The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink

The ISME Journal, Год журнала: 2012, Номер 7(2), С. 417 - 426

Опубликована: Ноя. 15, 2012

Язык: Английский

---

Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils

Proceedings of the National Academy of Sciences, Год журнала: 2012, Номер 109(48), С. 19709 - 19714

Опубликована: Ноя. 12, 2012

Agricultural and industrial practices more than doubled the intrinsic rate of terrestrial N fixation over past century with drastic consequences, including increased atmospheric nitrous oxide (N(2)O) concentrations. N(2)O is a potent greenhouse gas contributor to ozone layer destruction, its release from fixed almost entirely controlled by microbial activities. Mitigation emissions atmosphere has been attributed exclusively denitrifiers possessing NosZ, enzyme system catalyzing N(2) reduction. We demonstrate that diverse taxa possess divergent nos clusters genes are related yet evolutionarily distinct typical denitirifers. atypical nosZ occur in Bacteria Archaea denitrify (44% genomes), do not other denitrification (56%), or perform dissimilatory nitrate reduction ammonium (DNRA; (31%). Experiments DNRA soil bacterium Anaeromyxobacter dehalogenans demonstrated NosZ an effective reductase, PCR-based surveys suggested abundant environments. Bioinformatic analyses revealed distinctive regulatory functional components (e.g., Sec vs. Tat secretion pathway nos), previous nosZ-targeted PCR primers capture diversity. Collectively, our results suggest nondenitrifying populations broad range metabolisms habitats potentially significant contributors consumption. Apparently, large, previously unrecognized group environmental accounted for, characterizing their contributions consumption will advance understanding ecological controls on lead refined flux models.

Язык: Английский

---

Genomics and Ecology of Novel N2O-Reducing Microorganisms

Trends in Microbiology, Год журнала: 2017, Номер 26(1), С. 43 - 55

Опубликована: Авг. 10, 2017

Язык: Английский

---

Anaerobic Microbial Dehalogenation

Annual Review of Microbiology, Год журнала: 2004, Номер 58(1), С. 43 - 73

Опубликована: Окт. 1, 2004

▪ Abstract The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been likely driving force for evolution an unexpectedly high microbial capacity to dehalogenate different classes xenobiotic haloorganics. This contribution provides update on current knowledge metabolic phylogenetic diversity anaerobic microorganisms that are capable dehalogenating—or completely mineralizing—halogenated by fermentative, oxidative, or reductive pathways. In particular, research past decade focused halorespiring anaerobes, which couple dehalogenation dedicated enzyme systems generation energy electron transport–driven phosphorylation. Significant advances in biochemistry molecular genetics degradation pathways have revealed mechanistic structural similarities between dehalogenating enzymes from phylogenetically distinct anaerobes. availability two almost complete genome sequences isolates recently enabled comparative functional genomics approaches, setting stage further exploitation other microbes as degraders biological remediation processes.

Язык: Английский

---

Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions

PLoS ONE, Год журнала: 2014, Номер 9(12), С. e114118 - e114118

Опубликована: Дек. 1, 2014

Nitrous oxide (N2O) is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N2O nitrous reductase, encoded by nosZ gene, which present among bacteria archaea capable of either complete denitrification or reduction di-nitrogen gas. To determine whether occurrence nosZ, being proxy for trait reduction, differed taxonomic groups, preferred habitats organisms having NirK NirS nitrite reductases nirK nirS genes, respectively, 652 microbial genomes across 18 phyla were compared. Furthermore, association different co-occurrence patterns with enzymes reducing nitric nor genes was examined. We observed that not randomly distributed taxa, as specific found be more dominant absent than expected within groups. gene had significantly higher frequency presence absence largely explained this pattern, almost always co-occurred nor. This suggests type denitrifiers are likely thus contribute less emissions under favorable environmental conditions. Comparative phylogenetic analysis indicated greater degree shared evolutionary history between nirS. However 30% did possess nir several these also lacking nor, suggesting potentially important role in reduction. Co-occurrence non-randomly amongst habitat categories, showing significant differences frequencies denitrifiers. These results demonstrate pathway highly modular, underpinning importance community structure emissions.

Язык: Английский

---

Quantitative PCR Targeting 16S rRNA and Reductive Dehalogenase Genes Simultaneously Monitors Multiple Dehalococcoides Strains

Applied and Environmental Microbiology, Год журнала: 2006, Номер 72(4), С. 2765 - 2774

Опубликована: Апрель 1, 2006

ABSTRACT The 16S rRNA gene provides insufficient information to infer the range of chloroorganic electron acceptors used by different Dehalococcoides organisms. To overcome this limitation and provide enhanced diagnostic tools for growth measurements, site assessment, bioremediation monitoring, a quantitative real-time PCR (qPCR) approach targeting genes three reductive dehalogenase (RDase) with assigned function (i.e., tceA , bvcA vcrA ) was designed evaluated. qPCR standard curves generated RDase use genomic DNA from pure cultures correlated obtained both Bacteria - -targeted genes, suggesting that are useful targets assessment probe/primer pairs were specific strains known carry sequences, method allowed detection as few 1 20 quantification 50 100 or per volume. applied dechlorinating enrichment cultures, microcosms, samples contaminated site. In characterized where enumerated, sum equaled total cell numbers. chloroethane-dechlorinating much less than predicted qPCR, totaling 10 30% Hence, large number spp. contain as-yet-unidentified indicating our current understanding community is incomplete.

Язык: Английский

---

Succession of bacterial community structure and diversity in a paddy soil oxygen gradient

Environmental Microbiology, Год журнала: 2005, Номер 7(3), С. 382 - 395

Опубликована: Янв. 11, 2005

Summary Cultivation‐independent techniques were applied to assess the succession and phylogenetic composition of bacterial communities in a vertical oxygen gradient flooded, unplanted paddy soil microcosms. Microsensor measurements showed that within 6 h flooding, was depleted from 200 µM at floodwater‐soil interface undetectable amounts depth approximately 2 mm below. The quite stable over time, although depletion less pronounced 84 days than after flooding. Community fingerprint patterns obtained by terminal restriction fragment length polymorphism (T‐RFLP) analysis oxic, transition, anoxic zones triplicate microcosms 0, 1 h, 1, 2, 7, 21, 30, 42, 84, 168 Correspondence analyses revealed T‐RFLP using either community DNA or RNA affected time zone, there significant interaction between effects zone. temporal dynamics populations resolved more clearly DNA. At level, successional most 21 for both oxic zones. No effect zone on observed Dominant early identified cloning comparative sequence environmental 16S rRNA genes as members Betaproteobacteria (oxic zone) clostridial cluster I (anoxic zone). late belonged Verrucomicrobia Nitrospira (detected mainly zone), Myxococcales In conclusion, developed through stages, leading level almost This principal finding, combination with identity early‐ late‐appearing populations, suggests can be explained principles r‐ K‐selection.

Язык: Английский

---

Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment

Water Research, Год журнала: 2017, Номер 116, С. 268 - 295

Опубликована: Фев. 4, 2017

Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is assumption that degradation more energetically favorable than under Certain aerobically recalcitrant contaminants, however, are biodegraded little known about organisms enzymatic processes involved their degradation. This review provides a comprehensive survey characteristic biotransformation reactions for variety well-studied, structurally rather simple (SMOCs) bearing one or few different functional groups/structural moieties. Furthermore it summarizes complex groups (CMCs), soil, sediment wastewater treatment. While able promote transformation persistent observed limited, reductive dehalogenations cleavage ether bonds being most prevalent. Thus, becomes clear transferability mechanisms deduced from culture SMOCs predict CMCs, EOCs, matrices hampered due chemical structure groups, (e.g. matrix, redox, pH), microbial community adaptation, competition) low concentrations typical EOCs.

Язык: Английский

---

Respiratory Transformation of Nitrous Oxide (N2O) to Dinitrogen by Bacteria and Archaea

Advances in microbial physiology/Advances in Microbial Physiology, Год журнала: 2006, Номер unknown, С. 107 - 227

Опубликована: Янв. 1, 2006

Язык: Английский

---

Evolution of the Chaperone/Usher Assembly Pathway: Fimbrial Classification Goes Greek

Microbiology and Molecular Biology Reviews, Год журнала: 2007, Номер 71(4), С. 551 - 575

Опубликована: Дек. 1, 2007

SUMMARY Many Proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on bacterial surface. These can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule spore coat). This article reviews phylogeny of operons belonging assembly class explore utility establishing scheme for subdividing them clades phylogenetically related gene clusters. Based usher amino acid sequence comparisons, our analysis shows that is subdivided six major phylogenetic clades, which we have termed α-, β-, γ-, κ-, π-, and σ-fimbriae. Members each clade share operon encode subunits with similar protein domains. The proposed classification system offers simple convenient method assigning newly discovered systems one groups.

Язык: Английский

---