soil properties in four typical ecosystems of vegetation restoration (tussock (TK), shrub (SB), secondary forest (SF), and primary forest (PF)) in a karst region of southwest China. Abundance of AM fungi and nitrogen-fixing bacteria, plant species diversity, and soil nutrient levels increased from the tussock to the primary forest. The AM fungus, nitrogen-fixing bacterium, and plant community composition differed significantly between vegetation types (p < 0.05). Plant richness and pH were linked to the community composition of fungi and nitrogen-fixing bacteria, respectively. Available phosphorus, total nitrogen, and soil organic carbon levels and plant richness were positively correlated with the abundance of AM fungi and nitrogen-fixing bacteria (p < 0.05). The results suggested that abundance of AM fungi and nitrogen-fixing bacteria increased from the tussock to the primary forest and highlight the essentiality of these communities for vegetation restoration.

A congruent phylogenomic signal places eukaryotes within the Archaea.

PubMed

Williams, Tom A; Foster, Peter G; Nye, Tom M W; Cox, Cymon J; Embley, T Martin

2012-12-22

Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook 'three domains' tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.

Epizootiological characteristics of viable bacteria and fungi in indoor air from porcine, chicken, or bovine husbandry confinement buildings

PubMed Central

Roque, Katharine; Lim, Gyeong-Dong; Jo, Ji-Hoon; Shin, Kyung-Min; Song, Eun-Seob; Gautam, Ravi; Kim, Chang-Yul; Lee, Kyungsuk; Shin, Seungwon; Yoo, Han-Sang; Heo, Yong

2016-01-01

Microorganisms found in bioaerosols from animal confinement buildings not only foster the risk of spreading diseases among livestock buildings, but also pose health hazards to farm workers and nearby residents. This study identified the various microorganisms present in the air of swine, chicken, and cattle farms with different kinds of ventilation conditions in Korea. Microbial air samples were collected onto Petri dishes with bacterial or fungal growth media using a cascade impactor. Endotoxin levels in total dust were determined by the limulus amebocyte lysate kinetic QCL method. Prevalent Gram-positive bacteria were Staphylococcus (S.) lentus, S. chromogenes, Bacillus (B.) cereus, B. licheniformis, and Enterococcus faecalis, while the dominant fungi and Gram-negative bacteria were Candida albicans and Sphingomonas paucimobilis, respectively. Considering no significant relationship between the indoor dust endotoxin levels and the isolation of Gram-negative bacteria from the indoor air, monitoring the indoor airborne endotoxin level was found to be also critical for risk assessment on health for animals or workers. The present study confirms the importance of microbiological monitoring and control on animal husbandry indoor air to ensure animal and worker welfare. PMID:27456779

Increase in detectable opportunistic bacteria in the oral cavity of orthodontic patients.

PubMed

Kitada, K; de Toledo, A; Oho, T

2009-05-01

This study was performed to detect the opportunistic bacteria and fungi from the oral cavities of orthodontic patients and examine the ability of the organisms to adhere to saliva-coated metallic brackets. Opportunistic bacteria and fungi were isolated from 58 patients (orthodontic group: 42; non-orthodontic group: 16) using culture methods and were identified based on their biochemical and enzymatic profiles. Seven opportunistic and four streptococcal strains were tested for their ability to adhere to saliva-coated metallic brackets. More opportunistic bacteria and fungi were detected in the orthodontic group than in the non-orthodontic group (P < 0.05). Opportunistic bacteria adhered to saliva-coated metallic brackets to the same degree as oral streptococci. The isolation frequencies of opportunistic bacteria and fungi increase during orthodontic treatment, suggesting the importance of paying special attention to oral hygiene in orthodontic patients to prevent periodontal disease and the aggravation of systemic disease in immunocompromised conditions.

Tripartite symbiosis of Sophora tomentosa, rhizobia and arbuscular mycorhizal fungi.

PubMed

Toma, Maíra Akemi; Soares de Carvalho, Teotonio; Azarias Guimarães, Amanda; Martins da Costa, Elaine; Savana da Silva, Jacqueline; de Souza Moreira, Fatima Maria

Sophora tomentosa is a pantropical legume species with potential for recovery of areas degraded by salinization, and for stabilization of sand dunes. However, few studies on this species have been carried out, and none regarding its symbiotic relationship with beneficial soil microorganisms. Therefore, this study aimed to evaluate the diversity of nitrogen-fixing bacteria isolated from nodules of Sophora tomentosa, and to analyze the occurrence of colonization of arbuscular mycorrhizal fungi on the roots of this legume in seafront soil. Thus, seeds, root nodules, and soil from the rhizosphere of Sophora tomentosa were collected. From the soil samples, trap cultures with this species were established to extract spores and to evaluate arbuscular mycorhizal fungi colonization in legume roots, as well as to capture rhizobia. Rhizobia strains were isolated from nodules collected in the field or from the trap cultures. Representative isolates of the groups obtained in the similarity dendrogram, based on phenotypic characteristics, had their 16S rRNA genes sequenced. The legume species showed nodules with indeterminate growth, and reddish color, distributed throughout the root. Fifty-one strains of these nodules were isolated, of which 21 were classified in the genus Bacillus, Brevibacillus, Paenibacillus, Rhizobium and especially Sinorhizobium. Strains closely related to Sinorhizobium adhaerens were the predominant bacteria in nodules. The other genera found, with the exception of Rhizobium, are probably endophytic bacteria in the nodules. Arbuscular mycorrhizal fungi was observed colonizing the roots, but arbuscular mycorhizal fungi spores were not found in the trap cultures. Therefore Sophora tomentosa is associated with both arbuscular mycorhizal fungi and nodulating nitrogen-fixing bacteria. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae.

PubMed

Guo, Min; Yang, Ruifu; Huang, Chen; Liao, Qiwen; Fan, Guangyi; Sun, Chenghang; Lee, Simon Ming-Yuen

2017-04-04

The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization signal (NLS), a short stretch of amino acid sequence, destines to transport proteins from cytoplasm into nucleus, and is also associated with the development of nuclear envelope. We attempted to investigate the NLS motifs in Planctomycetaceae genomes to demonstrate the potential molecular transition in the development of intracellular membrane system. In this study, we identified NLS-like motifs that have the same amino acid compositions as experimentally identified NLSs in genomes of 11 representative species of family Planctomycetaceae. A total of 15 NLS types and 170 NLS-bearing proteins were detected in the 11 strains. To determine the molecular transformation, we compared NLS-bearing protein abundances in the 11 representative Planctomycetaceae genomes with them in genomes of 16 taxonomically varied microorganisms: nine bacteria, two archaea and five fungi. In the 27 strains, 29 NLS types and 1101 NLS-bearing proteins were identified, principal component analysis showed a significant transitional gradient from bacteria to Planctomycetaceae to fungi on their NLS-bearing protein abundance profiles. Then, we clustered the 993 non-redundant NLS-bearing proteins into 181 families and annotated their involved metabolic pathways. Afterwards, we aligned the ten types of NLS motifs from the 13 families containing NLS-bearing proteins among bacteria, Planctomycetaceae or fungi, considering their diversity, length and origin. A transition towards increased complexity from non-planctomycete bacteria to Planctomycetaceae to archaea and fungi was detected based on the complexity of the 10 types of NLS-like motifs in the 13 NLS-bearing proteins families. The results of this study reveal that

Community composition of ammonia-oxidizing bacteria and archaea in rice field soil as affected by nitrogen fertilization.

PubMed

Wang, Yanan; Ke, Xiubin; Wu, Liqin; Lu, Yahai

2009-02-01

Little information is available on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in flooded rice soils. Consequently, a microcosm experiment was conducted to determine the effect of nitrogen fertilizer on the composition of AOB and AOA communities in rice soil by using molecular analyses of ammonia monooxygenase gene (amoA) fragments. Experimental treatments included three levels of N (urea) fertilizer, i.e. 50, 100 and 150 mgNkg(-1) soil. Soil samples were operationally divided into four fractions: surface soil, bulk soil deep layer, rhizosphere and washed root material. NH(4)(+)-N was the dominant form of N in soil porewater and increased with N fertilization. Cloning and sequencing of amoA gene fragments showed that the AOB community in the rice soil consisted of three major groups, i.e. Nitrosomonas communis cluster, Nitrosospira cluster 3a and cluster 3b. The sequences related to Nitrosomonas were predominant. There was a clear effect of N fertilizer and soil depth on AOB community composition based on terminal restriction fragment length polymorphism fingerprinting. Nitrosomonas appeared to be more abundant in the potentially oxic or micro-oxic fractions, including surface soil, rhizosphere and washed root material, than the deep layer of anoxic bulk soil. Furthermore, Nitrosomonas increased relatively in the partially oxic fractions and that of Nitrosospira decreased with the increasing application of N fertilizer. However, AOA community composition remained unchanged according to the denaturing gradient gel electrophoresis analyses.

Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase.

PubMed

Rigden, Daniel J

2004-12-01

Aminoacyl-tRNA synthetases (AARSs) are key players in the maintenance of the genetic code through correct pairing of amino acids with their cognate tRNA molecules. To this end, some AARSs, as well as seeking to recognize the correct amino acid during synthesis of aminoacyl-tRNA, enhance specificity through recognition of mischarged aminoacyl-tRNA molecules in a separate editing reaction. Recently, an editing domain, of uncertain provenance, idiosyncratic to some archaeal ThrRSs has been characterized. Here, sequence analyses and molecular modeling are reported that clearly show a relationship of the archaea-specific ThrRS editing domains with d-Tyr-tRNATyr deacylases (DTDs). The model enables the identification of the catalytic site and other substrate binding residues, as well as the proposal of a likely catalytic mechanism. Interestingly, typical DTD sequences, common in bacteria and eukaryotes, are entirely absent in archaea, consistent with an evolutionary scheme in which DTD was co-opted to serve as a ThrRS editing domain in archaea soon after their divergence from eukaryotes. A group of present-day archaebacteria contain a ThrRS obtained from a bacterium by horizontal gene transfer. In some of these cases a vestigial version of the original archaeal ThrRS, of potentially novel function, is maintained.

Archaea recruited d-Tyr-tRNATyr deacylase for editing in Thr–tRNA synthetase

PubMed Central

RIGDEN, DANIEL J.

2004-01-01

Aminoacyl–tRNA synthetases (AARSs) are key players in the maintenance of the genetic code through correct pairing of amino acids with their cognate tRNA molecules. To this end, some AARSs, as well as seeking to recognize the correct amino acid during synthesis of aminoacyl–tRNA, enhance specificity through recognition of mischarged aminoacyl–tRNA molecules in a separate editing reaction. Recently, an editing domain, of uncertain provenance, idiosyncratic to some archaeal ThrRSs has been characterized. Here, sequence analyses and molecular modeling are reported that clearly show a relationship of the archaea-specific ThrRS editing domains with d-Tyr-tRNATyr deacylases (DTDs). The model enables the identification of the catalytic site and other substrate binding residues, as well as the proposal of a likely catalytic mechanism. Interestingly, typical DTD sequences, common in bacteria and eukaryotes, are entirely absent in archaea, consistent with an evolutionary scheme in which DTD was co-opted to serve as a ThrRS editing domain in archaea soon after their divergence from eukaryotes. A group of present-day archaebacteria contain a ThrRS obtained from a bacterium by horizontal gene transfer. In some of these cases a vestigial version of the original archaeal ThrRS, of potentially novel function, is maintained. PMID:15525705

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

Treesearch

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

2014-01-01

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

The life cycle of iron Fe(III) oxide: impact of fungi and bacteria

NASA Astrophysics Data System (ADS)

Bonneville, Steeve

2014-05-01

Iron oxides are ubiquitous reactive constituents of soils, sediments and aquifers. They exhibit vast surface areas which bind a large array of trace metals, nutrients and organic molecules hence controlling their mobility/reactivity in the subsurface. In this context, understanding the "life cycle" of iron oxide in soils is paramount to many biogeochemical processes. Soils environments are notorious for their extreme heterogeneity and variability of chemical, physical conditions and biological agents at play. Here, we present studies investigating the role of two biological agents driving iron oxide dynamics in soils, root-associated fungi (mycorrhiza) and bacteria. Mycorrhiza filaments (hypha) grow preferentially around, and on the surface of nutrient-rich minerals, making mineral-fungi contact zones, hot-spots of chemical alteration in soils. However, because of the microscopic nature of hyphae (only ~ 5 µm wide for up to 1 mm long) and their tendency to strongly adhere to mineral surface, in situ observations of this interfacial micro-environment are scarce. In a microcosm, ectomycorrhiza (Paxillus involutus) was grown symbiotically with a pine tree (Pinus sylvestris) in the presence of freshly-cleaved biotite under humid, yet undersaturated, conditions typical of soils. Using spatially-resolved ion milling technique (FIB), transmission electron microscopy and spectroscopy (TEM/STEM-EDS), synchrotron based X-ray microscopy (STXM), we were able to quantify the speciation of Fe at the biotite-hypha interface. The results shows that substantial oxidation of biotite structural-Fe(II) into Fe(III) subdomains occurs at the contact zone between mycorrhiza and biotite. Once formed, iron(III) oxides can reductively dissolve under suboxic conditions via several abiotic and microbial pathways. In particular, they serve as terminal electron acceptors for the oxidation of organic matter by iron reducing bacteria. We aimed here to understand the role of Fe(III) mineral

Effects of Different Regeneration Scenarios and Fertilizer Treatments on Soil Microbial Ecology in Reclaimed Opencast Mining Areas on the Loess Plateau, China

PubMed Central

Li, Junjian; Zheng, Yuanming; Yan, Junxia; Li, Hongjian; Wang, Xiang; He, Jizheng; Ding, Guangwei

2013-01-01

The soil microbial community in reclaimed mining areas is fundamental to vegetative establishment. However, how this community responds to different regeneration scenarios and fertilizer treatments is poorly understood. This research evaluated plant and soil microbial communities from different regeneration scenarios and different fertilizer treatments. Regeneration scenarios significantly influenced soil bacterial, archaeal, and fungal rDNA abundance. The ratios of fungi to bacteria or archaea were increased with fertilizer application. The diversity of both plants and microbes was lowest in Lotus corniculatus grasslands. Regeneration scenario, fertilizer treatment, and their interaction influenced soil microbial richness, diversity and evenness indices. Labile carbon pool 2 was a significant factor affected plant and microbe communities in July, suggesting that plants and microbes may be competing for nutrients. The higher ratios of positive to negative association were found in soil bacteria and total microbe than in archaea and fungi. Stronger clustering of microbial communities from the same regeneration scenario indicated that the vegetative composition of regeneration site may have a greater influence on soil microbial communities than fertilizer treatment. PMID:23658819

Cell division and the ESCRT complex: A surprise from the archaea.

PubMed

Ettema, Thijs Jg; Bernander, Rolf

2009-01-01

The Archaea constitute the third domain of life, a separate evolutionary lineage together with the Bacteria and the Eukarya.1 Species belonging to the Archaea contain a surprising mix of bacterial (metabolism, life style, genomic organization) and eukaryotic (replication, transcription, translation) features.2 The archaeal kingdom comprises two main phyla, the Crenarchaeota and the Euryarchaeota. Regarding the cell division process in archaeal species (reviewed in ref. 3), members of the Euryarchaeota rely on an FtsZ-based cell division mechanism4 whereas, previously, no division genes had been detected in the crenarchaea. However, we recently reported the discovery of the elusive cell division machinery in crenarchaea from the genus Sulfolobus.5 The minimal machinery consists of three genes, which we designated cdvA, B and C (for cell division), organized into an operon that is widely conserved among crenarchaea. The gene products polymerize between segregating nucleoids at the early mitotic stage, forming a complex that remains associated with the leading edge of constriction throughout cytokinesis. Interestingly, CdvB and CdvC were shown to be related to the eukaryotic ESCRT-III protein sorting machinery (reviewed in ref. 6), indicating shared common ancestry and mechanistic similarities to endosomal vesicle formation and viral (HIV) budding in eukaryotes. We also demonstrated that the cdv operon is subject to checkpoint-like regulation, and that the genes display a complementary phylogenetic distribution within the Archaea domain relative to FtsZ-dependent division systems.5 Here, the findings are further explored and discussed, and topics for further investigation are suggested.

Chromosome segregation in Archaea mediated by a hybrid DNA partition machine

PubMed Central

Kalliomaa-Sanford, Anne K.; Rodriguez-Castañeda, Fernando A.; McLeod, Brett N.; Latorre-Roselló, Victor; Smith, Jasmine H.; Reimann, Julia; Albers, Sonja V.; Barillà, Daniela

2012-01-01

Eukarya and, more recently, some bacteria have been shown to rely on a cytoskeleton-based apparatus to drive chromosome segregation. In contrast, the factors and mechanisms underpinning this fundamental process are underexplored in archaea, the third domain of life. Here we establish that the archaeon Sulfolobus solfataricus harbors a hybrid segrosome consisting of two interacting proteins, SegA and SegB, that play a key role in genome segregation in this organism. SegA is an ortholog of bacterial, Walker-type ParA proteins, whereas SegB is an archaea-specific factor lacking sequence identity to either eukaryotic or bacterial proteins, but sharing homology with a cluster of uncharacterized factors conserved in both crenarchaea and euryarchaea, the two major archaeal sub-phyla. We show that SegA is an ATPase that polymerizes in vitro and that SegB is a site-specific DNA-binding protein contacting palindromic sequences located upstream of the segAB cassette. SegB interacts with SegA in the presence of nucleotides and dramatically affects its polymerization dynamics. Our data demonstrate that SegB strongly stimulates SegA polymerization, possibly by promoting SegA nucleation and accelerating polymer growth. Increased expression levels of segAB resulted in severe growth and chromosome segregation defects, including formation of anucleate cells, compact nucleoids confined to one half of the cell compartment and fragmented nucleoids. The overall picture emerging from our findings indicates that the SegAB complex fulfills a crucial function in chromosome segregation and is the prototype of a DNA partition machine widespread across archaea. PMID:22355141

Chromosome segregation in Archaea mediated by a hybrid DNA partition machine.

PubMed

Kalliomaa-Sanford, Anne K; Rodriguez-Castañeda, Fernando A; McLeod, Brett N; Latorre-Roselló, Victor; Smith, Jasmine H; Reimann, Julia; Albers, Sonja V; Barillà, Daniela

2012-03-06

Eukarya and, more recently, some bacteria have been shown to rely on a cytoskeleton-based apparatus to drive chromosome segregation. In contrast, the factors and mechanisms underpinning this fundamental process are underexplored in archaea, the third domain of life. Here we establish that the archaeon Sulfolobus solfataricus harbors a hybrid segrosome consisting of two interacting proteins, SegA and SegB, that play a key role in genome segregation in this organism. SegA is an ortholog of bacterial, Walker-type ParA proteins, whereas SegB is an archaea-specific factor lacking sequence identity to either eukaryotic or bacterial proteins, but sharing homology with a cluster of uncharacterized factors conserved in both crenarchaea and euryarchaea, the two major archaeal sub-phyla. We show that SegA is an ATPase that polymerizes in vitro and that SegB is a site-specific DNA-binding protein contacting palindromic sequences located upstream of the segAB cassette. SegB interacts with SegA in the presence of nucleotides and dramatically affects its polymerization dynamics. Our data demonstrate that SegB strongly stimulates SegA polymerization, possibly by promoting SegA nucleation and accelerating polymer growth. Increased expression levels of segAB resulted in severe growth and chromosome segregation defects, including formation of anucleate cells, compact nucleoids confined to one half of the cell compartment and fragmented nucleoids. The overall picture emerging from our findings indicates that the SegAB complex fulfills a crucial function in chromosome segregation and is the prototype of a DNA partition machine widespread across archaea.

A Phylogenomic Census of Molecular Functions Identifies Modern Thermophilic Archaea as the Most Ancient Form of Cellular Life

PubMed Central

Kim, Kyung Mo; Caetano-Anollés, Gustavo

2014-01-01

The origins of diversified life remain mysterious despite considerable efforts devoted to untangling the roots of the universal tree of life. Here we reconstructed phylogenies that described the evolution of molecular functions and the evolution of species directly from a genomic census of gene ontology (GO) definitions. We sampled 249 free-living genomes spanning organisms in the three superkingdoms of life, Archaea, Bacteria, and Eukarya, and used the abundance of GO terms as molecular characters to produce rooted phylogenetic trees. Results revealed an early thermophilic origin of Archaea that was followed by genome reduction events in microbial superkingdoms. Eukaryal genomes displayed extraordinary functional diversity and were enriched with hundreds of novel molecular activities not detected in the akaryotic microbial cells. Remarkably, the majority of these novel functions appeared quite late in evolution, synchronized with the diversification of the eukaryal superkingdom. The distribution of GO terms in superkingdoms confirms that Archaea appears to be the simplest and most ancient form of cellular life, while Eukarya is the most diverse and recent. PMID:25249790

Bacterial biofilm formation on the hyphae of ectomycorrhizal fungi: a widespread ability under controls?

PubMed

Guennoc, Cora Miquel; Rose, Christophe; Labbé, Jessy; Deveau, Aurélie

2018-05-17

Ectomycorrhizal (ECM) fungi establish symbiosis with roots of most trees of boreal and temperate ecosystems and are major drivers of nutrient fluxes between trees and the soil. ECM fungi constantly interact with bacteria all along their life cycle and the extended networks of hyphae provide a habitat for complex bacterial communities. Despite the important effects these bacteria can have on the growth and activities of ECM fungi, little is known about the mechanisms by which these microorganisms interact. Here we investigated the ability of bacteria to form biofilm on the hyphae of the ECM fungus Laccaria bicolor. We showed that the ability to form biofilms on the hyphae of the ECM fungus is widely shared among soil bacteria. Conversely, some fungi, belonging to the Ascomycete class, did not allow for the formation of bacterial biofilms on their surfaces. The formation of biofilms was also modulated by the presence of tree roots and ectomycorrhizae, suggesting that biofilm formation does not occur randomly in soil but that it is regulated by several biotic factors. In addition, our study demonstrated that the formation of bacterial biofilm on fungal hyphae relies on the production of networks of filaments made of extracellular DNA.

Enigmatic, ultrasmall, uncultivated Archaea

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

Baker, Brett J.; Comolli, Luis; Dick, Gregory J.

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge particularly for Archaea that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher codingmore » density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISME J 3:159 167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged.« less

Enigmatic, ultrasmall, uncultivated Archaea

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

Baker, Brett J.; Comolli, Luis; Dick, Gregory J.

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete similar to 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher codingmore » density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISME J 3: 159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged.« less

Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil▿

PubMed Central

Kelly, John J.; Policht, Katherine; Grancharova, Tanya; Hundal, Lakhwinder S.

2011-01-01

The recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare−1 year−1) and double the agronomic rate (54 Mg hectare−1 year−1), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare−1 year−1). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterial amoA genes. In addition, only archaeal amoA gene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaeal amoA genes were significantly higher than copy numbers of bacterial amoA genes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches. PMID:21803892

Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients.

PubMed

Noon, Jason B; Baum, Thomas J

2016-04-12

Hoplolaimina plant-parasitic nematodes (PPN) are a lineage of animals with many documented cases of horizontal gene transfer (HGT). In a recent study, we reported on three likely HGT candidate genes in the soybean cyst nematode Heterodera glycines, all of which encode secreted candidate effectors with putative functions in the host plant. Hg-GLAND1 is a putative GCN5-related N-acetyltransferase (GNAT), Hg-GLAND13 is a putative invertase (INV), and Hg-GLAND16 is a putative chorismate mutase (CM), and blastp searches of the non-redundant database resulted in highest similarity to bacterial sequences. Here, we searched nematode and non-nematode sequence databases to identify all the nematodes possible that contain these three genes, and to formulate hypotheses about when they most likely appeared in the phylum Nematoda. We then performed phylogenetic analyses combined with model selection tests of alternative models of sequence evolution to determine whether these genes were horizontally acquired from bacteria. Mining of nematode sequence databases determined that GNATs appeared in Hoplolaimina PPN late in evolution, while both INVs and CMs appeared before the radiation of the Hoplolaimina suborder. Also, Hoplolaimina GNATs, INVs and CMs formed well-supported clusters with different rhizosphere bacteria in the phylogenetic trees, and the model selection tests greatly supported models of HGT over descent via common ancestry. Surprisingly, the phylogenetic trees also revealed additional, well-supported clusters of bacterial GNATs, INVs and CMs with diverse eukaryotes and archaea. There were at least eleven and eight well-supported clusters of GNATs and INVs, respectively, from different bacteria with diverse eukaryotes and archaea. Though less frequent, CMs from different bacteria formed supported clusters with multiple different eukaryotes. Moreover, almost all individual clusters containing bacteria and eukaryotes or archaea contained species that inhabit very similar

Responses of soil hydrolytic enzymes, ammonia-oxidizing bacteria and archaea to nitrogen applications in a temperate grassland in Inner Mongolia.

PubMed

Zhang, Xinyu; Tang, Yuqian; Shi, Yao; He, Nianpeng; Wen, Xuefa; Yu, Qiang; Zheng, Chunyu; Sun, Xiaomin; Qiu, Weiwen

2016-09-06

We used a seven-year urea gradient applied field experiment to investigate the effects of nitrogen (N) applications on soil N hydrolytic enzyme activity and ammonia-oxidizing microbial abundance in a typical steppe ecosystem in Inner Mongolia. The results showed that N additions inhibited the soil N-related hydrolytic enzyme activities, especially in 392 kg N ha(-1 )yr(-1) treatment. As N additions increased, the amoA gene copy ratios of ammonia-oxidizing archaea (AOA) to ammonia-oxidizing bacteria (AOB) decreased from 1.13 to 0.65. Pearson correlation analysis showed that the AOA gene copies were negatively related with NH4(+)-N content. However, the AOB gene copies were positively correlated with NO3(-)-N content. Moderate N application rates (56-224 kg N ha(-1 )yr(-1)) accompanied by P additions are beneficial to maintaining the abundance of AOB, as opposed to the inhibition of highest N application rate (392 kg N ha(-1 )yr(-1)) on the abundance of AOB. This study suggests that the abundance of AOB and AOA would not decrease unless N applications exceed 224 kg N ha(-1 )yr(-1) in temperate grasslands in Inner Mongolia.

Towards a mechanistic and physiological understanding of a ferredoxin disulfide reductase from the domains Archaea and Bacteria.

PubMed

Prakash, Divya; Walters, Karim A; Martinie, Ryan J; McCarver, Addison C; Kumar, Adepu K; Lessner, Daniel J; Krebs, Carsten; Golbeck, John H; Ferry, James G

2018-05-02

Disulfide reductases reduce other proteins and are critically important for cellular redox signaling and homeostasis. Methanosarcina acetivorans is a methane-producing microbe from the domain Archaea that produces a ferredoxin:disulfide reductase (FDR) for which the crystal structure has been reported, yet its biochemical mechanism and physiological substrates are unknown. FDR and the extensively characterized plant-type ferredoxin:thioredoxin reductase (FTR) belong to a distinct class of disulfide reductases that contain a unique active-site [4Fe-4S] cluster. The results reported here support a mechanism for FDR similar to that reported for FTR with notable exceptions. Unlike FTR, FDR contains a rubredoxin [1Fe-0S] center postulated to mediate electron transfer from ferredoxin to the active-site [4Fe-4S] cluster.  UV-Vis, EPR and Mӧssbauer spectroscopic data indicated that two-electron reduction of the active-site disulfide in FDR involves a one-electron-reduced [4Fe-4S]1+ intermediate previously hypothesized for FTR. Our results support a role for an active-site tyrosine in FDR that occupies the equivalent position of an essential histidine in the active-site of FTR. Of note, one of seven Trxs encoded in the genome (Trx5) and methanoredoxin, a glutaredoxin-like enzyme from M. acetivorans, were reduced by FDR advancing the physiological understanding of FDRs role in the redox metabolism of methanoarchaea. Finally, bioinformatics analyses show FDR homologs are widespread in diverse microbes from the domain Bacteria. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

PubMed Central

Wessén, Ella; Söderström, Mats; Stenberg, Maria; Bru, David; Hellman, Maria; Welsh, Allana; Thomsen, Frida; Klemedtson, Leif; Philippot, Laurent; Hallin, Sara

2011-01-01

Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms of nitrate leaching were determined. All measured community components for both AOB and AOA exhibited spatial patterns at the hectare scale. The patchy patterns of community structures did not reflect the farming systems, but the AOB community was weakly related to differences in soil pH and moisture, whereas the AOA community to differences in soil pH and clay content. Soil properties related differently to the size of the communities, with soil organic carbon and total nitrogen correlating positively to AOB abundance, while clay content and pH showed a negative correlation to AOA abundance. Contrasting spatial patterns were observed for the abundance distributions of the two groups indicating that the AOB and AOA may occupy different niches in agro-ecosystems. In addition, the two communities correlated differently to community and ecosystem functions. Our results suggest that the AOA, not the AOB, were contributing to nitrate leaching at the site by providing substrate for the nitrite oxidizers. PMID:21228891

Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

PubMed Central

2012-01-01

Background The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life. Results Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a ‘fourth supergroup’ along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity. Conclusions Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet’s biosphere. PMID:22920653

Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary*

PubMed Central

Li, Xiao-ran; Xiao, Yi-ping; Ren, Wen-wei; Liu, Zeng-fu; Shi, Jin-huan; Quan, Zhe-xue

2012-01-01

Tidal flats are soil resources of great significance. Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. We determined the abundance as well as composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in different soils during land reclamation process. The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction (PCR). The different abundances of AOB and AOA were negatively correlated with the salinity. The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene. Among AOB, nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process, i.e., tidal flats, while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process, farm land and wild land. The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate. As for AOA, there was no obvious correlation with the changes in the physicochemical properties of the soil. This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages. PMID:23024044

Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary.

PubMed

Li, Xiao-ran; Xiao, Yi-ping; Ren, Wen-wei; Liu, Zeng-fu; Shi, Jin-huan; Quan, Zhe-xue

2012-10-01

Tidal flats are soil resources of great significance. Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. We determined the abundance as well as composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in different soils during land reclamation process. The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction (PCR). The different abundances of AOB and AOA were negatively correlated with the salinity. The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene. Among AOB, nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process, i.e., tidal flats, while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process, farm land and wild land. The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate. As for AOA, there was no obvious correlation with the changes in the physicochemical properties of the soil. This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages.

Size-resolved emission rates of airborne bacteria and fungi in an occupied classroom

PubMed Central

Qian, J; Hospodsky, D; Yamamoto, N; Nazaroff, W W; Peccia, J

2012-01-01

The role of human occupancy as a source of indoor biological aerosols is poorly understood. Size-resolved concentrations of total and biological particles in indoor air were quantified in a classroom under occupied and vacant conditions. Per-occupant emission rates were estimated through a mass-balance modeling approach, and the microbial diversity of indoor and outdoor air during occupancy was determined via rDNA gene sequence analysis. Significant increases of total particle mass and bacterial genome concentrations were observed during the occupied period compared to the vacant case. These increases varied in magnitude with the particle size and ranged from 3 to 68 times for total mass, 12–2700 times for bacterial genomes, and 1.5–5.2 times for fungal genomes. Emission rates per person-hour because of occupancy were 31 mg, 37 × 106 genome copies, and 7.3 × 106 genome copies for total particle mass, bacteria, and fungi, respectively. Of the bacterial emissions, ∼18% are from taxa that are closely associated with the human skin microbiome. This analysis provides size-resolved, per person-hour emission rates for these biological particles and illustrates the extent to which being in an occupied room results in exposure to bacteria that are associated with previous or current human occupants. Practical Implications Presented here are the first size-resolved, per person emission rate estimates of bacterial and fungal genomes for a common occupied indoor space. The marked differences observed between total particle and bacterial size distributions suggest that size-dependent aerosol models that use total particles as a surrogate for microbial particles incorrectly assess the fate of and human exposure to airborne bacteria. The strong signal of human microbiota in airborne particulate matter in an occupied setting demonstrates that the aerosol route can be a source of exposure to microorganisms emitted from the skin, hair, nostrils, and mouths of other occupants

Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements

PubMed Central

Sauer-Heilborn, Annette; Welte, Tobias; Guzman, Carlos A.; Abraham, Wolf-Rainer; Höfle, Manfred G.

2015-01-01

The respiratory mycobiome is an important but understudied component of the human microbiota. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. This study compared the bacterial and fungal communities of sputum samples from a large cohort of 56 adult patients with cystic fibrosis (CF) during nonexacerbation periods and under continuous antibiotic treatment. Molecular fingerprinting based on single-strand conformation polymorphism (SSCP) analysis revealed fundamental differences between bacterial and fungal communities. Both groups of microorganisms were taxonomically classified by identification of gene sequences (16S rRNA and internal transcript spacer), and prevalences of single taxa were determined for the entire cohort. Major bacterial pathogens were frequently observed, whereas fungi of known pathogenicity in CF were detected only in low numbers. Fungal species richness increased without reaching a constant level (saturation), whereas bacterial richness showed saturation after 50 patients were analyzed. In contrast to bacteria, a large number of fungal species were observed together with high fluctuations over time and among patients. These findings demonstrated that the mycobiome was dominated by transient species, which strongly suggested that the main driving force was their presence in inhaled air rather than colonization. Considering the high exposure of human airways to fungal spores, we concluded that fungi have low colonization abilities in CF, and colonization by pathogenic fungal species may be considered a rare event. A comprehensive understanding of the conditions promoting fungal colonization may offer the opportunity to prevent colonization and substantially reduce or even eliminate fungus-related disease progression in CF. PMID:26135861

Prevalence of bacteria and fungi in athlete's foot of varying severity and response to topical antibacterial and antifungal therapies.

PubMed

Talwar, P; Kumar, B; Ayyagiri, A; Kaur, S

1985-08-01

Ninety-six patients with clinical evidence of interdigital lesions classified as mild, moderate and severe athlete's foot were investigated for bacterial and fungal populations in the interspaces. Gram-negative bacteria, which were not found in the toe spaces of 50 normal controls, were grown in increasing numbers and with increasing frequency as the symptoms progressed from mild to severe. Gram-positive bacteria were also isolated regularly and in increasing numbers commensurate with the severity of the disease. Similarly the isolation rates of dermatophytes and Candida species were higher in patients with moderate and severe disease compared to those with mild disease. Clinical and culture responses to topical applications with framycetin, tolnaftate, miconazole and clotrimazole were also studied. In some patients the prevalence of pathogenic fungi increased as bacterial numbers decreased. The pure antibacterial framycetin brought symptomatic relief, as did the purely anti-dermatophyte substance tolnaftate, but best results were seen with two azole compounds having mixed antibacterial and antifungal properties.

Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches

PubMed Central

Sartor, R. Balfour; Wu, Gary D.

2017-01-01

Intestinal microbiota are involved in the pathogenesis of Crohn’s disease, ulcerative colitis, and pouchitis. We review the mechanisms by which these gut bacteria, fungi, and viruses mediate mucosal homeostasis, via their composite genes (metagenome) and metabolic products (metabolome). We explain how alterations to their profiles and functions under conditions of dysbiosis contribute to inflammation and effector immune responses that mediate inflammatory bowel diseases (IBD) in humans and enterocolitis in mice. It could be possible to engineer the intestinal environment by modifying the microbiota community structure or function to treat patients with IBD— either with individual agents, via dietary management, or as adjuncts to immunosuppressive drugs. We summarize the latest information on therapeutic use of fecal microbial transplantation and propose improved strategies to selectively normalize the dysbiotic microbiome in personalized approaches to treatment. PMID:27769810

The role of bacteria and mycorrhiza in plant sulfur supply

PubMed Central

Gahan, Jacinta; Schmalenberger, Achim

2014-01-01

Plant growth is highly dependent on bacteria, saprophytic, and mycorrhizal fungi which facilitate the cycling and mobilization of nutrients. Over 95% of the sulfur (S) in soil is present in an organic form. Sulfate-esters and sulfonates, the major forms of organo-S in soils, arise through deposition of biological material and are transformed through subsequent humification. Fungi and bacteria release S from sulfate-esters using sulfatases, however, release of S from sulfonates is catalyzed by a bacterial multi-component mono-oxygenase system. The asfA gene is used as a key marker in this desulfonation process to study sulfonatase activity in soil bacteria identified as Variovorax, Polaromonas, Acidovorax, and Rhodococcus. The rhizosphere is regarded as a hot spot for microbial activity and recent studies indicate that this is also the case for the mycorrhizosphere where bacteria may attach to the fungal hyphae capable of mobilizing organo-S. While current evidence is not showing sulfatase and sulfonatase activity in arbuscular mycorrhiza, their effect on the expression of plant host sulfate transporters is documented. A revision of the role of bacteria, fungi and the interactions between soil bacteria and mycorrhiza in plant S supply was conducted. PMID:25566295

Bacteria and Fungi Respond Differently to Multifactorial Climate Change in a Temperate Heathland, Traced with 13C-Glycine and FACE CO2

PubMed Central

Andresen, Louise C.; Dungait, Jennifer A. J.; Bol, Roland; Selsted, Merete B.; Ambus, Per; Michelsen, Anders

2014-01-01

It is vital to understand responses of soil microorganisms to predicted climate changes, as these directly control soil carbon (C) dynamics. The rate of turnover of soil organic carbon is mediated by soil microorganisms whose activity may be affected by climate change. After one year of multifactorial climate change treatments, at an undisturbed temperate heathland, soil microbial community dynamics were investigated by injection of a very small concentration (5.12 µg C g−1 soil) of 13C-labeled glycine (13C2, 99 atom %) to soils in situ. Plots were treated with elevated temperature (+1°C, T), summer drought (D) and elevated atmospheric carbon dioxide (510 ppm [CO2]), as well as combined treatments (TD, TCO2, DCO2 and TDCO2). The 13C enrichment of respired CO2 and of phospholipid fatty acids (PLFAs) was determined after 24 h. 13C-glycine incorporation into the biomarker PLFAs for specific microbial groups (Gram positive bacteria, Gram negative bacteria, actinobacteria and fungi) was quantified using gas chromatography-combustion-stable isotope ratio mass spectrometry (GC-C-IRMS). Gram positive bacteria opportunistically utilized the freshly added glycine substrate, i.e. incorporated 13C in all treatments, whereas fungi had minor or no glycine derived 13C-enrichment, hence slowly reacting to a new substrate. The effects of elevated CO2 did suggest increased direct incorporation of glycine in microbial biomass, in particular in G+ bacteria, in an ecosystem subjected to elevated CO2. Warming decreased the concentration of PLFAs in general. The FACE CO2 was 13C-depleted (δ13C = 12.2‰) compared to ambient (δ13C = ∼−8‰), and this enabled observation of the integrated longer term responses of soil microorganisms to the FACE over one year. All together, the bacterial (and not fungal) utilization of glycine indicates substrate preference and resource partitioning in the microbial community, and therefore suggests a diversified response pattern to future

Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments.

PubMed

Wang, Linqiong; Li, Yi; Niu, Lihua; Zhang, Wenlong; Zhang, Huanjun; Wang, Longfei; Wang, Peifang

2018-01-01

Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1-100 mg kg -1 ) and copper (Cu, 50-500 mg kg -1 ) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg -1 BDE 209 with a 100 mg kg -1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Competition and coexistence of sulfate-reducing bacteria, acetogens and methanogens in a lab-scale anaerobic bioreactor as affected by changing substrate to sulfate ratio

PubMed Central

Dar, Shabir A.; Kleerebezem, Robbert; Stams, Alfons J. M.; Kuenen, J. Gijs

2008-01-01

The microbial population structure and function of natural anaerobic communities maintained in lab-scale continuously stirred tank reactors at different lactate to sulfate ratios and in the absence of sulfate were analyzed using an integrated approach of molecular techniques and chemical analysis. The population structure, determined by denaturing gradient gel electrophoresis and by the use of oligonucleotide probes, was linked to the functional changes in the reactors. At the influent lactate to sulfate molar ratio of 0.35 mol mol−1, i.e., electron donor limitation, lactate oxidation was mainly carried out by incompletely oxidizing sulfate-reducing bacteria, which formed 80–85% of the total bacterial population. Desulfomicrobium- and Desulfovibrio-like species were the most abundant sulfate-reducing bacteria. Acetogens and methanogenic Archaea were mostly outcompeted, although less than 2% of an acetogenic population could still be observed at this limiting concentration of lactate. In the near absence of sulfate (i.e., at very high lactate/sulfate ratio), acetogens and methanogenic Archaea were the dominant microbial communities. Acetogenic bacteria represented by Dendrosporobacter quercicolus-like species formed more than 70% of the population, while methanogenic bacteria related to uncultured Archaea comprising about 10–15% of the microbial community. At an influent lactate to sulfate molar ratio of 2 mol mol−1, i.e., under sulfate-limiting conditions, a different metabolic route was followed by the mixed anaerobic community. Apparently, lactate was fermented to acetate and propionate, while the majority of sulfidogenesis and methanogenesis were dependent on these fermentation products. This was consistent with the presence of significant levels (40–45% of total bacteria) of D. quercicolus-like heteroacetogens and a corresponding increase of propionate-oxidizing Desulfobulbus-like sulfate-reducing bacteria (20% of the total bacteria). Methanogenic

N-Linked Glycosylation in Archaea: a Structural, Functional, and Genetic Analysis

PubMed Central

Ding, Yan; Meyer, Benjamin H.; Albers, Sonja-Verena; Kaminski, Lina; Eichler, Jerry

2014-01-01

SUMMARY N-glycosylation of proteins is one of the most prevalent posttranslational modifications in nature. Accordingly, a pathway with shared commonalities is found in all three domains of life. While excellent model systems have been developed for studying N-glycosylation in both Eukarya and Bacteria, an understanding of this process in Archaea was hampered until recently by a lack of effective molecular tools. However, within the last decade, impressive advances in the study of the archaeal version of this important pathway have been made for halophiles, methanogens, and thermoacidophiles, combining glycan structural information obtained by mass spectrometry with bioinformatic, genetic, biochemical, and enzymatic data. These studies reveal both features shared with the eukaryal and bacterial domains and novel archaeon-specific aspects. Unique features of N-glycosylation in Archaea include the presence of unusual dolichol lipid carriers, the use of a variety of linking sugars that connect the glycan to proteins, the presence of novel sugars as glycan constituents, the presence of two very different N-linked glycans attached to the same protein, and the ability to vary the N-glycan composition under different growth conditions. These advances are the focus of this review, with an emphasis on N-glycosylation pathways in Haloferax, Methanococcus, and Sulfolobus. PMID:24847024

Biosynthesis of Ergothioneine and Hercynine by Fungi and Actinomycetales

PubMed Central

Genghof, Dorothy S.

1970-01-01

Unlike other bacteria, aerobic members of the order Actinomycetales show a close biochemical relationship to the fungi by their capacity to synthesize hercynine and ergothioneine. The myxomycete Physarum polycephalum, possessing the same synthetic ability, also shows this relationship. Contrariwise, the unusual position of yeasts as fungi is indicated by the inability of all yeastlike Ascomycetes and all except a few false yeasts to synthesize these two betaines. PMID:5432011

Effects of bioaugmentation in para-nitrophenol-contaminated soil on the abundance and community structure of ammonia-oxidizing bacteria and archaea.

PubMed

Chi, Xiang-Qun; Liu, Kun; Zhou, Ning-Yi

2015-07-01

Pseudomonas sp. strain WBC-3 mineralizes the priority pollutant para-nitrophenol (PNP) and releases nitrite (NO2 (-)), which is probably involved in the nitrification. In this study, the rate of PNP removal in soil bioaugmented with strain WBC-3 was more accelerated with more NO2 (-) accumulation than in uninoculated soils. Strain WBC-3 survived well and remained stable throughout the entire period. Real-time polymerase chain reaction (real-time PCR) indicated a higher abundance of ammonia-oxidizing bacteria (AOB) than ammonia-oxidizing archaea (AOA), suggesting that AOB played a greater role in nitrification in the original sampled soil. Real-time PCR and multivariate analysis based on the denaturing gradient gel electrophoresis showed that PNP contamination did not significantly alter the abundance and community structure of ammonia oxidizers except for inhibiting the AOB abundance. Bioaugmentation of PNP-contaminated soil showed a significant effect on AOB populations and community structure as well as AOA populations. In addition, ammonium (NH4 (+)) variation was found to be the primary factor affecting the AOB community structure, as determined by the correlation between the community structures of ammonia oxidizers and environmental factors. It is here proposed that the balance between archaeal and bacterial ammonia oxidation could be influenced significantly by the variation in NH4 (+) levels as caused by bioaugmentation of contaminated soil by a pollutant containing nitrogen.

Bacteria on housefly eggs, Musca domestica, suppress fungal growth in chicken manure through nutrient depletion or antifungal metabolites

NASA Astrophysics Data System (ADS)

Lam, Kevin; Thu, Kelsie; Tsang, Michelle; Moore, Margo; Gries, Gerhard

2009-09-01

Female houseflies, Musca domestica (Diptera: Muscidae), lay their eggs in ephemeral resources such as animal manure. Hatching larvae compete for essential nutrients with fungi that also colonize such resources. Both the well-known antagonistic relationship between bacteria and fungi and the consistent presence of the bacterium Klebsiella oxytoca on housefly eggs led us to hypothesize (1) that K. oxytoca, and possibly other bacteria on housefly eggs, help curtail the growth of fungal resource competitors and (2) that such fungi indeed adversely affect the development of housefly larvae. Bacteria washed from housefly eggs significantly reduced the growth of fungi in chicken manure. Nineteen bacterial strains and ten fungal strains were isolated from housefly eggs or chicken manure, respectively. Co-culturing each of all the possible bacterium-fungus pairs revealed that the bacteria as a group, but no single bacterium, significantly suppressed the growth of all fungal strains tested. The bacteria's adverse effect on fungi is due to resource nutrient depletion and/or the release of antifungal chemicals. Well-established fungi in resources significantly reduced the number of larval offspring that completed development to adult flies.

Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria

PubMed Central

Taylor, Anne E; Giguere, Andrew T; Zoebelein, Conor M; Myrold, David D; Bottomley, Peter J

2017-01-01

Soil nitrification potential (NP) activities of ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) were evaluated across a temperature gradient (4–42 °C) imposed upon eight soils from four different sites in Oregon and modeled with both the macromolecular rate theory and the square root growth models to quantify the thermodynamic responses. There were significant differences in response by the dominant AOA and AOB contributing to the NPs. The optimal temperatures (Topt) for AOA- and AOB-supported NPs were significantly different (P<0.001), with AOA having Topt>12 °C greater than AOB. The change in heat capacity associated with the temperature dependence of nitrification (ΔCP‡) was correlated with Topt across the eight soils, and the ΔCP‡ of AOB activity was significantly more negative than that of AOA activity (P<0.01). Model results predicted, and confirmatory experiments showed, a significantly lower minimum temperature (Tmin) and different, albeit very similar, maximum temperature (Tmax) values for AOB than for AOA activity. The results also suggested that there may be different forms of AOA AMO that are active over different temperature ranges with different Tmin, but no evidence of multiple Tmin values within the AOB. Fundamental differences in temperature-influenced properties of nitrification driven by AOA and AOB provides support for the idea that the biochemical processes associated with NH3 oxidation in AOA and AOB differ thermodynamically from each other, and that also might account for the difficulties encountered in attempting to model the response of nitrification to temperature change in soil environments. PMID:27996979

Distribution and structure of pranktonic Archaea in the Arctic Ocean using 2008 - 2010 R/V Mirai cruise samples

NASA Astrophysics Data System (ADS)

Amano (Sato), C.; Akiyama, S.; Uchida, M.; Utsumi, M.

2011-12-01

Recent molecular biological techniques indicate that there is widely spreading marine planktonic Archaea in the world's ocean under euphotic zone, and those microbial metabolisms are now recognized the drive forces of the world ocean geochemical cycling. In addition, after the discovery of large amount of marine Archaea, it is pointed out to an accurate calculation of the ocean carbon cycling that the grasp of the Archaea quantitive distribution and their methabolism are indispensable. Remarkably, part of marine Archaea (Crenarchaeota) certainly has carbon fixing ability, thus there is currently great interest in the marine Archaea for getting to understand the carbon cycling. In this study, we evaluated the Archaeal spatial distribution and their biomass in the Pacific sector of the Arctic Ocean, where is the Archaeal quantitative data was less and strongly needed to reveal the marine bacterial carbon cycling due to resent changing the Arctic region such as extensive melting ice. The Arctic Ocean cruise by R/V MIRAI was done from August to October in 2008 - 2010 in the Chukchi Sea, Canada Basin and East Siberian Sea. In these cruises, vertical seawater samples were collected with 12 L Niskin bottles with CTD system at total 30 stations to investigate the distributions of bacterial population density. The Catalyzed Reporter Deposition Fluorescence in situ hybridization (CARD-FISH) technique targeting Crenarchaeal, Euryarchaeal and Eubacterial rRNA was used for identifying and enumerating marine microbial cells under florescent microscope. These cells were counted and measured the size, and calculated the biomass. From the results, in the Pacific sector of the Arctic Ocean, it was determined that the fraction of Archaea was abundant under euphotic zone like as other oceans, and the vertical distribution of planktonic Archaea were obviously different by each sea area. Especially in East Siberian Sea, the fraction of Crenarchaeota was relatively high near bottom

Skin microbiome: genomics-based insights into the diversity and role of skin microbes

PubMed Central

Kong, Heidi H.

2011-01-01

Recent advances in DNA sequencing methodology have enabled studies of human skin microbes that circumvent difficulties in isolating and characterizing fastidious microbes. Sequence-based approaches have identified greater diversity of cutaneous bacteria than studies using traditional cultivation techniques. However, improved sequencing technologies and analytical methods are needed to study all skin microbes, including bacteria, archaea, fungi, viruses, and mites, and how they interact with each other and their human hosts. This review discusses current skin microbiome research, with a primary focus on bacteria, and the challenges facing investigators striving to understand how skin micro-organisms contribute to health and disease. PMID:21376666

Evolutionary origins of mechanosensitive ion channels.

PubMed

Martinac, Boris; Kloda, Anna

2003-01-01

According to the recent revision, the universal phylogenetic tree is composed of three domains: Eukarya (eukaryotes), Bacteria (eubacteria) and Archaea (archaebacteria). Mechanosensitive (MS) ion channels have been documented in cells belonging to all three domains suggesting their very early appearance during evolution of life on Earth. The channels show great diversity in conductance, selectivity and voltage dependence, while sharing the property of being gated by mechanical stimuli exerted on cell membranes. In prokaryotes, MS channels were first documented in Bacteria followed by their discovery in Archaea. The finding of MS channels in archaeal cells helped to recognize and establish the evolutionary relationship between bacterial and archaeal MS channels and to show that this relationship extends to eukaryotic Fungi (Schizosaccharomyces pombe) and Plants (Arabidopsis thaliana). Similar to their bacterial and archaeal homologues, MS channels in eukaryotic cell-walled Fungi and Plants may serve in protecting the cellular plasma membrane from excessive dilation and rupture that may occur during osmotic stress. This review summarizes briefly some of the recent developments in the MS channel research field that may ultimately lead to elucidation of the biophysical and evolutionary principles underlying the mechanosensory transduction in living cells.

Abundance and community structure of ammonia-oxidizing Archaea and Bacteria in response to fertilization and mowing in a temperate steppe in Inner Mongolia.

PubMed

Chen, Yong-Liang; Hu, Hang-Wei; Han, Hong-Yan; Du, Yue; Wan, Shi-Qiang; Xu, Zhu-Wen; Chen, Bao-Dong

2014-07-01

Based on a 6-year field trial in a temperate steppe in Inner Mongolia, we investigated the effects of nitrogen (N) and phosphorus (P) fertilization and mowing on the abundance and community compositions of ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) upon early (May) and peak (August) plant growth using quantitative PCR (qPCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing. The results showed that N fertilization changed AOB community composition and increased AOB abundance in both May and August, but significantly decreased AOA abundance in May. By contrast, P fertilization significantly influenced AOB abundance only in August. Mowing significantly decreased AOA abundance and had little effect on AOA community compositions in May, while significantly influencing AOB abundance in both May and August, Moreover, AOA and AOB community structures showed obvious seasonal variations between May and August. Phylogenetic analysis showed that all AOA sequences fell into the Nitrososphaera cluster, and the AOB community was dominated by Nitrosospira Cluster 3. The results suggest that fertilization and mowing play important roles in affecting the abundance and community compositions of AOA and AOB. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Insights into the phylogeny or arylamine N-acetyltransferases in fungi.

PubMed

Martins, Marta; Dairou, Julien; Rodrigues-Lima, Fernando; Dupret, Jean-Marie; Silar, Philippe

2010-08-01

Previous studies have shown that Eumycetes fungi can acylate arylamine thanks to arylamine N-acetyltransferases, xenobiotic-metabolizing enzymes also found in animals and bacteria. In this article, we present the results of mining 96 available fungal genome sequences for arylamine N-acetyltransferase genes and propose their phylogeny. The filamentous Pezizomycotina are shown to possess many putative N-acetyltransferases, whilst these are often lacking in other fungal groups. The evolution of the N-acetyltransferases is best explained by the presence of at least one gene in the opisthokont ancestor of the fungi and animal kingdoms, followed by recurrent gene losses and gene duplications. A possible horizontal gene transfer event may have occurred from bacteria to the basidiomycetous yeast Malassezia globosa.

Differences in composition of honey samples and their impact on the antimicrobial activities against drug multiresistant bacteria and pathogenic fungi.

PubMed

AL-Waili, Noori; Al Ghamdi, Ahmad; Ansari, Mohammad Javed; Al-Attal, Yehya; Al-Mubarak, Aarif; Salom, Khelod

2013-05-01

Antibiotic multiresistant microbes represent a challenging problem. Because honey has a potent antibacterial property, the antimicrobial effects of different honey samples against multiresistant pathogens and their compositions were investigated. Five honey samples were used: Talah, Dhahian, Sumra-1, Sidr, and Sumra-2. Samples were analyzed to determine chemical composition such as fructose, glucose, sucrose, pH, total flavonoids, total phenolics, hydrogen peroxide concentration, minerals and trace elements. Antimicrobial activities of the samples against 17 (16 were multiresistant) human pathogenic bacteria and three types of fungi were studied. Specimens of the isolates were cultured into 10 mL of 10-100% (volume/volume) honey diluted in broth. Microbial growth was assessed on a solid plate media after 24 h and 72 h incubation. The composition of honey samples varied considerably. Sumra 1 and 2 contained the highest level of flavonoids and phenolics and the lowest level of hydrogen peroxide, whereas Dhahian honey contained the highest level of hydrogen peroxide. Sixteen pathogens were antibiotic multiresistant. A single dose of each honey sample inhibited all the pathogens tested after 24 h and 72 h incubation. The most sensitive pathogens were Aspergillus nidulans, Salmonella typhimurum and Staphylococcus epidermidis (S. epidermidis). Although there was no statistically significant difference in the effectiveness of honey samples, the most effective honey against bacteria was Talah and against fungi were Dhahian and Sumra-2. Various honey samples collected from different geographical areas and plant origins showed almost similar antimicrobial activities against multiresistant pathogens despite considerable variation in their composition. Honey may represent an alternative candidate to be tested as part of management of drug multiresistant pathogens. Copyright © 2013 IMSS. Published by Elsevier Inc. All rights reserved.

Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea

PubMed Central

Brochier-Armanet, Céline; Deschamps, Philippe; López-García, Purificación; Zivanovic, Yvan; Rodríguez-Valera, Francisco; Moreira, David

2011-01-01

The extent of horizontal gene transfer (HGT) among marine pelagic prokaryotes and the role that HGT may have played in their adaptation to this particular environment remain open questions. This is partly due to the paucity of cultured species and genomic information for many widespread groups of marine bacteria and archaea. Molecular studies have revealed a large diversity and relative abundance of marine planktonic archaea, in particular of Thaumarchaeota (also known as group I Crenarchaeota) and Euryarchaeota of groups II and III, but only one species (the thaumarchaeote Candidatus Nitrosopumilus maritimus) has been isolated in pure culture so far. Therefore, metagenomics remains the most powerful approach to study these environmental groups. To investigate the impact of HGT in marine archaea, we carried out detailed phylogenetic analyses of all open reading frames of 21 archaeal 16S rRNA gene-containing fosmids and, to extend our analysis to other genomic regions, also of fosmid-end sequences of 12 774 fosmids from three different deep-sea locations (South Atlantic and Adriatic Sea at 1000 m depth, and Ionian Sea at 3000 m depth). We found high HGT rates in both marine planktonic Thaumarchaeota and Euryarchaeota, with remarkable converging values estimated from complete-fosmid and fosmid-end sequence analysis (25 and 21% of the genes, respectively). Most HGTs came from bacterial donors (mainly from Proteobacteria, Firmicutes and Chloroflexi) but also from other archaea and eukaryotes. Phylogenetic analyses showed that in most cases HGTs are shared by several representatives of the studied groups, implying that they are ancient and have been conserved over relatively long evolutionary periods. This, together with the functions carried out by these acquired genes (mostly related to energy metabolism and transport of metabolites across membranes), suggests that HGT has played an important role in the adaptation of these archaea to the cold and nutrient

Gene transfers can date the tree of life.

PubMed

Davín, Adrián A; Tannier, Eric; Williams, Tom A; Boussau, Bastien; Daubin, Vincent; Szöllősi, Gergely J

2018-05-01

Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use state-of-the-art species tree-aware phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukarya. We present the order of speciations according to lateral gene transfer data calibrated to geological time for three datasets comprising 40 genomes for Cyanobacteria, 60 genomes for Archaea and 60 genomes for Fungi. An inspection of discrepancies between transfers and clocks and a comparison with mammalian fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.

[Isolation of endophytic fungi from medicinal plant Brucea javanica and their microbial inhibition activity].

PubMed

Liang, Zi-Ning; Zhu, Hua; Lai, Kai-Ping; Chen, Long

2014-04-01

To isolate and identify endophytic fungi from Brucea javanica, and to detect the antimicrobial activity of these strains. Endophytic fungi were isolated by tissue inoculation culture and identified by conventional morphological characteristic method. Seven kinds of pathogenic fungi and three kinds of bacteria were used as targeting microbes to test microbial inhibition activities by agar plate antagonistic action and modified agar gel diffusion methods, respectively. A total of 83 endophytic fungi strains were isolated from the root, stem, leaf and fruit of Brucea javanica. 34 strains were obtained from the stem, 32 strains were obtained from the leaf, 15 strains were isolated from the root and 2 strains came from the fruit. These 73 strains which had been identified attribute to 5 orders, 6 families and 12 genera. For the isolated strains, 14 strains had antifungal activities against at least one pathogenic fungi, 9 strains showed antibacterial activities against one or more bacteria. Especially, the strain YJ-17 which belonged to Phomopsis genus showed the best inhibitory effect on the targeting microbes. The endophytic fungi from Brucea javanica show diversity and microbial inhibition activity, and are worthy for further study on plant disease controlling.

RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

PubMed Central

Grosjean, Henri; Gaspin, Christine; Marck, Christian; Decatur, Wayne A; de Crécy-Lagard, Valérie

2008-01-01

Background Naturally occurring RNAs contain numerous enzymatically altered nucleosides. Differences in RNA populations (RNomics) and pattern of RNA modifications (Modomics) depends on the organism analyzed and are two of the criteria that distinguish the three kingdoms of life. If the genomic sequences of the RNA molecules can be derived from whole genome sequence information, the modification profile cannot and requires or direct sequencing of the RNAs or predictive methods base on the presence or absence of the modifications genes. Results By employing a comparative genomics approach, we predicted almost all of the genes coding for the t+rRNA modification enzymes in the mesophilic moderate halophile Haloferax volcanii. These encode both guide RNAs and enzymes. Some are orthologous to previously identified genes in Archaea, Bacteria or in Saccharomyces cerevisiae, but several are original predictions. Conclusion The number of modifications in t+rRNAs in the halophilic archaeon is surprisingly low when compared with other Archaea or Bacteria, particularly the hyperthermophilic organisms. This may result from the specific lifestyle of halophiles that require high intracellular salt concentration for survival. This salt content could allow RNA to maintain its functional structural integrity with fewer modifications. We predict that the few modifications present must be particularly important for decoding, accuracy of translation or are modifications that cannot be functionally replaced by the electrostatic interactions provided by the surrounding salt-ions. This analysis also guides future experimental validation work aiming to complete the understanding of the function of RNA modifications in Archaeal translation. PMID:18844986

Comparative study of the fungicide Benomyl toxicity on some plant growth promoting bacteria and some fungi in pure cultures.

PubMed

Elslahi, Randa H; Osman, Awad G; Sherif, Ashraf M; Elhussein, Adil A

2014-03-01

Six laboratory experiments were carried out to investigate the effect of the fungicide Benomyl on pure cultures of some plant growth promoting bacteria (PGPB) and some fungi. The highest LD50 was recorded for Bacillus circulans and proved to be the most resistant to the fungicide, followed by Azospirillum braziliense, while Penicillium sp. was the most affected microorganism. LD50 values for the affected microorganisms were in 21-240 orders of magnitude lower in comparison with the LD50 value for Azospirillum braziliense. The results indicate a strong selectivity for Benomyl against Rhizobium meliloti and Penicillium sp. when compared to other microorganisms tested. The highest safety coefficient was recorded for Bacillus circulans followed by Azospirillum braziliense, while Rhizobium meliloti, showed the lowest safety coefficient value compared to other bacteria. The lowest toxicity index was recorded for Bacillus circulans and Azospirillum braziliense. The slope of the curves for Bacillus sp. and Rhizobium meliloti was steeper than that of the other curves, suggesting that even a slight increase of the dose of the fungicide can cause a very strong negative effect. In conclusion, Benomyl could be applied without restriction when using inocula based on growth promoting bacteria such as symbiotic nitrogen fixers (Rhizobium meliloti), non-symbiotic nitrogen fixers (Azospirillum braziliense) or potassium solibilizers (Bacillus circulans), given that the fungicide is applied within the range of the recommended field dose.

Sulfate- and Sulfur-Reducing Bacteria as Terrestrial Analogs for Microbial Life on Jupiter's Satellite Io

NASA Technical Reports Server (NTRS)

Pikuta, Elena V.; Hoover, Richard B.; Six, N. Frank (Technical Monitor)

2001-01-01

Observations from the Voyager and Galileo spacecraft have revealed Jupiter's moon Io to be the most volcanically active body of our Solar System. The Galileo Near Infrared Imaging Spectrometer (NIMS) detected extensive deposits of sulfur compounds, elemental sulfur and SO2 frost on the surface of Io. There are extreme temperature variations on Io's surface, ranging from -130 C to over 2000 C at the Pillan Patera volcanic vent. The active volcanoes, fumaroles, calderas, and lava lakes and vast sulfur deposits on this frozen moon indicate that analogs of sulfur- and sulfate-reducing bacteria might inhabit Io. Hence Io may have great significance to Astrobiology. Earth's life forms that depend on sulfur respiration are members of two domains: Bacteria and Archaea. Two basic links of the biogeochemical sulfur cycle of Earth have been studied: 1) the sulfur oxidizing process (occurring at aerobic conditions) and 2) the process of sulfur-reduction to hydrogen sulfide (anaerobic conditions). Sulfate-reducing bacteria (StRB) and sulfur-reducing bacteria (SrRB) are responsible for anaerobic reducing processes. At the present time the systematics of StRB include over 112 species distributed into 35 genera of Bacteria and Archaea. Moderately thermophilic and mesophilic SrRB belong to the Bacteria. The hyperthermophilic SrRB predominately belong to the domain Archaea and are included in the genera: Pyrodictium, Thermoproteus, Pyrobaculum, Thermophilum, Desulfurococcus, and Thermodiscus. The StRB and SrRB use a wide spectrum of substrates as electron donors for lithotrophic and heterotrophic type nutrition. The electron acceptors for the StRB include: sulfate, thiosulfate, sulfite, sulfur, arsenate, dithionite, tetrathionate, sulfur monoxide, iron, nitrite, selenite, fumarate, oxygen, carbon dioxide, and chlorine-containing phenol compounds. The Sulfate- and Sulfur-reducing bacteria are widely distributed in anaerobic ecosystems, including extreme environments like hot springs

Effects of chlorimuron-ethyl application with or without urea fertilization on soil ammonia-oxidizing bacteria and archaea.

PubMed

Tan, Huanbo; Xu, Mingkai; Li, Xinyu; Zhang, Huiwen; Zhang, Chenggang

2013-09-15

Chlorimuron-ethyl (CE) has been widely used in modern agriculture, but little is known regarding the influence of CE on ammonia-oxidizing bacteria (AOB) and archaea (AOA) populations in soils. In this study, microcosm incubation of aquic brown soil was conducted for 60 d. Associated changes in the population sizes of AOB and AOA in response to CE application with or without urea fertilization were examined via quantitative real-time PCR (qPCR) assays of the ammonia monooxygenase gene (amoA). The half-life of CE ranged from 11.80 d to 14.54 d in the tested soil. Compared to the untreated control, the application of CE alone had no strong effects on soil pH, and urea fertilization temporarily increased soil pH in the first 7 days. The abundance of the AOA amoA gene was greater than the abundance of the AOB amoA gene in all treatments, but both were significantly suppressed by CE application in a dose-dependent manner. Urea fertilization generally increased AOB and AOA amoA gene abundances, except that the AOA amoA gene level was slightly reduced at the early stage of the incubation period. AOB and AOA preferred different N levels for growth, with AOB only growing significantly at high NH4(+) levels and AOA growing substantially at low NH₄(+) levels. The stimulation effects of urea fertilization on AOA and AOB amoA gene abundances were strongly suppressed by the CE application. This study indicated that the CE application substantially suppressed soil nitrification via inhibiting the AOB and AOA population regardless of urea fertilization, which resulted in significant changes in the soil NH₄(+)-N and NO₃(-)-N levels. Furthermore, AOB and AOA inhabiting separate ecological niches with different NH₄(+) levels played various roles in N cycling. Copyright © 2013 Elsevier B.V. All rights reserved.

Twenty Species of Hypobarophilic Bacteria Recovered from Diverse Soils Exhibit Growth under Simulated Martian Conditions at 0.7 kPa

NASA Astrophysics Data System (ADS)

Schuerger, Andrew C.; Nicholson, Wayne L.

2016-12-01

Bacterial growth at low pressure is a new research area with implications for predicting microbial activity in clouds and the bulk atmosphere on Earth and for modeling the forward contamination of planetary surfaces like Mars. Here, we describe experiments on the recovery and identification of 20 species of bacterial hypobarophiles (def., growth under hypobaric conditions of approximately 1-2 kPa) in 10 genera capable of growth at 0.7 kPa. Hypobarophilic bacteria, but not archaea or fungi, were recovered from diverse soils, and high numbers of hypobarophiles were recovered from Arctic and Siberian permafrost soils. Isolates were identified through 16S rRNA sequencing to belong to the genera Bacillus, Carnobacterium, Clostridium, Cryobacterium, Exiguobacterium, Paenibacillus, Rhodococcus, Streptomyces, and Trichococcus. The highest population of culturable hypobarophilic bacteria (5.1 × 104 cfu/g) was recovered from Colour Lake soils from Axel Heiberg Island in the Canadian Arctic. In addition, we extend the number of hypobarophilic species in the genus Serratia to six type-strains that include S. ficaria, S. fonticola, S. grimesii, S. liquefaciens, S. plymuthica, and S. quinivorans. Microbial growth at 0.7 kPa suggests that pressure alone will not be growth-limiting on the martian surface, or in Earth's atmosphere up to an altitude of 34 km.

A novel pathway for the biosynthesis of heme in Archaea: genome-based bioinformatic predictions and experimental evidence.

PubMed

Storbeck, Sonja; Rolfes, Sarah; Raux-Deery, Evelyne; Warren, Martin J; Jahn, Dieter; Layer, Gunhild

2010-12-13

Heme is an essential prosthetic group for many proteins involved in fundamental biological processes in all three domains of life. In Eukaryota and Bacteria heme is formed via a conserved and well-studied biosynthetic pathway. Surprisingly, in Archaea heme biosynthesis proceeds via an alternative route which is poorly understood. In order to formulate a working hypothesis for this novel pathway, we searched 59 completely sequenced archaeal genomes for the presence of gene clusters consisting of established heme biosynthetic genes and colocalized conserved candidate genes. Within the majority of archaeal genomes it was possible to identify such heme biosynthesis gene clusters. From this analysis we have been able to identify several novel heme biosynthesis genes that are restricted to archaea. Intriguingly, several of the encoded proteins display similarity to enzymes involved in heme d(1) biosynthesis. To initiate an experimental verification of our proposals two Methanosarcina barkeri proteins predicted to catalyze the initial steps of archaeal heme biosynthesis were recombinantly produced, purified, and their predicted enzymatic functions verified.

Diversity and Phylogenetic Distribution of Extracellular Microbial Peptidases

NASA Astrophysics Data System (ADS)

Nguyen, Trang; Mueller, Ryan; Myrold, David

2017-04-01

Depolymerization of proteinaceous compounds by extracellular proteolytic enzymes is a bottleneck in the nitrogen cycle, limiting the rate of the nitrogen turnover in soils. Protein degradation is accomplished by a diverse range of extracellular (secreted) peptidases. Our objective was to better understand the evolution of these enzymes and how their functional diversity corresponds to known phylogenetic diversity. Peptidase subfamilies from 110 archaeal, 1,860 bacterial, and 97 fungal genomes were extracted from the MEROPS database along with corresponding SSU sequences for each genome from the SILVA database, resulting in 43,177 secreted peptidases belonging to 34 microbial phyla and 149 peptidase subfamilies. We compared the distribution of each peptidase subfamily across all taxa to the phylogenetic relationships of these organisms based on their SSU gene sequences. The occurrence and abundance of genes coding for secreted peptidases varied across microbial taxa, distinguishing the peptidase complement of the three microbial kingdoms. Bacteria had the highest frequency of secreted peptidase coding genes per 1,000 genes and contributed from 1% to 6% of the gene content. Fungi only had a slightly higher number of secreted peptidase gene content than archaea, standardized by the total genes. The relative abundance profiles of secreted peptidases in each microbial kingdom also varied, in which aspartic family was found to be the greatest in fungi (25%), whereas it was only 12% in archaea and 4% in bacteria. Serine, metallo, and cysteine families consistently contributed widely up to 75% of the secreted peptidase abundance across the three kingdoms. Overall, bacteria had a much wider collection of secreted peptidases, whereas fungi and archaea shared most of their secreted peptidase families. Principle coordinate analysis of the peptidase subfamily-based dissimilarities showed distinguishable clusters for different groups of microorganisms. The distribution of

Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life

NASA Technical Reports Server (NTRS)

Margulis, L.

1996-01-01

A symbiosis-based phylogeny leads to a consistent, useful classification system for all life. "Kingdoms" and "Domains" are replaced by biological names for the most inclusive taxa: Prokarya (bacteria) and Eukarya (symbiosis-derived nucleated organisms). The earliest Eukarya, anaerobic mastigotes, hypothetically originated from permanent whole-cell fusion between members of Archaea (e.g., Thermoplasma-like organisms) and of Eubacteria (e.g., Spirochaeta-like organisms). Molecular biology, life-history, and fossil record evidence support the reunification of bacteria as Prokarya while subdividing Eukarya into uniquely defined subtaxa: Protoctista, Animalia, Fungi, and Plantae.

Significant contribution of Archaea to extant biomass in marine subsurface sediments.

PubMed

Lipp, Julius S; Morono, Yuki; Inagaki, Fumio; Hinrichs, Kai-Uwe

2008-08-21

Deep drilling into the marine sea floor has uncovered a vast sedimentary ecosystem of microbial cells. Extrapolation of direct counts of stained microbial cells to the total volume of habitable marine subsurface sediments suggests that between 56 Pg (ref. 1) and 303 Pg (ref. 3) of cellular carbon could be stored in this largely unexplored habitat. From recent studies using various culture-independent techniques, no clear picture has yet emerged as to whether Archaea or Bacteria are more abundant in this extensive ecosystem. Here we show that in subsurface sediments buried deeper than 1 m in a wide range of oceanographic settings at least 87% of intact polar membrane lipids, biomarkers for the presence of live cells, are attributable to archaeal membranes, suggesting that Archaea constitute a major fraction of the biomass. Results obtained from modified quantitative polymerase chain reaction and slot-blot hybridization protocols support the lipid-based evidence and indicate that these techniques have previously underestimated archaeal biomass. The lipid concentrations are proportional to those of total organic carbon. On the basis of this relationship, we derived an independent estimate of amounts of cellular carbon in the global marine subsurface biosphere. Our estimate of 90 Pg of cellular carbon is consistent, within an order of magnitude, with previous estimates, and underscores the importance of marine subsurface habitats for global biomass budgets.

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland.

PubMed

He, Yuan; Hu, Wenge; Ma, Decao; Lan, Hongzhu; Yang, Yang; Gao, Yan

2017-07-01

Ammonia oxidation is carried out by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The Ebinur Lake wetland is the best example of a temperate arid zone wetland ecosystem in China. Soil samples were collected from rhizosphere and non-rhizosphere soil containing Halocnemum strobilaceum (samples H and H'), Phragmites australis (samples R and R'), and Karelinia caspia (samples K and K') to study the relationship between environmental factors and the community structure of AOB and AOA. Phylogenetic analysis showed that the AOA sequences belonged to the Nitrosopumilus and Nitrososphaera clusters. AOB were grouped into Nitrosospira sp. and Nitrosomonas sp. Quantitative polymerase chain reaction results showed that the AOA abundance ranged from 2.09 × 10 4 to 2.94 × 10 5 gene copies/g soil. The highest number of AOA was detected in sample K, followed by samples R and H. AOB abundance varied between 2.91 × 10 5 and 1.05 × 10 6 gene copies/g soil, which was higher than that of AOA. Redundancy analysis indicated that electrical conductivity, pH, and NH 4 + -N might influence the community structure of AOA and AOB. AOB might play a more crucial role than AOA in ammonia oxidation based on AOB's higher diversity and abundance in the Ebinur Lake wetland in Xinjiang.

Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil.

PubMed

Scharko, Nicole K; Schütte, Ursel M E; Berke, Andrew E; Banina, Lauren; Peel, Hannah R; Donaldson, Melissa A; Hemmerich, Chris; White, Jeffrey R; Raff, Jonathan D

2015-12-01

Nitrous acid (HONO) is a photochemical source of hydroxyl radical and nitric oxide in the atmosphere that stems from abiotic and biogenic processes, including the activity of ammonia-oxidizing soil microbes. HONO fluxes were measured from agricultural and urban soil in mesocosm studies aimed at characterizing biogenic sources and linking them to indigenous microbial consortia. Fluxes of HONO from agricultural and urban soil were suppressed by addition of a nitrification inhibitor and enhanced by amendment with ammonium (NH4(+)), with peaks at 19 and 8 ng m(-2) s(-1), respectively. In addition, both agricultural and urban soils were observed to convert (15)NH4(+) to HO(15)NO. Genomic surveys of soil samples revealed that 1.5-6% of total expressed 16S rRNA sequences detected belonged to known ammonia oxidizing bacteria and archaea. Peak fluxes of HONO were directly related to the abundance of ammonia-oxidizer sequences, which in turn depended on soil pH. Peak HONO fluxes under fertilized conditions are comparable in magnitude to fluxes reported during field campaigns. The results suggest that biogenic HONO emissions will be important in soil environments that exhibit high nitrification rates (e.g., agricultural soil) although the widespread occurrence of ammonia oxidizers implies that biogenic HONO emissions are also possible in the urban and remote environment.

Urediospores of rust fungi are ice nucleation active at > -10 °C and harbor ice nucleation active bacteria

NASA Astrophysics Data System (ADS)

Morris, C. E.; Sands, D. C.; Glaux, C.; Samsatly, J.; Asaad, S.; Moukahel, A. R.; Gonçalves, F. L. T.; Bigg, E. K.

2013-04-01

Various features of the biology of the rust fungi and of the epidemiology of the plant diseases they cause illustrate the important role of rainfall in their life history. Based on this insight we have characterized the ice nucleation activity (INA) of the aerially disseminated spores (urediospores) of this group of fungi. Urediospores of this obligate plant parasite were collected from natural infections of 7 species of weeds in France, from coffee in Brazil and from field and greenhouse-grown wheat in France, the USA, Turkey and Syria. Immersion freezing was used to determine freezing onset temperatures and the abundance of ice nuclei in suspensions of washed spores. Microbiological analyses of spores from France, the USA and Brazil, and subsequent tests of the ice nucleation activity of the bacteria associated with spores were deployed to quantify the contribution of bacteria to the ice nucleation activity of the spores. All samples of spores were ice nucleation active, having freezing onset temperatures as high as -4 °C. Spores in most of the samples carried cells of ice nucleation-active strains of the bacterium Pseudomonas syringae (at rates of less than 1 bacterial cell per 100 urediospores), but bacterial INA accounted for only a small fraction of the INA observed in spore suspensions. Changes in the INA of spore suspensions after treatment with lysozyme suggest that the INA of urediospores involves a polysaccharide. Based on data from the literature, we have estimated the concentrations of urediospores in air at cloud height and in rainfall. These quantities are very similar to those reported for other biological ice nucleators in these same substrates. However, at cloud level convective activity leads to widely varying concentrations of particles of surface origin, so that mean concentrations can underestimate their possible effects on clouds. We propose that spatial and temporal concentrations of biological ice nucleators active at temperatures > -10 �

Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria.

PubMed

Taylor, Anne E; Giguere, Andrew T; Zoebelein, Conor M; Myrold, David D; Bottomley, Peter J

2017-04-01

Soil nitrification potential (NP) activities of ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) were evaluated across a temperature gradient (4-42 °C) imposed upon eight soils from four different sites in Oregon and modeled with both the macromolecular rate theory and the square root growth models to quantify the thermodynamic responses. There were significant differences in response by the dominant AOA and AOB contributing to the NPs. The optimal temperatures (T opt ) for AOA- and AOB-supported NPs were significantly different (P<0.001), with AOA having T opt >12 °C greater than AOB. The change in heat capacity associated with the temperature dependence of nitrification (ΔC P ‡ ) was correlated with T opt across the eight soils, and the ΔC P ‡ of AOB activity was significantly more negative than that of AOA activity (P<0.01). Model results predicted, and confirmatory experiments showed, a significantly lower minimum temperature (T min ) and different, albeit very similar, maximum temperature (T max ) values for AOB than for AOA activity. The results also suggested that there may be different forms of AOA AMO that are active over different temperature ranges with different T min , but no evidence of multiple T min values within the AOB. Fundamental differences in temperature-influenced properties of nitrification driven by AOA and AOB provides support for the idea that the biochemical processes associated with NH 3 oxidation in AOA and AOB differ thermodynamically from each other, and that also might account for the difficulties encountered in attempting to model the response of nitrification to temperature change in soil environments.

A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea.

PubMed

Liu, Ying; Ishino, Sonoko; Ishino, Yoshizumi; Pehau-Arnaudet, Gérard; Krupovic, Mart; Prangishvili, David

2017-07-01

Encapsidation of genetic material into polyhedral particles is one of the most common structural solutions employed by viruses infecting hosts in all three domains of life. Here, we describe a new virus of hyperthermophilic archaea, Sulfolobus polyhedral virus 1 (SPV1), which condenses its circular double-stranded DNA genome in a manner not previously observed for other known viruses. The genome complexed with virion proteins is wound up sinusoidally into a spherical coil which is surrounded by an envelope and further encased by an outer polyhedral capsid apparently composed of the 20-kDa virion protein. Lipids selectively acquired from the pool of host lipids are integral constituents of the virion. None of the major virion proteins of SPV1 show similarity to structural proteins of known viruses. However, minor structural proteins, which are predicted to mediate host recognition, are shared with other hyperthermophilic archaeal viruses infecting members of the order Sulfolobales The SPV1 genome consists of 20,222 bp and contains 45 open reading frames, only one-fifth of which could be functionally annotated. IMPORTANCE Viruses infecting hyperthermophilic archaea display a remarkable morphological diversity, often presenting architectural solutions not employed by known viruses of bacteria and eukaryotes. Here we present the isolation and characterization of Sulfolobus polyhedral virus 1, which condenses its genome into a unique spherical coil. Due to the original genomic and architectural features of SPV1, the virus should be considered a representative of a new viral family, "Portogloboviridae." Copyright © 2017 American Society for Microbiology.

Chaperonin Polymers in Archaea: The Cytoskeleton of Prokaryotes?

DOE R&D Accomplishments Database

Trent, J. D.; Kagawa, H. K.; Zaluzec, N. J.

1997-07-01

Chaperonins are protein complexes that play a critical role in folding nascent polypeptides under normal conditions and refolding damaged proteins under stress conditions. In all organisms these complexes are composed of evolutionarily conserved 60-kDa proteins arranged in double-ring structures with between 7 and 9 protein subunits per ring. These double ring structures are assumed to be the functional units in vivo, although they have never been observed inside cells. Here the authors show that the purified chaperonin from the hyperthermophilic archaeon Sulfolobus shibatae, which is closely related to chaperonins in eukaryotes, has a double ring structure at low concentrations (0.1 mg/ml), but at more physiological concentrations, the rings stack end to end to form polymers. The polymers are stable at physiological temperatures (75 C) and closely resemble structures observed inside unfixed S. shibatae cells. The authors suggest that in vivo chaperonin activity may be regulated by polymerization and that chaperonin polymers may act as a cytoskeleton-like structure in archaea and bacteria.

Discrimination of Pigments of Microalgae, Bacteria and Yeasts Using Lightweight Handheld Raman Spectrometers: Prospects for Astrobiology

NASA Astrophysics Data System (ADS)

Jehlicka, J.; Osterrothova, K.; Nedbalova, L.; Gunde-Cimerman, N.; Oren, A.

2014-06-01

Handheld Raman instrumentation with 532 nm lasers can be used to distinguish carotenoids of autotrophic microalgae, purple sulfur bacteria, halophilic Archaea and pigmented yeasts. Pigments are proposed as biomarkers for astrobiology of Mars.

Biology Students’ Initial Mental Model about Microorganism

NASA Astrophysics Data System (ADS)

Hamdiyati, Y.; Sudargo, F.; Redjeki, S.; Fitriani, A.

2017-02-01

The purpose of this study was to identify biology students’ initial mental model about microorganism. This research used descriptive method with 32 sixth semester biology students at Biology Education Departement-Universitas Pendidikan Indonesia as its respondents. Data was taken at the beginning of the 6th semester before respondents endure microbiology course. Instrument used to assess mental model was drawing-writing test in which it contains concepts such as structure of bacteria, archaea, virus, and fungi. Students were asked to describe their imagination about the structure of microorganisms and subsequently asked to explain the structure of microorganisms in writing through open-ended questions. Students’ response was then compared to scientists or experts’ mental models as the targeted mental model. Student mental models were categorized into five levels (levels 1-5), namely “there is no drawing/writing,” “wrong or irrelevant drawing/writing of question,” “partially correct drawing/writing,” “the drawing/writing that has some deficiencies,” and “completely correct and complete drawing/writing.” Results showed that the level of mental models through drawing or writing about the four concepts were varied. The highest level of mental models through drawing (D5) was found in the concept of bacteria, while the highest level of mental models through writing (W3) was found in the concept of bacteria, virus, and fungi. Mental model levels most commonly found in each concept through drawing-writing tests (D/W) were bacteria (D2/W2), Archaea (D1/W1 and D2/W2), virus (D3/W3), and fungi (D2/W1). From these results it is advisable to improve lectures and assessment strategy to enhance or complement students’ mental models about microorganisms.

[Features of adhesion of anaerobic periodontopathogenic bacteria and Candida albicans fungi to experimental samples of basis dental plastic depending on surface roughness and polishing method].

PubMed

Tsarev, V N; Ippolitov, E V; Trefilov, A G; Arutiunov, S D; Pivovarov, A A

2014-01-01

Study the main surface parameters of milled polyacrylic materials using atomic force microscopy and primary microbial adhesion of periodontopathogenic group bacteria and Candida albicans fungi taking into consideration the method of sample polishing. Studied samples: mill-treated without polishing (control); ergobox polished; polished in dental laboratory conditions; polished by a rubber brush in dentists' office. Microbial strains belonging to periodontopathogenic species (clinical isolates) that had been isolated from periodontal pockets of periodontitis patients: Porphyromonas gingivalis, Fusobacterium nucleatum, Streptococcus sanguis, C. albicans fungi were used for modelling experiments of primary adhesion of microbes to the material samples. S. sanguis had the highest degree of adhesion to polymer after milling, P. gingivalis, C. albicans--medium, F. nucleatum--low. A significant reduction of adhesion is observed during polishing in dental laboratory conditions or ergobox, less significant--during polishing in dental office. The data obtained allow to make a conclusion that the samples from polymer materials for preparation of prosthesis basis have varying degree of intensity of microbial adhesion of members of periodontopathogenic microflora and C. albicans fungi that depends on the polishing method, that accordingly determined the differences in colonization resistance against formation of microbial biofilm during polymer use in clinical conditions. . ,

Diversity and activity of nitrogen fixing archaea and bacteria associated with micro-environments of wetland rice

NASA Astrophysics Data System (ADS)

Schmidt, Hannes; Woebken, Dagmar

2017-04-01

Wetland rice is one of the world's most important crop plants. The cultivation on waterlogged paddy soils is strongly limited by nitrogen (N), which is typically supplied by industrial fertilizers that are not only costly but also exhibit hazardous effects on the environment. It has been reported that "Biological Nitrogen Fixation" through N2-fixing bacteria and archaea (diazotrophs) can alleviate the N-shortage in rice cultivation, thus carrying out an important ecosystem function. However, our understanding of the diversity and in situ N2 fixation activity of diazotrophs in flooded rice fields is still rudimentary. Moreover, knowledge on the impact of biochemical gradients established by root activity (i.e. exudation, radial oxygen loss) on the functioning of N-fixing microorganisms in paddy soil ecosystems is limited. We aimed at studying underlying processes on biologically relevant scales. Greenhouse studies were performed to identify key factors that control rice-diazotroph association and related N2 fixation activities. Paddy soils of different geographical origin were cultivated with two commercially used genotypes of wetland rice. Samples were separated into bulk soil, rhizosphere soil, rhizoplane, and roots at flowering stage of rice plant development. These samples were subjected to functional assays and various molecular biological techniques in order to analyze the associated diazotroph communities. Based on Illumina amplicon sequencing of nifH genes and transcripts, we show that the diversity and potential activity of diazotroph communities varies according to micro-environments. We will comparatively discuss the influence of (a) the soil microbial "seed bank" and (b) plant genotype in shaping the respective microbiomes and selecting for potentially active diazotrophs. Actual N2 fixation activities of soil-genotype combinations and micro-environments will be shown on the basis of incubation assays using 15N2-containing atmospheres. Areas of potential

The Diversity and Distribution of Fungi on Residential Surfaces

PubMed Central

Adams, Rachel I.; Miletto, Marzia; Taylor, John W.; Bruns, Thomas D.

2013-01-01

The predominant hypothesis regarding the composition of microbial assemblages in indoor environments is that fungal assemblages are structured by outdoor air with a moderate contribution by surface growth, whereas indoor bacterial assemblages represent a mixture of bacteria entered from outdoor air, shed by building inhabitants, and grown on surfaces. To test the fungal aspect of this hypothesis, we sampled fungi from three surface types likely to support growth and therefore possible contributors of fungi to indoor air: drains in kitchens and bathrooms, sills beneath condensation-prone windows, and skin of human inhabitants. Sampling was done in replicated units of a university-housing complex without reported mold problems, and sequences were analyzed using both QIIME and the new UPARSE approach to OTU-binning, to the same result. Surfaces demonstrated a mycological profile similar to that of outdoor air from the same locality, and assemblages clustered by surface type. “Weedy” genera typical of indoor air, such as Cladosporium and Cryptococcus, were abundant on sills, as were a diverse set of fungi of likely outdoor origin. Drains supported more depauperate assemblages than the other surfaces and contained thermotolerant genera such as Exophiala, Candida, and Fusarium. Most surprising was the composition detected on residents’ foreheads. In addition to harboring Malassezia, a known human commensal, skin also possessed a surprising richness of non-resident fungi, including plant pathogens such as ergot (Claviceps purperea). Overall, fungal richness across indoor surfaces was high, but based on known autecologies, most of these fungi were unlikely to be growing on surfaces. We conclude that while some endogenous fungal growth on typical household surfaces does occur, particularly on drains and skin, all residential surfaces appear – to varying degrees – to be passive collectors of airborne fungi of putative outdoor origin, a view of the origins of the

The diversity and distribution of fungi on residential surfaces.

PubMed

Adams, Rachel I; Miletto, Marzia; Taylor, John W; Bruns, Thomas D

2013-01-01

The predominant hypothesis regarding the composition of microbial assemblages in indoor environments is that fungal assemblages are structured by outdoor air with a moderate contribution by surface growth, whereas indoor bacterial assemblages represent a mixture of bacteria entered from outdoor air, shed by building inhabitants, and grown on surfaces. To test the fungal aspect of this hypothesis, we sampled fungi from three surface types likely to support growth and therefore possible contributors of fungi to indoor air: drains in kitchens and bathrooms, sills beneath condensation-prone windows, and skin of human inhabitants. Sampling was done in replicated units of a university-housing complex without reported mold problems, and sequences were analyzed using both QIIME and the new UPARSE approach to OTU-binning, to the same result. Surfaces demonstrated a mycological profile similar to that of outdoor air from the same locality, and assemblages clustered by surface type. "Weedy" genera typical of indoor air, such as Cladosporium and Cryptococcus, were abundant on sills, as were a diverse set of fungi of likely outdoor origin. Drains supported more depauperate assemblages than the other surfaces and contained thermotolerant genera such as Exophiala, Candida, and Fusarium. Most surprising was the composition detected on residents' foreheads. In addition to harboring Malassezia, a known human commensal, skin also possessed a surprising richness of non-resident fungi, including plant pathogens such as ergot (Claviceps purperea). Overall, fungal richness across indoor surfaces was high, but based on known autecologies, most of these fungi were unlikely to be growing on surfaces. We conclude that while some endogenous fungal growth on typical household surfaces does occur, particularly on drains and skin, all residential surfaces appear - to varying degrees - to be passive collectors of airborne fungi of putative outdoor origin, a view of the origins of the indoor

Isolation of Bacteria with Antifungal Activity against the Phytopathogenic Fungi Stenocarpella maydis and Stenocarpella macrospora

PubMed Central

Petatán-Sagahón, Iván; Anducho-Reyes, Miguel Angel; Silva-Rojas, Hilda Victoria; Arana-Cuenca, Ainhoa; Tellez-Jurado, Alejandro; Cárdenas-Álvarez, Isabel Oyuki; Mercado-Flores, Yuridia

2011-01-01

Stenocarpella maydis and Stenocarpella macrospora are the causal agents of ear rot in corn, which is one of the most destructive diseases in this crop worldwide. These fungi are important mycotoxin producers that cause different pathologies in farmed animals and represent an important risk for humans. In this work, 160 strains were isolated from soil of corn crops of which 10 showed antifungal activity against these phytopathogens, which, were identified as: Bacillus subtilis, Pseudomonas spp., Pseudomonas fluorescens, and Pantoea agglomerans by sequencing of 16S rRNA gene and the phylogenetic analysis. From cultures of each strain, extracellular filtrates were obtained and assayed to determine antifungal activity. The best filtrates were obtained in the stationary phase of B. subtilis cultures that were stable to the temperature and extreme pH values; in addition they did not show a cytotoxicity effect against brine shrimp and inhibited germination of conidia. The bacteria described in this work have the potential to be used in the control of white ear rot disease. PMID:22016606

Diversity of bacteria and archaea from a landfill in Chandigarh, India as revealed by culture-dependent and culture-independent molecular approaches.

PubMed

Krishnamurthi, S; Chakrabarti, T

2013-02-01

The bacterial community structure of a municipal landfill in Chandigarh, India was analysed by culture-dependent as well as culture-independent molecular approaches, and archaeal structure by the latter method. Samples were collected in two phases from the surface and a depth of 0.91 m in June, 2004 and from 0.91 m, 1.52 m and 1.68 m in May, 2005. After serial dilutions, samples were plated onto tryptic soy agar (TSA), plate count agar (PCA), tryptic soy broth agar (TSBA) and TSBA100 (TSBA diluted 100 times and solidified with agarose), and incubated aerobically at 30°C. The number of bacteria (CFU) on different media ranged between 9.4×10⁵g⁻¹ (on PCA) and 1.9×10⁷g⁻¹ (on TSA) (wet weight). The numbers of bacteria enumerated from plates incubated anaerobically (anaerobic agar and reinforced clostridial agar) were 2.1×10⁷and 1.7×10⁶g⁻¹, respectively. Of the 468 isolated and purified bacteria (183 in the first phase and 285 in the second phase), 135 were characterised using phenotypic characteristics as well as 16S rRNA gene sequence analysis. It was found that members of the phylum Firmicutes were overwhelmingly predominant (86.6%) in the landfill, followed by Actinobacteria (9.6%) and Proteobacteria (3.7%). Among the Firmicutes, at least 17 species from the single genus Bacillus were the most abundant inhabitants of the landfill. Detailed polyphasic characterisation of many of these isolates led to the discovery of a novel genus Paenisporosarcina (and the species P. quisquiliarum), a novel species of Microbacterium, M. immunditiarum, and reclassification of Sporosarcina macmurdoensis, Pelagibacillus goriensis, Bacillus silvestris, Bacillus insolitus, Bacillus psychrotolerans and Bacillus psychrodurans. Culture-independent analysis of two 16S rRNA gene libraries also revealed that the phylum Firmicutes was the predominant group in this community. The diversity of Archaea was found to be limited mainly to members of two orders: Methanosarcinales

[Fungi in the gut - the gut mycobiome].

PubMed

Hof, Herbert

2017-08-01

Many different fungi, including yeasts and molds, can be found in the intestinal tract of humans constituting the gut mycobiome. In case the bacterial flora is altered, the fungal flora may react inversely. By a so-called fungal diet, however, the composition of the mycobiome can hardly be influenced. Whereas some fungi are only transiently present in the gut after oral uptake, others, such as Candida, Saccharomyces, Rhodotorula, Trichosporon, Geotrichum, amongst others, are members of the residential, autochthonous gut flora. Some of these fungi exert beneficial effects, for example by synthesizing useful materials. Rhodotorula can produce fatty acids and carotenoids. Others are able to metabolize toxic compounds, for example mycotoxins as well as procarcinogenic items in food. Toxins, as well as pathogenic bacteria, can be bound to mannans on the surface of fungi und can consequently be exported. Some fungi are said to exert probiotic activities. Certain fungal constituents, such as glucans, may even stimulate the immune system. On the other hand, some fungi cannot only colonize the gut asymptomatically but can also be noxious under certain conditions when, for example, the bacterial flora is disturbed. By means of their virulence factors, they can damage the gut epithelium and even penetrate into the Mukosa inducing inflammation, They can also aggravate chronic inflammatory processes. Fungi play a role in the development of obesity. Lastly, fungi in the gut represent a reservoir from which they may spread to other sites when the conditions are favorable. © Georg Thieme Verlag KG Stuttgart · New York.

Influence of plant origin natural α-pinene with different enantiomeric composition on bacteria, yeasts and fungi.

PubMed

Ložienė, Kristina; Švedienė, Jurgita; Paškevičius, Algimantas; Raudonienė, Vita; Sytar, Oksana; Kosyan, Anatoliy

2018-04-22

Although the nature-identical chemical compounds are cheaper, they not always repeat biological activity of plant origin natural chemical compounds, often react allergies and resistance of microorganisms. The aim of this study was to investigate effects of Juniperus communis origin α-pinene with different enantiomeric composition on bacteria, yeasts and fungi. Results showed that different enantiomeric composition of α-pinene have different activities on microorganisms: essential oil with (1S)-(-) ≈ (1R)-(+) enantiomeric composition of α-pinene influenced on some microorganisms stronger than essential oil with (1S)-(-) < (1R)-(+) enantiomeric composition of α-pinene; the pure natural α-pinene with enantiomeric composition S < R more strongly inhibited growth of investigated bacteria and Candida yeasts, α-pinene with enantiomeric composition S ≈ R - growth of Trichophyton and Aspergillus. (1S)-(-) and (1R)-(+) enantiomeric forms of α-pinene can have also different synergistic effects with other compounds of essential oil. The results of study showed that the same amount of α-pinene with different enantiomeric composition can have diverse antimicrobial potential due different specific interactions with other chemical compounds of essential oil. Therefore, it is very important to determine and present the enantiomeric composition of those plant origin compounds, which are characterized by enantiomerisation, during the course of research of biological activities of natural plant products (essential oils and other) and their isolated compounds. Copyright © 2018 Elsevier B.V. All rights reserved.

The Interaction between Arbuscular Mycorrhizal Fungi and Endophytic Bacteria Enhances Plant Growth of Acacia gerrardii under Salt Stress

PubMed Central

Hashem, Abeer; Abd_Allah, Elsayed F.; Alqarawi, Abdulaziz A.; Al-Huqail, Asma A.; Wirth, Stephan; Egamberdieva, Dilfuza

2016-01-01

Microbes living symbiotically in plant tissues mutually cooperate with each other by providing nutrients for proliferation of the partner organism and have a beneficial effect on plant growth. However, few studies thus far have examined the interactive effect of endophytic bacteria and arbuscular mycorrhizal fungi (AMF) in hostile conditions and their potential to improve plant stress tolerance. In this study, we investigated how the synergistic interactions of endophytic bacteria and AMF affect plant growth, nodulation, nutrient acquisition and stress tolerance of Acacia gerrardii under salt stress. Plant growth varied between the treatments with both single inoculants and was higher in plants inoculated with the endophytic B. subtilis strain than with AMF. Co-inoculated A. gerrardii had a significantly greater shoot and root dry weight, nodule number, and leghemoglobin content than those inoculated with AMF or B. subtilis alone under salt stress. The endophytic B. subtilis could alleviate the adverse effect of salt on AMF colonization. The differences in nitrate and nitrite reductase and nitrogenase activities between uninoculated plants and those inoculated with AMF and B. subtilis together under stress were significant. Both inoculation treatments, either B. subtilis alone or combined with AMF, enhanced the N, P, K, Mg, and Ca contents and phosphatase activities in salt-stressed A. gerrardii tissues and reduced Na and Cl concentration, thereby protecting salt-stressed plants from ionic and osmotic stress-induced changes. In conclusion, our results indicate that endophytic bacteria and AMF contribute to a tripartite mutualistic symbiosis in A. gerrardii and are coordinately involved in the plant adaptation to salt stress tolerance. PMID:27486442

In-Vitro Archaeacidal Activity of Biocides against Human-Associated Archaea

PubMed Central

Khelaifia, Saber; Michel, Jean Brunel; Drancourt, Michel

2013-01-01

Background Several methanogenic archaea have been detected in the human intestinal microbiota. These intestinal archaea may contaminate medical devices such as colonoscopes. However, no biocide activity has been reported among these human-associated archaea. Methodology The minimal archaeacidal concentration (MAC) of peracetic acid, chlorhexidine, squalamine and twelve parent synthetic derivatives reported in this study was determined against five human-associated methanogenic archaea including Methanobrevibacter smithii, Methanobrevibacter oralis, Methanobrevibacter arboriphilicus, Methanosphaera stadtmanae, Methanomassiliicoccus luminyensis and two environmental methanogens Methanobacterium beijingense and Methanosaeta concilii by using a serial dilution technique in Hungates tubes. Principal Findings MAC of squalamine derivative S1 was 0.05 mg/L against M. smithii strains, M. oralis, M. arboriphilicus, M. concilii and M. beijingense whereas MAC of squalamine and derivatives S2–S12 varied from 0.5 to 5 mg/L. For M. stadtmanae and M. luminyensis, MAC of derivative S1 was 0.1 mg/L and varied from 1 to ≥10 mg/L for squalamine and its parent derivatives S2–S12. Under the same experimental conditions, chlorhexidine and peracetic acid lead to a MAC of 0.2 and 1.5 mg/L, respectively against all tested archaea. Conclusions/Significance Squalamine derivative S1 exhibited a 10–200 higher archaeacidal activity than other tested squalamine derivatives, on the majority of human-associated archaea. As previously reported and due to their week corrosivity and their wide spectrum of antibacterial and antifungal properties, squalamine and more precisely derivative S1 appear as promising compounds to be further tested for the decontamination of medical devices contaminated by human-associated archaea. PMID:23658767

Overview of Archaea

NASA Astrophysics Data System (ADS)

Pikuta, Elena V.

2011-10-01

Archaea were separated from Eubacteria after discovery of their specifics in cell outer membrane that usually not affected by common antibiotics. Phylogenetic analysis introduced by Karl Wöese supported this separation. Presently, only two phyla Crenarchaeota and Euryarchaeota include the valid representatives. Another three phyla that were proposed based on the sequence analysis of environmental samples, do not contain validly published species, and for this reason they are not included in this review. The phylum Euryarchaeota currently includes eight classes and ten orders, while the Crenarchaeota phylum contains the only class with five orders. Members of the phyla Crenarchaeota have two or three family B and no family D DNA polymerases, but members of the Euryarchaeota contain the only family B polymerases and the only family D polymerases, and it is still not clear, which is the main functional enzyme in the replication process. In this article, we are present an update and comparative analysis for this domain, discussing unique features of this group and Evolution, estimating their physiology within the matrix of physic-chemical factors, and outlining future perspectives in their study. Rules of the diagonal for the diagrams with all Archaea are presented and discussed.

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

PubMed Central

2017-01-01

Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea. We briefly review the GEM construction process and the genealogy of the archaeal models. The major insights gained during the construction of these models are then reviewed with specific focus on novel metabolic pathway predictions and growth characteristics. Metabolic pathway usage is discussed in the context of the composition of each organism's biomass and their specific energy and growth requirements. We show how the metabolic models can be used to study the evolution of metabolism in archaea. Conservation of particular metabolic pathways can be studied by comparing reactions using the genes associated with their enzymes. This demonstrates the utility of GEMs to evolutionary studies, far beyond their original purpose of metabolic modeling; however, much needs to be done before archaeal models are as extensively complete as those for bacteria. PMID:28133437

Halophilic archaea cultivated from surface sterilized middle-late eocene rock salt are polyploid.

PubMed

Jaakkola, Salla T; Zerulla, Karolin; Guo, Qinggong; Liu, Ying; Ma, Hongling; Yang, Chunhe; Bamford, Dennis H; Chen, Xiangdong; Soppa, Jörg; Oksanen, Hanna M

2014-01-01

Live bacteria and archaea have been isolated from several rock salt deposits of up to hundreds of millions of years of age from all around the world. A key factor affecting their longevity is the ability to keep their genomic DNA intact, for which efficient repair mechanisms are needed. Polyploid microbes are known to have an increased resistance towards mutations and DNA damage, and it has been suggested that microbes from deeply buried rock salt would carry several copies of their genomes. Here, cultivable halophilic microbes were isolated from a surface sterilized middle-late Eocene (38-41 million years ago) rock salt sample, drilled from the depth of 800 m at Yunying salt mine, China. Eight unique isolates were obtained, which represented two haloarchaeal genera, Halobacterium and Halolamina. We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11-14 genomes per cell in exponential growth phase. The ploidy level was slightly downregulated in stationary growth phase, but the cells still had an average genome copy number of 6-8. The polyploidy of halophilic archaea living in ancient rock salt might be a factor explaining how these organisms are able to overcome the challenge of prolonged survival during their entombment.

Fungi contamination of drinking water.

PubMed

Al-Gabr, Hamid Mohammad; Zheng, Tianling; Yu, Xin

2014-01-01

Aquatic fungi commonly infest various aqueous environments and play potentially crucial roles in nutrient and carbon cycling. Aquatic fungi also interact with other organisms to influence food web dynamics. In recent decades, numerous studies have been conducted to address the problem of microorganism contamination of water. The major concern has been potential effects on human health from exposure to certain bacteria, viruses, and protozoa that inhabit water and the microbial metabolites,pigments, and odors which are produced in the water, and their effects on human health and animals. Fungi are potentially important contaminants because they produce certain toxic metabolites that can cause severe health hazards to humans and animals. Despite the potential hazard posed by fungi, relatively few studies on them as contaminants have been reported for some countries.A wide variety of fungi species have been isolated from drinking water, and some of them are known to be strongly allergenic and to cause skin irritation, or immunosuppression in immunocompromised individuals (e.g., AIDS, cancer, or organ transplant patients). Mycotoxins are naturally produced as secondary metabolites by some fungi species, and exposure of humans or animals to them can cause health problems. Such exposure is likely to occur from dietary intake of either food,water or beverages made with water. However, mycotoxins, as residues in water,may be aerosolized when showering or when being sprayed for various purposes and then be subject to inhalation. Mycotoxins, or at least some of them, are regarded to be carcinogenic. There is also some concern that toxic mycotoxins or other secondary metabolites of fungi could be used by terrorists as a biochemical weapon by adding amounts of them to drinking water or non drinking water. Therefore, actions to prevent mycotoxin contaminated water from affecting either humans or animals are important and are needed. Water treatment plants may serve to partially

Archaea in the foregut of macropod marsupials: PCR and amplicon sequence-based observations.

PubMed

Klieve, A V; Ouwerkerk, D; Maguire, A J

2012-11-01

To investigate, using culture-independent techniques, the presence and diversity of methanogenic archaea in the foregut of kangaroos. DNA was extracted from forestomach contents of 42 kangaroos (three species), three sheep and three cattle. Four qualitative and quantitative PCR assays targeting the archaeal domain (16S rRNA gene) or the functional methanogenesis gene, mcrA, were used to determine the presence and population density of archaea in kangaroos and whether they were likely to be methanogens. All ruminal samples were positive for archaea, produced PCR product of expected size, contained high numbers of archaea and high numbers of cells with mcrA genes. Kangaroos were much more diverse and contradictory. Fourteen kangaroos had detectable archaea with numbers 10- to 1000-fold fewer than sheep and cattle. Many kangaroos that did not possess archaea were positive for the mcrA gene and had detectable numbers of cells with this gene and vice versa. DNA sequence analysis of kangaroos' archaeal 16S rRNA gene clones show that many methanogens were related to Methanosphaera stadmanae. Other sequences were related to non-methanogenic archaea (Thermoplasma sp.), and a number of kangaroos had mcrA gene sequences related to methane oxidising archaea (ANME). Discrepancies between qualitative and quantitative PCR assays for archaea and the mcrA gene suggest that the archaeal communities are very diverse and it is possible that novel species exist. Archaea (in general) were below detectable limits in many kangaroos, especially Red kangaroos; when present they are in lower numbers than in ruminants, and the archaea are not necessarily methanogenic. The determination of why this is the case in the kangaroo foregut could assist in reducing emissions from other ecosystems in the future. © 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Antimicrobial activity of filamentous fungi isolated from highly antibiotic-contaminated river sediment

PubMed Central

Svahn, K. Stefan; Göransson, Ulf; El-Seedi, Hesham; Bohlin, Lars; Larsson, D.G. Joakim; Olsen, Björn; Chryssanthou, Erja

2012-01-01

Background Filamentous fungi are well known for their production of substances with antimicrobial activities, several of which have formed the basis for the development of new clinically important antimicrobial agents. Recently, environments polluted with extraordinarily high levels of antibiotics have been documented, leading to strong selection pressure on local sentinel bacterial communities. In such microbial ecosystems, where multidrug-resistant bacteria are likely to thrive, it is possible that certain fungal antibiotics have become less efficient, thus encouraging alternative strategies for fungi to compete with bacteria. Methods In this study, sediment of a highly antibiotic-contaminated Indian river was sampled in order to investigate the presence of cultivable filamentous fungi and their ability to produce substances with antimicrobial activity. Results Sixty one strains of filamentous fungi, predominantly various Aspergillus spp. were identified. The majority of the Aspergillus strains displayed antimicrobial activity against methicillin-resistant Staphylococcus aureus, extended-spectrum beta-lactamase-producing Escherichia coli, vancomycin-resistant Enterococcus faecalis and Candida albicans. Bioassay-guided isolation of the secondary metabolites of A. fumigatus led to the identification of gliotoxin. Conclusion This study demonstrated proof of principle of using bioassay-guided isolation for finding bioactive molecules. PMID:22957125

Microbial fouling and corrosion of carbon steel in deep anoxic alkaline groundwater.

PubMed

Rajala, Pauliina; Bomberg, Malin; Vepsäläinen, Mikko; Carpén, Leena

2017-02-01

Understanding the corrosion of carbon steel materials of low and intermediate level radioactive waste under repository conditions is crucial to ensure the safe storage of radioactive contaminated materials. The waste will be in contact with the concrete of repository silos and storage containers, and eventually with groundwater. In this study, the corrosion of carbon steel under repository conditions as well as the microbial community forming biofilm on the carbon steel samples, consisting of bacteria, archaea, and fungi, was studied over a period of three years in a groundwater environment with and without inserted concrete. The number of biofilm forming bacteria and archaea was 1,000-fold lower, with corrosion rates 620-times lower in the presence of concrete compared to the natural groundwater environment. However, localized corrosion was detected in the concrete-groundwater environment indicating the presence of local microenvironments where the conditions for pitting corrosion were favorable.

Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils

PubMed Central

Zhang, Li-Mei; Hu, Hang-Wei; Shen, Ju-Pei; He, Ji-Zheng

2012-01-01

Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. 13CO2-DNA-stable isotope probing results showed significant assimilation of 13C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO2 fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active 13CO2-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils. PMID:22134644

Characterization and quantification of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a nitrogen-removing reactor using T-RFLP and qPCR

PubMed Central

Jin, Tao; Yan, Qingmei

2010-01-01

Using ammonia monooxygenase α-subunit (amoA) gene and 16S rRNA gene, the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a nitrogen-removing reactor, which was operated for five phases, were characterized and quantified by cloning, terminal restriction fragment length polymorphism (T-RFLP), and quantitative polymerase chain reaction (qPCR). The results suggested that the dominant AOB in the reactor fell to the genus Nitrosomonas, while the dominant AOA belonged to Crenarchaeotal Group I.1a in phylum Crenarchaeota. Real-time PCR results demonstrated that the levels of AOB amoA varied from 2.9 × 103 to 2.3 × 105 copies per nanogram DNA, greatly (about 60 times) higher than those of AOA, which ranged from 1.7 × 102 to 3.8 × 103 copies per nanogram DNA. This indicated the possible leading role of AOB in the nitrification process in this study. T-RFLP results showed that the AOB community structure significantly shifted in different phases while AOA only showed one major peak for all the phases. The analyses also suggested that the AOB community was more sensitive than that of AOA to operational conditions, such as ammonia loading and dissolved oxygen. PMID:20405121

Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene.

PubMed

Offre, Pierre; Prosser, James I; Nicol, Graeme W

2009-10-01

Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 degrees C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.

Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea

PubMed Central

2017-01-01

ABSTRACT All organisms must adapt to ever-changing environmental conditions and accordingly have evolved diverse signal transduction systems. In bacteria, the most abundant networks are built around the two-component signal transduction systems that include histidine kinases and receiver domains. In contrast, eukaryotic signal transduction is dominated by serine/threonine/tyrosine protein kinases. Both of these systems are also found in archaea, but they are not as common and diversified as their bacterial and eukaryotic counterparts, suggesting the possibility that archaea have evolved other, still uncharacterized signal transduction networks. Here we propose a role for KaiC family ATPases, known to be key components of the circadian clock in cyanobacteria, in archaeal signal transduction. The KaiC family is notably expanded in most archaeal genomes, and although most of these ATPases remain poorly characterized, members of the KaiC family have been shown to control archaellum assembly and have been found to be a stable component of the gas vesicle system in Halobacteria. Computational analyses described here suggest that KaiC-like ATPases and their homologues with inactivated ATPase domains are involved in many other archaeal signal transduction pathways and comprise major hubs of complex regulatory networks. We predict numerous input and output domains that are linked to KaiC-like proteins, including putative homologues of eukaryotic DEATH domains that could function as adapters in archaeal signaling networks. We further address the relationships of the archaeal family of KaiC homologues to the bona fide KaiC of cyanobacteria and implications for the existence of a KaiC-based circadian clock apparatus in archaea. PMID:29208747

Ether Lipids of Planktonic Archaea in the Marine Water Column

PubMed Central

Hoefs, M.; Schouten, S.; De Leeuw, J. W.; King, L. L.; Wakeham, S. G.; Damste, J.

1997-01-01

Acyclic and cyclic biphytanes derived from the membrane ether lipids of archaea were found in water column particulate and sedimentary organic matter from several oxic and anoxic marine environments. Compound-specific isotope analyses of the carbon skeletons suggest that planktonic archaea utilize an isotopically heavy carbon source such as algal carbohydrates and proteins or dissolved bicarbonate. Due to their high preservation potential, these lipids provide a fossil record of planktonic archaea and suggest that they have thrived in marine environments for more than 50 million years. PMID:16535669

Indole-3-acetic acid: A widespread physiological code in interactions of fungi with other organisms

PubMed Central

Fu, Shih-Feng; Wei, Jyuan-Yu; Chen, Hung-Wei; Liu, Yen-Yu; Lu, Hsueh-Yu; Chou, Jui-Yu

2015-01-01

Plants as well as microorganisms, including bacteria and fungi, produce indole-3-acetic acid (IAA). IAA is the most common plant hormone of the auxin class and it regulates various aspects of plant growth and development. Thus, research is underway globally to exploit the potential for developing IAA-producing fungi for promoting plant growth and protection for sustainable agriculture. Phylogenetic evidence suggests that IAA biosynthesis evolved independently in bacteria, microalgae, fungi, and plants. Present studies show that IAA regulates the physiological response and gene expression in these microorganisms. The convergent evolution of IAA production leads to the hypothesis that natural selection might have favored IAA as a widespread physiological code in these microorganisms and their interactions. We summarize recent studies of IAA biosynthetic pathways and discuss the role of IAA in fungal ecology. PMID:26179718

Effect of pH buffering capacity and sources of dietary sulfur on rumen fermentation, sulfide production, methane production, sulfate reducing bacteria, and total Archaea in in vitro rumen cultures.

PubMed

Wu, Hao; Meng, Qingxiang; Yu, Zhongtang

2015-06-01

The effects of three types of dietary sulfur on in vitro fermentation characteristics, sulfide production, methane production, and microbial populations at two different buffer capacities were examined using in vitro rumen cultures. Addition of dry distilled grain with soluble (DDGS) generally decreased total gas production, degradation of dry matter and neutral detergent fiber, and concentration of total volatile fatty acids, while increasing ammonia concentration. High buffering capacity alleviated these adverse effects on fermentation. Increased sulfur content resulted in decreased methane emission, but total Archaea population was not changed significantly. The population of sulfate reducing bacteria was increased in a sulfur type-dependent manner. These results suggest that types of dietary sulfur and buffering capacity can affect rumen fermentation and sulfide production. Diet buffering capacity, and probably alkalinity, may be increased to alleviate some of the adverse effects associated with feeding DDGS at high levels. Copyright © 2015 Elsevier Ltd. All rights reserved.

Implications of Antimicrobial Combinations in Complex Wound Biofilms Containing Fungi.

PubMed

Townsend, Eleanor M; Sherry, Leighann; Kean, Ryan; Hansom, Donald; Mackay, William G; Williams, Craig; Butcher, John; Ramage, Gordon

2017-09-01

Diabetic foot ulcer treatment currently focuses on targeting bacterial biofilms, while dismissing fungi. To investigate this, we used an in vitro biofilm model containing bacteria and fungi, reflective of the wound environment, to test the impact of antimicrobials. Here we showed that while monotreatment approaches influenced biofilm composition, this had no discernible effect on overall quantity. Only by combining bacterium- and fungus-specific antibiotics were we able to decrease the biofilm bioburden, irrespective of composition. Copyright © 2017 American Society for Microbiology.

Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru

PubMed Central

Biddle, Jennifer F.; Lipp, Julius S.; Lever, Mark A.; Lloyd, Karen G.; Sørensen, Ketil B.; Anderson, Rika; Fredricks, Helen F.; Elvert, Marcus; Kelly, Timothy J.; Schrag, Daniel P.; Sogin, Mitchell L.; Brenchley, Jean E.; Teske, Andreas; House, Christopher H.; Hinrichs, Kai-Uwe

2006-01-01

Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane–carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100–2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea. PMID:16505362

A Novel Pathway for the Biosynthesis of Heme in Archaea: Genome-Based Bioinformatic Predictions and Experimental Evidence

PubMed Central

Storbeck, Sonja; Rolfes, Sarah; Raux-Deery, Evelyne; Warren, Martin J.; Jahn, Dieter; Layer, Gunhild

2010-01-01

Heme is an essential prosthetic group for many proteins involved in fundamental biological processes in all three domains of life. In Eukaryota and Bacteria heme is formed via a conserved and well-studied biosynthetic pathway. Surprisingly, in Archaea heme biosynthesis proceeds via an alternative route which is poorly understood. In order to formulate a working hypothesis for this novel pathway, we searched 59 completely sequenced archaeal genomes for the presence of gene clusters consisting of established heme biosynthetic genes and colocalized conserved candidate genes. Within the majority of archaeal genomes it was possible to identify such heme biosynthesis gene clusters. From this analysis we have been able to identify several novel heme biosynthesis genes that are restricted to archaea. Intriguingly, several of the encoded proteins display similarity to enzymes involved in heme d 1 biosynthesis. To initiate an experimental verification of our proposals two Methanosarcina barkeri proteins predicted to catalyze the initial steps of archaeal heme biosynthesis were recombinantly produced, purified, and their predicted enzymatic functions verified. PMID:21197080

Perspectives on biotechnological applications of archaea.

PubMed

Schiraldi, Chiara; Giuliano, Mariateresa; De Rosa, Mario

2002-09-01

Many archaea colonize extreme environments. They include hyperthermophiles, sulfur-metabolizing thermophiles, extreme halophiles and methanogens. Because extremophilic microorganisms have unusual properties, they are a potentially valuable resource in the development of novel biotechnological processes. Despite extensive research, however, there are few existing industrial applications of either archaeal biomass or archaeal enzymes. This review summarizes current knowledge about the biotechnological uses of archaea and archaeal enzymes with special attention to potential applications that are the subject of current experimental evaluation. Topics covered include cultivation methods, recent achievements in genomics, which are of key importance for the development of new biotechnological tools, and the application of wild-type biomasses, engineered microorganisms, enzymes and specific metabolites in particular bioprocesses of industrial interest.

Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices.

PubMed

He, Ji-Zheng; Shen, Ju-Pei; Zhang, Li-Mei; Zhu, Yong-Guan; Zheng, Yuan-Ming; Xu, Ming-Gang; Di, Hongjie

2007-09-01

The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated by using quantitative real-time polymerase chain reaction, cloning and sequencing approaches based on amoA genes. The soil, classified as agri-udic ferrosols with pH (H(2)O) ranging from 3.7 to 6.0, was sampled in summer and winter from long-term field experimental plots which had received 16 years continuous fertilization treatments, including fallow (CK0), control without fertilizers (CK) and those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK, PK, NPK and NPK plus organic manure (OM). Population sizes of AOB and AOA changed greatly in response to the different fertilization treatments. The NPK + OM treatment had the highest copy numbers of AOB and AOA amoA genes among the treatments that received mineral fertilizers, whereas the lowest copy numbers were recorded in the N treatment. Ammonia-oxidizing archaea were more abundant than AOB in all the corresponding treatments, with AOA to AOB ratios ranging from 1.02 to 12.36. Significant positive correlations were observed among the population sizes of AOB and AOA, soil pH and potential nitrification rates, indicating that both AOB and AOA played an important role in ammonia oxidation in the soil. Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from different treatments were affiliated with Nitrosospira or Nitrosospira-like species and grouped into cluster 3, and little difference in AOB community composition was recorded among different treatments. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). Cluster M dominated exclusively in the N, NP, NK and PK treatments, indicating a pronounced difference in the community composition of AOA in response to the long-term fertilization treatments. These findings could be fundamental to improve our understanding of the importance of

Phylogenetic characterization of culturable bacteria and fungi associated with tarballs from Betul beach, Goa, India.

PubMed

Shinde, Varsha Laxman; Meena, Ram Murti; Shenoy, Belle Damodara

2018-03-01

Tarballs are semisolid blobs of crude oil, normally formed due to weathering of crude-oil in the sea after any kind of oil spills. Microorganisms are believed to thrive on hydrocarbon-rich tarballs and possibly assist in biodegradation. The taxonomy of ecologically and economically important tarball-associated microbes, however, needs improvement as DNA-based identification and phylogenetic characterization have been scarcely incorporated into it. In this study, bacteria and fungi associated with tarballs from touristic Betul beach in Goa, India were isolated, followed by phylogenetic analyses of 16S rRNA gene and the ITS sequence-data to decipher their clustering patterns with closely-related taxa. The gene-sequence analyses identified phylogenetically diverse 20 bacterial genera belonging to the phyla Proteobacteria (14), Actinobacteria (3), Firmicutes (2) and Bacteroidetes (1), and 8 fungal genera belonging to the classes Eurotiomycetes (6), Sordariomycetes (1) and Leotiomycetes (1) associated with the Betul tarball samples. Future studies employing a polyphasic approach, including multigene sequence-data, are needed for species-level identification of culturable tarball-associated microbes. This paper also discusses potentials of tarball-associated microbes to degrade hydrocarbons. Copyright © 2018 Elsevier Ltd. All rights reserved.

Chaperonin polymers in archaea: The cytoskeleton of prokaryotes?

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

Trent, J.D.; Kagawa, H.K.; Zaluzec, N.J.

Chaperonins are protein complexes that play a critical role in folding nascent polypeptides under normal conditions and refolding damaged proteins under stress conditions. In all organisms these complexes are composed of evolutionarily conserved 60-kDa proteins arranged in double-ring structures with between 7 and 9 protein subunits per ring. These double ring structures are assumed to be the functional units in vivo, although they have never been observed inside cells. Here the authors show that the purified chaperonin from the hyperthermophilic archaeon Sulfolobus shibatae, which is closely related to chaperonins in eukaryotes, has a double ring structure at low concentrations (0.1more » mg/ml), but at more physiological concentrations, the rings stack end to end to form polymers. The polymers are stable at physiological temperatures (75 C) and closely resemble structures observed inside unfixed S. shibatae cells. The authors suggest that in vivo chaperonin activity may be regulated by polymerization and that chaperonin polymers may act as a cytoskeleton-like structure in archaea and bacteria.« less

Extreme halophilic archaea derive from two distinct methanogen Class II lineages.

PubMed

Aouad, Monique; Taib, Najwa; Oudart, Anne; Lecocq, Michel; Gouy, Manolo; Brochier-Armanet, Céline

2018-04-20

Phylogenetic analyses of conserved core genes have disentangled most of the ancient relationships in Archaea. However, some groups remain debated, like the DPANN, a deep-branching super-phylum composed of nanosized archaea with reduced genomes. Among these, the Nanohaloarchaea require high-salt concentrations for growth. Their discovery in 2012 was significant because they represent, together with Halobacteria (a Class belonging to Euryarchaeota), the only two described lineages of extreme halophilic archaea. The phylogenetic position of Nanohaloarchaea is highly debated, being alternatively proposed as the sister-lineage of Halobacteria or a member of the DPANN super-phylum. Pinpointing the phylogenetic position of extreme halophilic archaea is important to improve our knowledge of the deep evolutionary history of Archaea and the molecular adaptive processes and evolutionary paths that allowed their emergence. Using comparative genomic approaches, we identified 258 markers carrying a reliable phylogenetic signal. By combining strategies limiting the impact of biases on phylogenetic inference, we showed that Nanohaloarchaea and Halobacteria represent two independent lines that derived from two distinct but related methanogens Class II lineages. This implies that adaptation to high salinity emerged twice independently in Archaea and indicates that their emergence within DPANN in previous studies is likely the consequence of a tree reconstruction artifact, challenging the existence of this super-phylum. Copyright © 2018. Published by Elsevier Inc.

Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea

PubMed Central

Duszenko, Nikolas

2017-01-01

ABSTRACT Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role as quinones in the electron transport chain. To extend the analogy between quinones and MPh, we compared the MPh pool sizes between two well-studied Methanosarcina species, Methanosarcina acetivorans C2A and Methanosarcina barkeri Fusaro, to the quinone pool size in the bacterium Escherichia coli. We found the quantity of MPh per cell increases as cultures transition from exponential growth to stationary phase, and absolute quantities of MPh were 3-fold higher in M. acetivorans than in M. barkeri. The concentration of MPh suggests the cell membrane of M. acetivorans, but not of M. barkeri, is electrically quantized as if it were a single conductive metal sheet and near optimal for rate of electron transport. Similarly, stationary (but not exponentially growing) E. coli cells also have electrically quantized membranes on the basis of quinone content. Consistent with our hypothesis, we demonstrated that the exogenous addition of phenazine increases the growth rate of M. barkeri three times that of M. acetivorans. Our work suggests electron flux through MPh is naturally higher in M. acetivorans than in M. barkeri and that hydrogen cycling is less efficient at conserving energy than scalar proton translocation using MPh. IMPORTANCE Can we grow more from less? The ability to optimize and manipulate metabolic efficiency in cells is the difference between commercially viable and nonviable renewable technologies. Much can be learned from methane-producing archaea (methanogens) which evolved a successful metabolic lifestyle under extreme thermodynamic constraints. Methanogens use highly efficient electron transport

Composition of ammonia-oxidizing archaea and their contribution to nitrification in a high-temperature hot spring

NASA Astrophysics Data System (ADS)

Chen, S.; Peng, X.-T.; Xu, H.-C.; Ta, K.-W.

2015-10-01

The oxidation of ammonia by microbes and associated organisms has been shown to occur in diverse natural environments. However, the contribution of ammonia-oxidizing archaea to nitrification in high-temperature environments remains unclear. Here, we studied in situ ammonia oxidation rates and the abundance of ammonia-oxidizing archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3- pool dilution technique in the surface sinter and bottom sediments were 4.8 and 5.3 nmol N g-1 h-1, respectively. Relative abundances of Crenarchaea in both samples were determined by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic "Candidatus Nitrosocaldus yellowstonii", which represented the most abundant operation taxonomic units (OTU) in both sediments. Furthermore, bacterial amoA was not detected in this study. Quantitative PCR (qPCR) indicated that AOA and 16S rRNA genes were present in the range of 2.75 to 9.80 × 105 and 0.128 to 1.96 × 108 gene copies g-1 sediment. The cell-specific nitrification rates were estimated to be in the range of 0.41 to 0.79 fmol N archaeal cell-1 h-1, which is consistent with earlier estimates in estuary environments. This study demonstrated that AOA were widely involved in nitrification in this hot spring. It further indicated the importance of archaea rather than bacteria in driving the nitrogen cycle in terrestrial geothermal environments.

CRISPR-Cas Technologies and Applications in Food Bacteria.

PubMed

Stout, Emily; Klaenhammer, Todd; Barrangou, Rodolphe

2017-02-28

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity.

Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria

PubMed Central

Mukai, Takahito; Reynolds, Noah M.; Crnković, Ana; Söll, Dieter

2017-01-01

The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNATyr and tRNATrp genes reveal bacterial or archaeal origins. We identified a trace of domain fusion and swapping in the archaeal-type TyrRS gene of a bacterial lineage, suggesting that CPR bacteria may have used this mechanism to create diverse proteins. Archaeal-type TrpRS of bacteria and a few TrpRS species of DPANN archaea represent a new phylogenetic clade (named TrpRS-A). The TrpRS-A open reading frames (ORFs) are always associated with another ORF (named ORF1) encoding an unknown protein without global sequence identity to any known protein. However, our protein structure prediction identified a putative HIGH-motif and KMSKS-motif as well as many α-helices that are characteristic of class I aminoacyl-tRNA synthetase (aaRS) homologs. These results provide another example of the diversity of molecular components that implement the genetic code and provide a clue to the early evolution of life and the genetic code. PMID:28230768

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures.

PubMed

Pride, David T; Schoenfeld, Thomas

2008-09-17

Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs

Physical methods for genetic transformation of fungi and yeast

NASA Astrophysics Data System (ADS)

Rivera, Ana Leonor; Magaña-Ortíz, Denis; Gómez-Lim, Miguel; Fernández, Francisco; Loske, Achim M.

2014-06-01

The production of transgenic fungi is a routine process. Currently, it is possible to insert genes from other fungi, viruses, bacteria and even animals, albeit with low efficiency, into the genomes of a number of fungal species. Genetic transformation requires the penetration of the transgene through the fungal cell wall, a process that can be facilitated by biological or physical methods. Novel methodologies for the efficient introduction of specific genes and stronger promoters are needed to increase production levels. A possible solution to this problem is the recently discovered shock-wave-mediated transformation. The objective of this article is to review the state of the art of the physical methods used for genetic fungi transformation and to describe some of the basic physics and molecular biology behind them.

The identification of fungi collected from the ceca of commercial poultry.

PubMed

Byrd, J A; Caldwell, D Y; Nisbet, D J