scholarly journals Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches

2017 ◽  
Vol 14 (10) ◽  
pp. 2697-2714 ◽  
Author(s):  
Valérie F. Schwab ◽  
Martina Herrmann ◽  
Vanessa-Nina Roth ◽  
Gerd Gleixner ◽  
Robert Lehmann ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Functional Diversity ◽  
Iron Reduction ◽  
Rrna Genes ◽  
Anammox Bacteria ◽  
Iron Reducing Bacteria ◽  
Nitrite Oxidizing Bacteria ◽  
Relative Abundances ◽  
Reducing Bacteria ◽  
Nitrospira Moscoviensis

Abstract. Microorganisms in groundwater play an important role in aquifer biogeochemical cycles and water quality. However, the mechanisms linking the functional diversity of microbial populations and the groundwater physico-chemistry are still not well understood due to the complexity of interactions between surface and subsurface. Within the framework of Hainich (north-western Thuringia, central Germany) Critical Zone Exploratory of the Collaborative Research Centre AquaDiva, we used the relative abundances of phospholipid-derived fatty acids (PLFAs) to link specific biochemical markers within the microbial communities to the spatio-temporal changes of the groundwater physico-chemistry. The functional diversities of the microbial communities were mainly correlated with groundwater chemistry, including dissolved O2, Fet and NH4+ concentrations. Abundances of PLFAs derived from eukaryotes and potential nitrite-oxidizing bacteria (11Me16:0 as biomarker for Nitrospira moscoviensis) were high at sites with elevated O2 concentration where groundwater recharge supplies bioavailable substrates. In anoxic groundwaters more rich in Fet, PLFAs abundant in sulfate-reducing bacteria (SRB), iron-reducing bacteria and fungi increased with Fet and HCO3− concentrations, suggesting the occurrence of active iron reduction and the possible role of fungi in meditating iron solubilization and transport in those aquifer domains. In more NH4+-rich anoxic groundwaters, anammox bacteria and SRB-derived PLFAs increased with NH4+ concentration, further evidencing the dependence of the anammox process on ammonium concentration and potential links between SRB and anammox bacteria. Additional support of the PLFA-based bacterial communities was found in DNA- and RNA-based Illumina MiSeq amplicon sequencing of bacterial 16S rRNA genes, which showed high predominance of nitrite-oxidizing bacteria Nitrospira, e.g. Nitrospira moscoviensis, in oxic aquifer zones and of anammox bacteria in more NH4+-rich anoxic groundwater. Higher relative abundances of sequence reads in the RNA-based datasets affiliated with iron-reducing bacteria in more Fet-rich groundwater supported the occurrence of active dissimilatory iron reduction. The functional diversity of the microbial communities in the biogeochemically distinct groundwater assemblages can be largely attributed to the redox conditions linked to changes in bioavailable substrates and input of substrates with the seepage. Our results demonstrate the power of complementary information derived from PLFA-based and sequencing-based approaches.

scholarly journals Functional diversity of microbial communities in pristine aquifers inferred by PLFA – and sequencing – based approaches

2016 ◽  
Author(s):  
Valerie F. Schwab ◽  
Martina Hermann ◽  
Vanessa-Nina Roth ◽  
Gerd Gleixner ◽  
Robert Lehmann ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Functional Diversity ◽  
Iron Reduction ◽  
Rrna Genes ◽  
Anammox Bacteria ◽  
Iron Reducing Bacteria ◽  
Nitrite Oxidizing Bacteria ◽  
Relative Abundances ◽  
Reducing Bacteria ◽  
Nitrospira Moscoviensis

Abstract. Microorganisms in groundwater play an important role in aquifer biogeochemical cycles and water quality. However, the mechanisms linking the functional diversity of microbial populations and the groundwater physicochemistry are still not well understood due to the complexity of interactions between surface and subsurface. Here, we used phospholipid fatty acids (PLFAs) relative abundances to link specific biochemical markers within the microbial communities to the spatio-temporal changes of the groundwater physicochemistry. PLFAs were isolated from groundwater of two physicochemically distinct aquifer assemblages in central Germany (Thuringia). The functional diversities of the microbial communities were mainly correlated with groundwater chemistry, including dissolved O2, Fet and NH4+ concentrations. Abundances of PLFAs derived from eukaryotes and potential nitrite oxidizing bacteria (11MeC16:0 as biomarker for Nitrospira moscoviensis) were high at sites with elevated O2 concentration where groundwater recharge supplies both bioavailable organic substrates and NH4+ needed to sustain heterotrophic growth and nitrification processes. In anoxic groundwaters more rich in Fet, PLFAs abundant in sulphate reducing bacteria (SRB), iron-reducing bacteria and fungi increased with Fet and HCO3− concentrations suggesting the occurrence of active iron-reduction and the possible role of fungi in meditating iron solubilisation and transport in those aquifer domains. In NH4+ richer anoxic groundwaters, anammox bacteria and SRB- derived PLFAs increased with NH4+ concentration further evidencing the dependence of the anammox process on ammonium concentration and potential links between SRB and anammox bacteria. Additional support of the PLFA-based bacterial communities was found in DNA and RNA-based Illumina MiSeq amplicon sequencing of bacterial 16S rRNA genes, which evidenced high predominance of nitrite-oxidizing bacteria Nitrospira e.g. Nitrospira moscoviensis in oxic zones of the aquifers and of anammox bacteria in NH4+ richer anoxic groundwater. Higher relative abundances of sequence reads in the RNA-based data sets affiliated with iron-reducing bacteria in Fet richer groundwater supported the occurrence of active dissimilatory iron-reduction. The functional diversity of the microbial communities in these biogeochemically distinct groundwater assemblages can be largely attributed to the redox conditions linked to changes in bioavailable substrates and input of substrates with the seepage. Our results demonstrate the power of complementary information derived from PLFA-based and sequencing-based approaches.

scholarly journals Can Primary Ferroan Dolomite and Ankerite Be Precipitated? Its Implications for Formation of Submarine Methane-Derived Authigenic Carbonate (MDAC) Chimney

Minerals ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 413 ◽  
Author(s):  
Fan Xu ◽  
Xuelian You ◽  
Qing Li ◽  
Yi Liu
Keyword(s):  
Iron Reduction ◽  
Extracellular Polymeric Substances ◽  
Microbial Culture ◽  
Reduction Zone ◽  
Secondary Products ◽  
Iron Reducing Bacteria ◽  
Sulfate Reducing ◽  
Dolomite Problem ◽  
Reducing Bacteria ◽  
Ferroan Dolomite

Microbes can mediate the precipitation of primary dolomite under surface conditions. Meanwhile, primary dolomite mediated by microbes often contains more Fe2+ than standard dolomite in modern microbial culture experiments. Ferroan dolomite and ankerite have been regarded as secondary products. This paper reviews the process and possible mechanisms of microbial mediated precipitation of primary ferroan dolomite and/or ankerite. In the microbial geochemical Fe cycle, many dissimilatory iron-reducing bacteria (DIRB), sulfate-reducing bacteria (SRB), and methanogens can reduce Fe3+ to Fe2+, while SRB and methanogens can also promote the precipitation of primary dolomite. There are an oxygen respiration zone (ORZ), an iron reduction zone (IRZ), a sulfate reduction zone (SRZ), and a methanogenesis zone (MZ) from top to bottom in the muddy sediment diagenesis zone. DIRB in IRZ provide the lower section with Fe2+, which composes many enzymes and proteins to participate in metabolic processes of SRB and methanogens. Lastly, heterogeneous nucleation of ferroan dolomite on extracellular polymeric substances (EPS) and cell surfaces is mediated by SRB and methanogens. Exploring the origin of microbial ferroan dolomite may help to solve the “dolomite problem”.

scholarly journals Effect of Sub-Stoichiometric Fe(III) Amounts on LCFA Degradation by Methanogenic Communities

2020 ◽  
Vol 8 (9) ◽  
pp. 1375
Author(s):  
Ana J. Cavaleiro ◽  
Ana P. Guedes ◽  
Sérgio A. Silva ◽  
Ana L. Arantes ◽  
João C. Sequeira ◽  
...  
Keyword(s):  
Iron Reduction ◽  
Anaerobic Bacteria ◽  
Granular Sludge ◽  
Microbial Interactions ◽  
Methanogenic Activity ◽  
Iron Reducing Bacteria ◽  
Hydrogenotrophic Methanogenesis ◽  
Degrading Bacteria ◽  
Acetoclastic Methanogenesis ◽  
Reducing Bacteria

Long-chain fatty acids (LCFA) are common contaminants in municipal and industrial wastewater that can be converted anaerobically to methane. A low hydrogen partial pressure is required for LCFA degradation by anaerobic bacteria, requiring the establishment of syntrophic relationships with hydrogenotrophic methanogens. However, high LCFA loads can inhibit methanogens, hindering biodegradation. Because it has been suggested that anaerobic degradation of these compounds may be enhanced by the presence of alternative electron acceptors, such as iron, we investigated the effect of sub-stoichiometric amounts of Fe(III) on oleate (C18:1 LCFA) degradation by suspended and granular methanogenic sludge. Fe(III) accelerated oleate biodegradation and hydrogenotrophic methanogenesis in the assays with suspended sludge, with H2-consuming methanogens coexisting with iron-reducing bacteria. On the other hand, acetoclastic methanogenesis was delayed by Fe(III). These effects were less evident with granular sludge, possibly due to its higher initial methanogenic activity relative to suspended sludge. Enrichments with close-to-stoichiometric amounts of Fe(III) resulted in a microbial community mainly composed of Geobacter, Syntrophomonas, and Methanobacterium genera, with relative abundances of 83–89%, 3–6%, and 0.2–10%, respectively. In these enrichments, oleate was biodegraded to acetate and coupled to iron-reduction and methane production, revealing novel microbial interactions between syntrophic LCFA-degrading bacteria, iron-reducing bacteria, and methanogens.

Newly designed high-coverage degenerate primers for nitrogen removal mechanism analysis in a partial nitrification-anammox (PN/A) process

2019 ◽  
Vol 96 (1) ◽  
Author(s):  
Qingkun Wang ◽  
Jianzhong He
Keyword(s):  
Nitrogen Removal ◽  
Partial Nitrification ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Anammox Bacteria ◽  
Mechanism Analysis ◽  
Reactor Performance ◽  
Degenerate Primers ◽  
High Coverage ◽  
Nitrite Oxidizing Bacteria

ABSTRACT Reliable tools for quantification of different functional populations are required to achieve stable, effective nutrients removal in partial nitrification and anammox (PN/A) processes. Here we report the design and validation of degenerate PCR primer pairs targeting anammox bacteria, aerobic ammonium-oxidizing bacteria (AeAOB) and nitrite-oxidizing bacteria (NOB) with high coverage but without sacrificing specificity. The new primer pairs are able to cover a broader range of the targeted populations (58.4 vs 21.7%, 49.5 vs 47.6%, 80.7 vs 57.2% and 70.5 vs 42.3% of anammox bacteria, AeAOB, Nitrobacter and Nitrospina, respectively) than previously published primers. Particularly, the Amx719F/875R primer can retrieve a larger number of 16S rRNA genes from different types of samples with amplicons covering all known anammox bacteria genera (100% coverage) including the recently found novel genus, Asahi BRW. These newly desinged primers will provide a more reliable molecular tool to investigate the mechanisms of nitrogen removal in PN/A processes, which can provide clearer links between reactor performance, the metabolic activities and abundances of functional populations, shedding light on conditions that are favorable to the establishment of stable PN/A.

scholarly journals Humic Acid Reduction by Propionibacterium freudenreichii and Other Fermenting Bacteria

1998 ◽  
Vol 64 (11) ◽  
pp. 4507-4512 ◽  
Author(s):  
Marcus Benz ◽  
Bernhard Schink ◽  
Andreas Brune
Keyword(s):  
Molecular Weight ◽  
Humic Acids ◽  
Iron Reduction ◽  
Ferric Iron ◽  
Hydrogen Oxidation ◽  
Low Molecular Weight ◽  
Propionibacterium Freudenreichii ◽  
Iron Reducing Bacteria ◽  
Fermenting Bacteria ◽  
Reducing Bacteria

ABSTRACT Iron-reducing bacteria have been reported to reduce humic acids and low-molecular-weight quinones with electrons from acetate or hydrogen oxidation. Due to the rapid chemical reaction of amorphous ferric iron with the reduced reaction products, humic acids and low-molecular-weight redox mediators may play an important role in biological iron reduction. Since many anaerobic bacteria that are not able to reduce amorphous ferric iron directly are known to transfer electrons to other external acceptors, such as ferricyanide, 2,6-anthraquinone disulfonate (AQDS), or molecular oxygen, we tested several physiologically different species of fermenting bacteria to determine their abilities to reduce humic acids.Propionibacterium freudenreichii, Lactococcus lactis, and Enterococcus cecorum all shifted their fermentation patterns towards more oxidized products when humic acids were present; P. freudenreichii even oxidized propionate to acetate under these conditions. When amorphous ferric iron was added to reoxidize the electron acceptor, humic acids were found to be equally effective when they were added in substoichiometric amounts. These findings indicate that in addition to iron-reducing bacteria, fermenting bacteria are also capable of channeling electrons from anaerobic oxidations via humic acids towards iron reduction. This information needs to be considered in future studies of electron flow in soils and sediments.

scholarly journals Viable cold-tolerant iron-reducing microorganisms in geographically-isolated subglacial environments

2016 ◽  
Author(s):  
Sophie L. Nixon ◽  
Jon Telling ◽  
Jemma L. Wadham ◽  
Charles S. Cockell
Keyword(s):  
Microbial Communities ◽  
Chemical Weathering ◽  
Iron Reduction ◽  
Enrichment Culture ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Microbial Iron Reduction ◽  
Cold Tolerant ◽  
Subglacial Environments ◽  
Geographically Isolated

Abstract. Subglacial environments are known to harbor metabolically-diverse microbial communities. These microbial communities drive chemical weathering of underlying bedrock and influence the geochemistry of glacial meltwaters. Despite its importance in weathering reactions, the microbial cycling of iron in subglacial environments, in particular the role of microbial iron reduction, is poorly understood. In this study we address the prevalence of viable iron-reducing microorganisms in subglacial sediments from five geographically isolated glaciers. Iron-reducing enrichment cultures were established with sediment from beneath Engabreen (Norway), Finsterwalderbreen (Svalbard), Leverett and Russell Glaciers (Greenland) and Lower Wright Glacier (Antarctica). Rates of iron reduction were higher at 4 °C compared with 15 °C in all but one duplicated second-generation enrichment culture, indicative of cold-tolerant and perhaps cold-adapted iron-reducers. Analysis of bacterial 16S rRNA genes indicate Desulfosporosinus were the dominant iron-reducing microorganisms in low-temperature Engabreen, Finsterwalderbreen and Lower Wright Glacier enrichments, and Geobacter dominated in Russell and Leverett enrichments. Results from this study suggest microbial iron reduction is widespread in subglacial environments, and may have important implications for global biogeochemical iron cycling and export to marine ecosystems.

Authigenic nanoscale magnetite within methanic marine sediments

2021 ◽  
Author(s):  
Zhiyong Lin ◽  
Xiaoming Sun ◽  
Andrew Roberts ◽  
Harald Strauss ◽  
Benjamin Brunner ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Iron Reduction ◽  
Iron Sulfide ◽  
Anaerobic Oxidation Of Methane ◽  
Magnetic Studies ◽  
Iron Reducing Bacteria ◽  
Fine Grained ◽  
Oxidation Of Methane ◽  
New Type ◽  
Reducing Bacteria

<p>Magnetic studies of methanic sediments focus mainly on magnetic iron sulfide (greigite, 3C pyrrhotite) formation and magnetic iron oxide (magnetite, titanomagnetite) dissolution, which mainly result from the release of hydrogen sulfide during sulfate-driven anaerobic oxidation of methane. In some instances, authigenic fine-grained magnetite within methanic environments is recognized from magnetic parameters, but the mechanisms for explaining its occurrence remain unclear. We report a novel authigenic nanoscale magnetite source in methanic marine sediments. The magnetite occurs in large concentrations in multiple horizons in a 230-m long sediment core with gas hydrate-bearing intervals. In contrast to typical biogenic magnetite produced by magnetotactic bacteria and dissimilatory iron-reducing bacteria, most particles have sizes of 200-800 nm and many are aligned in distinctive structures that resemble microbial precipitates. This new type of magnetite is interpreted to be a by-product of microbial iron reduction within methanic sediments. It will record younger paleomagnetic signals than surrounding sediments, which is important for paleomagnetic interpretations in methanic sediments.</p>

scholarly journals Metagenomics: Read Length Matters

2008 ◽  
Vol 74 (5) ◽  
pp. 1453-1463 ◽  
Author(s):  
K. Eric Wommack ◽  
Jaysheel Bhavsar ◽  
Jacques Ravel
Keyword(s):  
Microbial Communities ◽  
Functional Diversity ◽  
16S Rrna Genes ◽  
Metagenomic Analysis ◽  
Read Length ◽  
Rrna Genes ◽  
Short Read ◽  
Short Reads ◽  
Long Read

ABSTRACT Obtaining an unbiased view of the phylogenetic composition and functional diversity within a microbial community is one central objective of metagenomic analysis. New technologies, such as 454 pyrosequencing, have dramatically reduced sequencing costs, to a level where metagenomic analysis may become a viable alternative to more-focused assessments of the phylogenetic (e.g., 16S rRNA genes) and functional diversity of microbial communities. To determine whether the short (∼100 to 200 bp) sequence reads obtained from pyrosequencing are appropriate for the phylogenetic and functional characterization of microbial communities, the results of BLAST and COG analyses were compared for long (∼750 bp) and randomly derived short reads from each of two microbial and one virioplankton metagenome libraries. Overall, BLASTX searches against the GenBank nr database found far fewer homologs within the short-sequence libraries. This was especially pronounced for a Chesapeake Bay virioplankton metagenome library. Increasing the short-read sampling depth or the length of derived short reads (up to 400 bp) did not completely resolve the discrepancy in BLASTX homolog detection. Only in cases where the long-read sequence had a close homolog (low BLAST E-score) did the derived short-read sequence also find a significant homolog. Thus, more-distant homologs of microbial and viral genes are not detected by short-read sequences. Among COG hits, derived short reads sampled at a depth of two short reads per long read missed up to 72% of the COG hits found using long reads. Noting the current limitation in computational approaches for the analysis of short sequences, the use of short-read-length libraries does not appear to be an appropriate tool for the metagenomic characterization of microbial communities.

scholarly journals Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes

2018 ◽  
Vol 84 (23) ◽  
Author(s):  
Andrea G. Bravo ◽  
Sari Peura ◽  
Moritz Buck ◽  
Omneya Ahmed ◽  
Alejandro Mateos-Rivera ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Lake Sediments ◽  
Aquatic Ecosystems ◽  
Sulfate Reducing Bacteria ◽  
Boreal Lakes ◽  
Mercury Methylation ◽  
Content Type ◽  
Iron Reducing Bacteria ◽  
Sulfate Reducing ◽  
Reducing Bacteria

ABSTRACTMethylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing thehgcAgene potentially mediate the formation of methylmercury in natural environments, the diversity of these mercury-methylating microbial communities remains largely unexplored. Previous studies have implicated sulfate-reducing bacteria as the main mercury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments using high-throughput sequencing of 16S rRNA andhgcAgenes. Our results show that in the lake sediments,MethanomicrobialesandGeobacteraceaealso represent abundant members of the mercury-methylating communities. In fact, incubation experiments with a mercury isotopic tracer and molybdate revealed that only between 38% and 45% of mercury methylation was attributed to sulfate reduction. These results suggest that methanogens and iron-reducing bacteria may contribute to more than half of the mercury methylation in boreal lakes.IMPORTANCEDespite the global awareness that mercury, and methylmercury in particular, is a neurotoxin to which millions of people continue to be exposed, there are sizable gaps in the understanding of the processes and organisms involved in methylmercury formation in aquatic ecosystems. In the present study, we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal lake sediments. All the microorganisms identified are associated with the processing of organic matter in aquatic systems. Moreover, our results show that the well-known mercury-methylating sulfate-reducing bacteria constituted only a minor portion of the potential mercury methylators. In contrast, methanogens and iron-reducing bacteria were important contributors to methylmercury formation, highlighting their role in mercury cycling in the environment.

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