Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T

Seleniivibrio woodruffii strain S4T is an obligate anaerobe belonging to the phylum Deferribacterota. It was isolated for its ability to respire selenate and was also found to respire arsenate. The high-quality draft genome of this bacterium is 2.9 Mbp, has a G+C content of 48%, 2762 predicted genes of which 2709 are protein-coding, and 53 RNA genes. An analysis of the genome focusing on the genes encoding for molybdenum-containing enzymes (molybdoenzymes) uncovered a remarkable number of genes encoding for members of the dimethylsulfoxide reductase family of proteins (DMSOR), including putative reductases for selenate and arsenate respiration, as well as genes for nitrogen fixation. Respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that can act as terminal electron acceptors for energy generation. Seleniivibrio woodruffii strain S4T also has essential genes for molybdate transporters and the biosynthesis of the molybdopterin guanine dinucleotide cofactors characteristic of the active centers of DMSORs. Phylogenetic analysis revealed candidate respiratory DMSORs spanning nine subfamilies encoded within the genome. Our analysis revealed the untapped potential of this interesting microorganism and expanded our knowledge of molybdoenzyme co-occurrence.

Bacterial and fungal communities in sub-Arctic tundra heaths are shaped by contrasting snow accumulation and nutrient availability

Climate change is affecting winter snow conditions significantly in northern ecosystems but the effects of the changing conditions for soil microbial communities are not well-understood. We utilized naturally occurring differences in snow accumulation to understand how the wintertime subnivean conditions shape bacterial and fungal communities in dwarf shrub-dominated sub-Arctic Fennoscandian tundra sampled in mid-winter, early, and late growing season. Phospholipid fatty acid (PLFA) and quantitative PCR analyses indicated that fungal abundance was higher in windswept tundra heaths with low snow accumulation and lower nutrient availability. This was associated with clear differences in the microbial community structure throughout the season. Members of Clavaria spp. and Sebacinales were especially dominant in the windswept heaths. Bacterial biomass proxies were higher in the snow-accumulating tundra heaths in the late growing season but there were only minor differences in the biomass or community structure in winter. Bacterial communities were dominated by members of Alphaproteobacteria, Actinomycetota, and Acidobacteriota and were less affected by the snow conditions than the fungal communities. The results suggest that small-scale spatial patterns in snow accumulation leading to a mosaic of differing tundra heath vegetation shapes bacterial and fungal communities as well as soil carbon and nutrient availability.

Microbial colonization and chemically influenced selective enrichment of bacterial pathogens on polycarbonate plastic

Plastic pollution in aquatic environments poses significant concerns due to its potential to serve as a refuge for aquatic pathogens. However, the role of plastic surfaces and microbial biofilm interfaces in facilitating pathogen development remains poorly understood. In this study, a microcosm setup was employed to investigate the interactions between plastics and the microbial community and examine the differences in bacterial community composition and potential pathogen occurrences between the plastisphere-biofilm and surrounding seawater. Community composition analysis combined with SEM observations over time indicated that biofilm extracellular polymeric substance formation over 14 days had a link with the relative abundance and succession patterns of pathogen taxa. Colony clusters were observed on biofilms from day 7 and coincided with higher bacterial pathogen dominance. On day 14, pathogen abundance overall decreased with a potentially degrading biofilm. Pseudomonas and Pseudoalteromonas were the dominant potential pathogen groups observed in the microcosm. When further subjected to chemical treatment as an imposed environmental stress over time, biofilm-associated Psuedoalteromonas sharply increased in abundance after three days of exposure, but quickly diminished by 14 days in favor of genera such as Acinetobacter, Pseudomonas, and Staphylococcus. These results suggest that environmental plastisphere-biofilms can promote the early selection, enrichment, and spread of pathogenic bacteria in the aquatic environment and could be later worsened under chemical and long-term pressure. This study provided new insights into the succession of pathogens in plastisphere biofilms, contributing to the understanding of pathogen risks involved in emerging plastisphere biofilms in light of global plastic pollution.

The Role of Fatty Acids from Plant Surfaces in the Infectivity of Colletotrichum fioriniae

Aqueous extracts derived from flowers stimulate germination, secondary conidiation, and appressorial formation of various latent fruit rotting fungi. Even raindrops passing over flowers accumulate sufficient activity to influence the infectivity of fruit rotting fungi. Using a spore germination bioassay, high levels of bioactivity were found in chloroform extracts from plant tissues, implicating the nonpolar components of the cuticle. The fatty acid (FA) and fatty acid methyl ester (FAME) composition (C9-C20) of blueberry and cranberry tissues as well as aqueous flower extracts were characterized using a gas chromatography-mass spectrometry (GC-MS) method. The FAs and FAMEs found in the plant extracts were then tested for bioactivity using a spore germination bioassay. The C16:0 and C18:2 FAs and FAMEs, as well as the C18:0 FAME and the C20:0 FA, all stimulated appressorial formation while the C10:0 FA stimulated secondary conidiation. The C10:0 and C16:0 FAs were the only two bioactive components also identified from the aqueous floral extracts of both blueberry and cranberry and are therefore considered as contributors to the bioactivity observed in these extracts. The aqueous extracts from surfaces other than flowers showed little or no activity, and it is speculated that the movement of FAs may be related to the level of polymerization and cutin polyester development in flowers versus other plant organs. This study highlights the importance of the bloom period for infection and that the apparent effects on host susceptibility may therefore depend on the availability of specific FAs or combinations thereof.

Immobile Iron-Rich Particles Promote Arsenic Retention and Regulate Arsenic Biotransformation in Treatment Wetlands

Remediation of arsenic (As)-contaminated wastewater by treatment wetlands (TWs) remains a technological challenge due to the low As adsorption capacity of wetland substrates and the release of adsorbed As to pore water. This study investigated the feasibility of using immobile iron-rich particles (IIRP) to promote As retention and to regulate As biotransformation in TWs. Iron-rich particles prepared were immobilized in the interspace of a gravel substrate. TWs with IIRP amendment (IIRP-TWs) achieved a stable As removal efficiency of 63 ± 4% over 300 days, while no As removal or release was observed in TWs without IIRP after 180 days of continuous operation. IIRP amendment provided additional adsorption sites and increased the stability of adsorbed As due to the strong binding affinity between As and Fe oxides. Microbially mediated As(III) oxidation was intensified by iron-rich particles in the anaerobic bottom layer of IIRP-TWs. Myxococcus and Fimbriimonadaceae were identified as As(III) oxidizers. Further, metagenomic binning suggested that these two bacterial taxa may have the capability for anaerobic As(III) oxidation. Overall, this study demonstrated that abiotic and biotic effects of IIRP contribute to As retention in TWs and provided insights into the role of IIRP for the remediation of As contamination.

Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis)

BACKGROUND

Phytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations, especially the deficiency of nitrogen (N), can hinder the growth of plants and impair the phytoremediation of mine tailings. Nevertheless, pioneer plants can successfully colonize mine tailings and exhibit potential for tailing phytoremediation. Diazotrophs, especially diazotrophic endophytes, can promote the growth of their host plants. This was tested in a mine-tailing habitat by a combination of field sampling, DNA-stable isotope probing (SIP) analysis, and pot experiments.

RESULTS

Bacteria belonging to the genera Herbaspirillum, Rhizobium, Devosia, Pseudomonas, Microbacterium, and Delftia are crucial endophytes for Chinese silvergrass (Miscanthus sinensis) grown in the tailing, the model pioneer plant selected in this study. Further, DNA-SIP using ¹⁵N₂ identified Pseudomonas, Rhizobium, and Exiguobacterium as putative diazotrophic endophytes of M. sinensis. Metagenomic-binning suggested that these bacteria contained essential genes for nitrogen fixation and plant growth promotion. Finally, two diazotrophic endophytes Rhizobium sp. G-14 and Pseudomonas sp. Y-5 were isolated from M. sinensis. Inoculation of another pioneer plant in mine tailings, Bidens pilosa, with diazotrophic endophytes resulted in successful plant colonization, significantly increased nitrogen fixation activity, and promotion of plant growth.

CONCLUSIONS

This study indicated that diazotrophic endophytes have the potential to promote the growth of pioneer plant B. pilosa in mine tailings. Video Abstract.

Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning

Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F₄₂₀H₂ dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.

Spatial responses of soil carbon stocks, total nitrogen, and microbial indices to post-wildfire in the Mediterranean red pine forest

Wildfire is a key ecological event that alters vegetation and soil quality attributes including biochemical attributes at spatial scale. This knowledge can provide insights into the development of better rehabilitation or restoration strategies that depend on the ecological dynamics of vegetation, fungi, and animals. The present study aimed to understand the causes and consequences of spatial variability of soil organic carbon, microbial biomass C concentrations, and soil quality indices as impacted by wildfire in a red pine forest. This study was conducted using kriging and inverse distance neighborhood similarity (IDW) interpolations methods. The carbon stocks were significantly (P = 0.002) higher in burned areas compared to those of unburned areas by 255% whereas microbial biomass carbon and microbial respiration were significantly (P < 0.0001 and P = 0.02) lower in burned areas by 66% and 90%, The Pearson's correlation analysis showed that carbon stocks were positively correlated with pH (0.61), total nitrogen (0.60) and ash quantity (0.41), but negatively correlated with microbial biomass carbon (-0.46) and nitrogen (-0.61), and microbial respiration (-0.48). The IDW interpolation method better-predicted pH, bulk density, and microbial biomass carbon and nitrogen compared to kriging interpolation, whereas the kriging interpolation method was better than IDW interpolation for the other studied soil properties. We concluded that pH, EC, SOC, C/N, MR, MBC/SOC, and MBC/MBN can be reliable indicators to monitor the effect of wildfire on forest soils. The wildfire event increased soil carbon stocks, TN, pH, and _qCO₂, but decreased MBC and MBN.

Desulfoluna spp. form a cosmopolitan group of anaerobic dehalogenating bacteria widely distributed in marine sponges

Host-specific microbial communities thrive within sponge tissues and this association between sponge and associated microbiota may be driven by the organohalogen chemistry of the sponge animal. Several sponge species produce diverse organobromine secondary metabolites (e.g. brominated phenolics, indoles, and pyrroles) that may function as a chemical defense against microbial fouling, infection or predation. In this study, anaerobic cultures prepared from marine sponges were amended with 2,6-dibromophenol as the electron acceptor and short chain organic acids as electron donors. We observed reductive dehalogenation from diverse sponge species collected at disparate temperate and tropical waters suggesting that biogenic organohalides appear to enrich for populations of dehalogenating microorganisms in the sponge animal. Further enrichment by successive transfers with 2,6-dibromophenol as the sole electron acceptor demonstrated the presence of dehalogenating bacteria in over 20 sponge species collected from temperate and tropical ecoregions in the Atlantic and Pacific Oceans and the Mediterranean Sea. The enriched dehalogenating strains were closely related to Desulfoluna spongiiphila and Desulfoluna butyratoxydans, suggesting a cosmopolitan association between Desulfoluna spp. and various marine sponges. In vivo reductive dehalogenation in intact sponges was also demonstrated. Organobromide-rich sponges may thus provide a specialized habitat for organohalide-respiring microbes and D. spongiiphila and/or its close relatives are responsible for reductive dehalogenation in geographically widely distributed sponge species.

Serratia spp. Are Responsible for Nitrogen Fixation Fueled by As(III) Oxidation, a Novel Biogeochemical Process Identified in Mine Tailings

Biological nitrogen fixation (BNF) has important environmental implications in tailings by providing bioavailable nitrogen to these habitats and sustaining ecosystem functions. Previously, chemolithotrophic diazotrophs that dominate in mine tailings were shown to use reduced sulfur (S) as the electron donor. Tailings often contain high concentrations of As(III) that might function as an alternative electron donor to fuel BNF. Here, we tested this hypothesis and report on BNF fueled by As(III) oxidation as a novel biogeochemical process in addition to BNF fueled by S. Arsenic (As)-dependent BNF was detected in cultures inoculated from As-rich tailing samples derived from the Xikuangshan mining area in China, as suggested by nitrogenase activity assays, quantitative polymerase chain reaction, and ¹⁵N₂ enrichment incubations. As-dependent BNF was also active in eight other As-contaminated tailings and soils, suggesting that the potential for As-dependent BNF may be widespread in As-rich habitats. DNA-stable isotope probing identified Serratia spp. as the bacteria responsible for As-dependent BNF. Metagenomic binning indicated that the essential genes for As-dependent BNF [i.e., nitrogen fixation, As(III) oxidation, and carbon fixation] were present in Serratia-associated metagenome-assembled genomes. Over 20 Serratia genomes obtained from NCBI also contained essential genes for both As(III) oxidation and BNF (i.e., aioA and nifH), suggesting that As-dependent BNF may be a widespread metabolic trait in Serratia spp.

A ribosomal operon database and MegaBLAST settings for strain-level resolution of microbiomes

Current methods to characterize microbial communities generally employ sequencing of the 16S rRNA gene (<500 bp) with high accuracy (∼99%) but limited phylogenetic resolution. However, long-read sequencing now allows for the profiling of near-full-length ribosomal operons (16S-ITS-23S rRNA genes) on platforms such as the Oxford Nanopore MinION. Here, we describe an rRNA operon database with >300 ,000 entries, representing >10 ,000 prokaryotic species and ∼ 150, 000 strains. Additionally, BLAST parameters were identified for strain-level resolution using in silico mutated, mock rRNA operon sequences (70-95% identity) from four bacterial phyla and two members of the Euryarchaeota, mimicking MinION reads. MegaBLAST settings were determined that required <3 s per read on a Mac Mini with strain-level resolution for sequences with >84% identity. These settings were tested on rRNA operon libraries from the human respiratory tract, farm/forest soils and marine sponges ( n = 1, 322, 818 reads for all sample sets). Most rRNA operon reads in this data set yielded best BLAST hits (95 ± 8%). However, only 38-82% of library reads were compatible with strain-level resolution, reflecting the dominance of human/biomedical-associated prokaryotic entries in the database. Since the MinION and the Mac Mini are both portable, this study demonstrates the possibility of rapid strain-level microbiome analysis in the field.

Characterization of Microplastic-Associated Biofilm Development along a Freshwater-Estuarine Gradient

Microplastic contamination is an increasing concern worldwide. Biofilms rapidly develop on surfaces in aquatic habitats, but the processes of biofilm formation and variation in bacterial community succession on different microplastics introduced into freshwater and estuarine environments are not well understood. In this study, the biofilm bacterial communities that developed on three different types of microplastics that are prevalent in the environment, high-density polyethylene (HDPE), polyethylene terephthalate (PET), and polystyrene (PS), was investigated. Virgin microplastics were incubated in microcosms over a period of 31 days with water collected along a freshwater-estuarine gradient of the Raritan River in New Jersey. Through long-read MinION sequencing of bacterial ribosomal operons, we were able to examine biofilm bacterial communities at a species- and strain-level resolution. Results indicated that both salinity level and microplastic type impacted biofilm formation and promoted colonization by distinct microbial communities. Limnobacter thiooxidans was found to be one of the most abundant microplastics colonizing-bacteria, and it is hypothesized that different types of microplastics could select for different strains. Our findings indicate that multiple groups of highly similar L. thiooxidans rRNA operons could be discerned within the community profiles. Phylogenetic reconstruction further established that various Linmobacter species uniquely colonized the different microplastics from the different sampling sites. Our findings indicate that microplastics support abundant and diverse bacterial communities and that the various types of microplastics can influence how different bacterial biofilms develop, which may have ecological impacts on aquatic ecosystems.

Identification of Antimonate Reducing Bacteria and Their Potential Metabolic Traits by the Combination of Stable Isotope Probing and Metagenomic-Pangenomic Analysis

Microorganisms play an important role in altering antimony (Sb) speciation, mobility, and bioavailability, but the understanding of the microorganisms responsible for Sb(V) reduction has been limited. In this study, DNA-stable isotope probing (DNA-SIP) and metagenomics analysis were combined to identify potential Sb(V)-reducing bacteria (SbRB) and predict their metabolic pathways for Sb(V) reduction. Soil slurry cultures inoculated with Sb-contaminated paddy soils from two Sb-contaminated sites demonstrated the capability to reduce Sb(V). DNA-SIP identified bacteria belonging to the genera Pseudomonas and Geobacter as putative SbRB in these two Sb-contaminated sites. In addition, bacteria such as Lysinibacillus and Dechloromonas may potentially participate in Sb(V) reduction. Nearly complete draft genomes of putative SbRB (i.e., Pseudomonas and Geobacter) were obtained, and the genes potentially responsible for arsenic (As) and Sb reduction (i.e., respiratory arsenate reductase (arrA) and antimonate reductase (anrA)) were examined. Notably, bins affiliated with Geobacter contained arrA and anrA genes, supporting our hypothesis that they are putative SbRB. Further, pangenomic analysis indicated that various Geobacter-associated genomes obtained from diverse habitats also contained arrA and anrA genes. In contrast, Pseudomonas may use a predicted DMSO reductase closely related to sbrA (Sb(V) reductase gene) clade II to reduce Sb(V), which may need further experiments to verify. This current work represents a demonstration of using DNA-SIP and metagenomic-binning to identify SbRB and their key genes involved in Sb(V) reduction and provides valuable data sets to link bacterial identities with Sb(V) reduction.

Efficacy of rhizobacteria for degradation of profenofos and improvement in tomato growth

Pesticides are widely used for managing pathogens and pests for sustainable agricultural output to feed around seven billion people worldwide. After their targeted role, residues of these compounds may build up and persist in soils and in the food chain. This study evaluated the efficiency of bacterial strains capable of plant growth promotion and biodegradation of profenofos. To execute this, bacteria were isolated from an agricultural area with a history of repeated application of profenofos. The profenofos degrading bacterial strains with growth-promoting characteristics were identified based on biochemical and molecular approaches through partial 16S ribosomal rRNA gene sequencing. The results revealed that one strain, Enterobacter cloacae MUG75, degraded over 90% profenofos after 9 days of incubation. Similarly, plant growth was significantly increased in plants grown in profenofos (100 mg L^-1) contaminated soil inoculated with the same strain. The study demonstrated that inoculation of profenofos degrading bacterial strains increased plant growth and profenofos degradation. Novelty statementPesticides are extensively applied in the agriculture sector to overcome pest attacks and to increase food production to fulfill the needs of the growing world population. Residues of these pesticides can persist in the environment for long periods, may enter the groundwater reservoirs and cause harmful effects on living systems highlighting the need for bioremediation of pesticide-contaminated environments. Microbes can use pesticides as a source of carbon and energy and convert them into less toxic and non-toxic products. Application of profenofos degrading rhizobacteria in interaction with the plants in the rhizosphere can remediate the pesticide-contaminated soils and minimize their uptake into the food chain. Hence, this approach can improve soil health and food quality without compromising the environment.

Genome analysis of Thauera chlorobenzoica strain 3CB-1T, a halobenzoate-degrading bacterium isolated from aquatic sediment

The genus Thauera is characterized by several species and strains with the ability to degrade a variety of aromatic compounds under denitrifying conditions. Thauera chlorobenzoica strain 3CB-1^T, isolated from river sediment, has the unique ability to degrade a variety of halobenzoates, such as 3-chlorobenzoate, 3-bromobenzoate, 3-iodobenzoate, and 2-fluorobenzoate, coupled to nitrate reduction. The genome of T. chlorobenzoica strain 3CB-1^T has been sequenced, allowing us to gain insights into the molecular basis for the anaerobic degradation of (halo)aromatic compounds. The 3.77-Mb genome contains 3584 genes; 3514 are protein-coding genes of which 198 are likely associated with degradation of aromatic compounds. It has a G + C content of 67.25%. The genome contains two sets of CoA reductase gene clusters, both belonging to class I benzoate-CoA reductases (BCRs). The genes in one of the two clusters differ from the typical BCRs, with low sequence identities, suggesting they might have different substrate specificities. The genome also contains four benzoate-CoA ligase genes. One likely encodes a 3-hydroxybenzoate-CoA ligase, and two others group together with benzoate-CoA ligases from Thauera aromatica. The fourth has a 77% identity to the mbdA gene from Azoarcus sp. CIB, is absent in the T. aromatica genome, and potentially encodes a halobenzoate-CoA ligase. 3-Chlorobenzoate is reductively dechlorinated in T. chlorobenzoica by a benzoyl-CoA reductase.

Metabolic potentials of members of the class Acidobacteriia in metal-contaminated soils revealed by metagenomic analysis

The relative abundance of Acidobacteriia correlated positively with the concentrations of arsenic (As), mercury (Hg), chromium (Cr), copper (Cu) and other metals, suggesting their adaptation of the metal-rich environments. Metagenomic binning reconstructed 29 high-quality metagenome-assembled genomes (MAGs) associated with Acidobacteriia, providing an opportunity to study their metabolic potentials. These MAGs contained genes to transform As, Hg and Cr through oxidation, reduction, efflux and demethylation, suggesting the potential of Acidobacteriia to transform such metal(loid)s. Additionally, genes associated with alleviation of acidic and metal stress were also detected in these MAGs. Acidobacteriia may have the capabilities to resist or transform metal(loid)s in acidic metal-contaminated sites. Moreover, these genes encoding metal transformation could be also identified in the Acidobacteriia-associated MAGs from five additional metal-contaminated sites across Southwest China, as well as Acidobacteriia-associated reference genomes from the NCBI database, suggesting that the capability of metal transformation may be widespread among Acidobacteriia members. This discovery provides an understanding of metabolic potentials of the Acidobacteriia in acidic metal-rich sites.

Paneth Cell-Derived Lysozyme Defines the Composition of Mucolytic Microbiota and the Inflammatory Tone of the Intestine

Paneth cells are the primary source of C-type lysozyme, a β-1,4-N-acetylmuramoylhydrolase that enzymatically processes bacterial cell walls. Paneth cells are normally present in human cecum and ascending colon, but are rarely found in descending colon and rectum; Paneth cell metaplasia in this region and aberrant lysozyme production are hallmarks of inflammatory bowel disease (IBD) pathology. Here, we examined the impact of aberrant lysozyme production in colonic inflammation. Targeted disruption of Paneth cell lysozyme (Lyz1) protected mice from experimental colitis. Lyz1-deficiency diminished intestinal immune responses to bacterial molecular patterns and resulted in the expansion of lysozyme-sensitive mucolytic bacteria, including Ruminococcus gnavus, a Crohn's disease-associated pathobiont. Ectopic lysozyme production in colonic epithelium suppressed lysozyme-sensitive bacteria and exacerbated colitis. Transfer of R. gnavus into Lyz1^-/- hosts elicited a type 2 immune response, causing epithelial reprograming and enhanced anti-colitogenic capacity. In contrast, in lysozyme-intact hosts, processed R. gnavus drove pro-inflammatory responses. Thus, Paneth cell lysozyme balances intestinal anti- and pro-inflammatory responses, with implications for IBD.

Characterization of Nitrate-Dependent As(III)-Oxidizing Communities in Arsenic-Contaminated Soil and Investigation of Their Metabolic Potentials by the Combination of DNA-Stable Isotope Probing and Metagenomics

Arsenite (As(III)) oxidation has important environmental implications by decreasing both the mobility and toxicity of As in the environment. Microbe-mediated nitrate-dependent As(III) oxidation (NDAO) may be an important process for As(III) oxidation in anoxic environments. Our current knowledge of nitrate-dependent As(III)-oxidizing bacteria (NDAB), however, is largely based on isolates, and thus, the diversity of NDAB may be underestimated. In this study, DNA-stable isotope probing (SIP) with ¹³C-labeled NaHCO₃ as the sole carbon source, amplicon sequencing, and shotgun metagenomics were combined to identify NDAB and investigate their NDAO metabolism. As(III) oxidation was observed in the treatment amended with nitrate, while no obvious As(III) oxidation was observed without nitrate addition. The increase in the gene copies of aioA in the nitrate-amended treatment suggested that As(III) oxidation was mediated by microorganisms containing the aioA genes. Furthermore, diverse putative NDAB were identified in the As-contaminated soil cultures, such as Azoarcus, Rhodanobacter, Pseudomonas, and Burkholderiales-related bacteria. Metagenomic analysis further indicated that most of these putative NDAB contained genes for As(III) oxidation and nitrate reduction, confirming their roles in NDAO. The identification of novel putative NDAB expands current knowledge regarding the diversity of NDAB. The current study also suggests the proof of concept of using DNA-SIP to identify the slow-growing NDAB.

Enhanced Current Production by Exogenous Electron Mediators via Synergy of Promoting Biofilm Formation and the Electron Shuttling Process

Exogenous electron mediators (EMs) can facilitate extracellular electron transfer (EET) via electron shuttling processes, but it is still unclear whether and how biofilm formation is affected by the presence of EMs. Here, the impacts of EMs on EET and biofilm formation were investigated in bioelectrochemical systems (BESs) with Shewanella oneidensis MR-1, and the results showed that the presence of five different EMs led to high density current production. All the EMs substantially promoted biofilm formation with 15-36 times higher total biofilm DNA with EMs than without EMs, and they also increased the production of extracellular polymeric substances, which was favorable for biofilm formation. The current decreased substantially after removing EMs from the medium or by replacing electrodes without biofilm, suggesting that both biofilm and EMs are required for high density current production. EET-related gene expression was upregulated with EMs, resulting in the high flux of cell electron output. A synergistic mechanism was proposed: EMs in suspension were quickly reduced by the cells and reoxidized rapidly by the electrode, resulting in a microenvironment with sufficient oxidized EMs for biofilm formation, and thus, besides the well-known electron shuttling process, the EM-induced high biofilm formation and high Mtr gene expression could jointly contribute to the EET and subsequently produce a high density current. This study provides a new insight into EM-enhanced current production via regulating the biofilm formation and EET-related gene expression.

Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings

Nutrient deficiency, especially bio-available nitrogen deficiency, often impedes the bioremediation efforts of mining generated tailings. Biological nitrogen fixation is a critical process necessary for the initial nitrogen buildup in tailings. Current knowledge regarding the diazotrophs that inhabit tailings is still in its infancy. Therefore, in this study, a comprehensive investigation combining geochemical characterization, sequence analyses, molecular techniques, and activity measurements was conducted to characterize the diazotrophic community residing in tailing environments. Significant differences between tailings and their adjacent soils in prokaryotic and diazotrophic communities were detected. Meanwhile, strong and significant correlations between the absolute abundance of the nitrogen fixation (nifH), carbon fixation (cbbL), sulfur oxidation (soxB), and arsenite oxidation (aioA) genes were observed in the tailings but not in the soils. The reconstructed nif-containing metagenome-assembled genomes (MAGs) suggest that the carbon fixation and sulfur oxidation pathways were important for potential diazotrophs inhabiting the tailings. Activity measurements further confirmed that diazotrophs inhabiting tailings preferentially use inorganic electron donors (e.g., elemental sulfur) compared to organic electron donors (e.g., sucrose), while diazotrophs inhabiting soils preferred organic carbon sources. Collectively, these findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.

Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor

Organohalide respiration is an important process in the global halogen cycle and for bioremediation. In this study, we compared the global transcriptomic and proteomic analyses of Desulfoluna spongiiphila strain AA1, an organohalide-respiring member of the Desulfobacterota isolated from a marine sponge, with 2,6-dibromophenol or with sulfate as an electron acceptor. The most significant difference of the transcriptomic analysis was the expression of one reductive dehalogenase gene cluster (rdh16), which was significantly upregulated with the addition of 2,6-dibromophenol. The corresponding protein, reductive dehalogenase RdhA16032, was detected in the proteome under treatment with 2,6-dibromophenol but not with sulfate only. There was no significant difference in corrinoid biosynthesis gene expression levels between the two treatments, indicating that the production of corrinoid in D. spongiiphila is constitutive or not specific for organohalide versus sulfate respiration. Electron-transporting proteins or mediators unique for reductive dehalogenation were not revealed in our analysis, and we hypothesize that reductive dehalogenation may share an electron-transporting system with sulfate reduction. The metabolism of D. spongiiphila, predicted from transcriptomic and proteomic results, demonstrates high metabolic versatility and provides insights into the survival strategies of a marine sponge symbiont in an environment rich in organohalide compounds and other secondary metabolites.IMPORTANCE Respiratory reductive dehalogenation is an important process in the overall cycling of both anthropogenic and natural organohalide compounds. Marine sponges produce a vast array of bioactive compounds as secondary metabolites, including diverse halogenated compounds that may enrich for dehalogenating bacteria. Desulfoluna spongiiphila strain AA1 was originally enriched and isolated from the marine sponge Aplysina aerophoba and can grow with both brominated compounds and sulfate as electron acceptors for respiration. An understanding of the overall gene expression and the protein production profile in response to organohalides is needed to identify the full complement of genes or enzymes involved in organohalide respiration. Elucidating the metabolic capacity of this sponge-associated bacterium lays the foundation for understanding how dehalogenating bacteria may control the fate of organohalide compounds in sponges and their role in a symbiotic organobromine cycle.

Bacterial Communities and Functional Genes Stimulated During Anaerobic Arsenite Oxidation and Nitrate Reduction in a Paddy Soil

Microbial arsenite (As(III)) oxidation associated with nitrate (NO₃^-) reduction might be an important process in diminishing arsenic bioavailability and toxicity to rice when paddy soils are contaminated by arsenic. In a noncontaminated soil, however, the responses of bacterial communities and functional genes to As(III) under nitrate-reducing conditions are poorly understood. In this study, anaerobic paddy soil microcosms were established with As(III) and/or NO₃^- to investigate how the bacterial communities and their functional genes were stimulated during As(III) oxidation and nitrate reduction. Microbial oxidation of As(III) to As(V) was substantially accelerated by nitrate addition, while nitrate reduction was not affected by As(III) addition. Metagenomic analysis revealed that nitrate-reducing bacteria were principally affiliated with Pseudogulbenkiania, with narG, nirS, and norBC genes. Putative As(III)-oxidizing bacteria were dominated by an Azoarcus sp. with As(III) oxidase genes aioA and aioB detected in its draft genome, which also had complete sets of denitrification genes (mainly, napA, nirK, and nosZ). Quantitive PCR analysis confirmed that the abundance of Azoarcus spp., aioA, and nosZ genes was enhanced by As(III) addition. These findings suggest the importance of Azoarcus- and Pseudogulbenkiania-related spp., both of which showed various physio-ecological characteristics for arsenic and nitrogen biogeochemistry, in coupling As(III) oxidation and nitrate reduction in flooded paddy soil.

Identification of a Chlorodibenzo-p-dioxin Dechlorinating Dehalococcoides mccartyi by Stable Isotope Probing

Polychlorinated dibenzo-p-dioxins (PCDDs) are released into the environment from a variety of both anthropogenic and natural sources. While highly chlorinated dibenzo-p-dioxins are persistent under oxic conditions, in anoxic environments, these organohalogens can be reductively dechlorinated to less chlorinated compounds that are then more amenable to subsequent aerobic degradation. Identifying the microorganisms responsible for dechlorination is an important step in developing bioremediation approaches. In this study, we demonstrated the use of a DNA-stable isotope probing (SIP) approach to identify the bacteria active in dechlorination of PCDDs in river sediments, with 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) as a model. In addition, pyrosequencing of reverse transcribed 16S rRNA of TeCDD dechlorinating enrichment cultures was used to reveal active members of the bacterial community. A set of operational taxonomic units (OTUs) responded positively to the addition of 1,2,3,4-TeCDD in SIP microcosms assimilating ¹³C-acetate as the carbon source. Analysis of bacterial community profiles of the ¹³C labeled heavy DNA fraction revealed that an OTU corresponding to Dehalococcoides mccartyi accounted for a significantly greater abundance in cultures amended with 1,2,3,4-TeCDD than in cultures without 1,2,3,4-TeCDD. This implies the involvement of this Dehalococcoides mccartyi strain in the reductive dechlorination of 1,2,3,4-TeCDD and suggests the applicability of SIP for a robust assessment of the bioremediation potential of organohalogen contaminated sites.

Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing

Arctic soils store vast amounts of carbon and are subject to intense climate change. While the effects of thaw on the composition and activities of Arctic tundra microorganisms has been examined extensively, little is known about the consequences of temperature fluctuations within the subzero range in seasonally frozen or permafrost soils. This study identified tundra soil bacteria active at subzero temperatures using stable isotope probing (SIP). Soils from Kilpisjärvi, Finland, were amended with 13C-cellobiose and incubated at 0, −4 and −16°C for up to 40 weeks. 16S rRNA gene sequence analysis of 13C-labelled DNA revealed distinct subzero-active bacterial taxa. The SIP experiments demonstrated that diverse bacteria, including members of Candidatus Saccharibacteria, Melioribacteraceae, Verrucomicrobiaceae, Burkholderiaceae, Acetobacteraceae, Armatimonadaceae and Planctomycetaceae, were capable of synthesising 13C-DNA at subzero temperatures. Differences in subzero temperature optima were observed, for example, with members of Oxalobacteraceae and Rhizobiaceae found to be more active at 0°C than at −4°C or −16°C, whereas Melioribacteriaceae were active at all subzero temperatures tested. Phylogeny of 13C-labelled 16S rRNA genes from the Melioribacteriaceae, Verrucomicrobiaceae and Candidatus Saccharibacteria suggested that these taxa formed subzero-active clusters closely related to members from other cryo-environments. This study demonstrates that subzero temperatures impact active bacterial community composition and activity, which may influence biogeochemical cycles.

Bacterial response to antimony and arsenic contamination in rice paddies during different flooding conditions

Rice is more vulnerable to arsenic (As) and antimony (Sb) contamination than other cereals due to the special cultivation methods, during which irrigation conditions are adjusted depending upon the growth stages. The changes in irrigation conditions may alter the oxidation states of Sb and As, which influences their mobility and bioavailability and hence uptake by rice. In this study, bacterial responses to As and Sb contamination in rice fields were investigated during two different stages of rice growth: the vegetative stage (flooded conditions), and the ripening stage (drained conditions). The substantial changes in the irrigation conditions caused a variation in geochemical parameters including the As- and Sb-extractable fractions. As and Sb were more mobile and bioaccessible during the flooded than under drained conditions. The microbial communities varied during two irrigation conditions, suggesting that the geochemical conditions may have different effects on the innate paddy microbiota. Therefore, various statistical tools including co-occurrence network and random forest (RF) were performed to reveal the environment-microbe interactions in two different irrigation conditions. One of the notable findings is that Sb- and As-related parameters exerted more influences during the flooded than under drained conditions. Furthermore, a detailed RF analysis indicated that the individual bacterial taxa may also respond differently to contaminant fractions during the two irrigation conditions. Notably, RF indicated that individual taxa such as Clostridiaceae and Geobacter may be responsible for biotransformation of As and Sb (e.g., As and Sb reduction). The results provided knowledge for As and Sb transformation during contrasting irrigation conditions and the potential mitigation strategy for contaminant removal.

Evaluation of carbon isotope fractionation during anaerobic reductive dehalogenation of chlorinated and brominated benzenes

Compound specific stable isotope analysis (CSIA) has been established as a useful tool to evaluate in situ biodegradation. Here, CSIA was used to determine microbial dehalogenation of chloro- and bromobenzenes in microcosms derived from Hackensack River sediments. Gas chromatography-isotope ratio mass spectrometry (GC-IRMS) was used to measure carbon isotope fractionation during reductive dehalogenation of hexachlorobenzene (HCB), pentachlorobenzene (PeCB), 1,2,3,5-tetrachlorobenzene (TeCB), 1,2,3,5-tetrabromobenzene (TeBB), and 1,3,5-tribromobenzene (TriBB). Strong evidence of isotope fractionation coupled to dehalogenation was not observed in the substrate, possibly due to the low solubilities of the highly halogenated benzene substrates and a dilution of the isotope signal. Nonetheless, we could measure a depletion of the δ¹³C value in the dichlorobenzene product during dechlorination of HCB, the sequential depletion and enrichment of δ¹³C value for trichlorobenzene in TeCB dechlorinating cultures, and the enrichment of δ¹³C during debromination of TriBB. This indicates that a measurable isotope fractionation occurred during reductive dehalogenation of highly halogenated chloro- and bromobenzenes in aquatic sediments. Thus, although more quantitative measurements will be needed, the data suggests that CSIA may have application for monitoring in situ microbial reductive dehalogenation of highly halogenated benzenes.

Organohalide respiration in pristine environments: implications for the natural halogen cycle

Halogenated organic compounds, also termed organohalogens, were initially considered to be of almost exclusively anthropogenic origin. However, over 5000 naturally synthesized organohalogens are known today. This has also fuelled the hypothesis that the natural and ancient origin of organohalogens could have primed development of metabolic machineries for their degradation, especially in microorganisms. Among these, a special group of anaerobic microorganisms was discovered that could conserve energy by reducing organohalogens as terminal electron acceptor in a process termed organohalide respiration. Originally discovered in a quest for biodegradation of anthropogenic organohalogens, these organohalide-respiring bacteria (OHRB) were soon found to reside in pristine environments, such as the deep subseafloor and Arctic tundra soil with limited/no connections to anthropogenic activities. As such, accumulating evidence suggests an important role of OHRB in local natural halogen cycles, presumably taking advantage of natural organohalogens. In this minireview, we integrate current knowledge regarding the natural origin and occurrence of industrially important organohalogens and the evolution and spread of OHRB, and describe potential implications for natural halogen and carbon cycles.

Dechlorinating bacteria are abundant but anaerobic dechlorination of weathered polychlorinated dibenzo-p-dioxins and dibenzofurans in contaminated sediments is limited

The potential for microbial dechlorination of the weathered polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) was determined in sediments with historical contamination by the chlorophenol wood preservative Ky-5 and its associated dimeric impurities. Sediments were collected from four sites of the Kymijoki River in South-Eastern Finland located at 0, 20, 30, and 60 km downstream from the source of contamination, and at a reference site. We examined the congener profiles of historical PCDD/Fs, including non-2,3,7,8-substituted congeners, and determined the dechlorination potential in sediments at the different sites of the river. The measured mean total concentrations for 2,3,7,8-PCDD/Fs were extremely high, 1200 mg/kg dw, at the most contaminated site, Kuusankoski. The mean concentrations for the predominant 2,3,7,8-congeners were 1,2,3,4,6,7,8-HpCDF 780 mg/kg dw, and for OCDF 380 mg/kg dw at Kuusankoski. At all other study sites of the river the mean total concentrations for 2,3,7,8-PCDD/Fs varied between 9 and 96 mg/kg dw, (6-80 mg/kg dw for 1,2,3,4,6,7,8-HpCDF, 3-13 mg/kg dw for OCDF). The sediment PCDD/F composition was similar to that of Ky-5, indicating that no or only minimal biodegradation of PCDD/F congeners has occurred in the river sediments over the last few decades since the contamination events. Microbes capable of PCDD/F dechlorination were present at all study sites based on Dehalococcoides-like Chloroflexi community determination and dechlorination of spiked 1,2,3,4-tetrachlorodibenzofuran. However, no substantial changes in the relative abundances of PCDD/Fs were observed over 2.5 years in laboratory microcosm studies, indicating that anaerobic dechlorination of weathered PCDD/Fs was limited over the course of the experiment. Therefore, concentrations of weathered PCDD/Fs in the sediments of the Kymijoki River are expected to remain at the same level for decades or centuries with further migration towards the Baltic Sea.

Novel reductive dehalogenases from the marine sponge associated bacterium Desulfoluna spongiiphila

Desulfoluna spongiiphila strain AA1 is an organohalide respiring bacterium, isolated from the marine sponge Aplysina aerophoba, that can use brominated and iodinated phenols, in addition to sulfate and thiosulfate as terminal electron acceptors. The genome of Desulfoluna spongiiphila strain AA1 is approximately 6.5 Mb. Three putative reductive dehalogenase (rdhA) genes involved in respiratory metabolism of organohalides were identified within the sequence. Conserved motifs found in respiratory reductive dehalogenases (a twin arginine translocation signal sequence and two iron-sulfur clusters) were present in all three putative AA1 rdhA genes. Transcription of one of the three rdhA genes was significantly upregulated during respiration of 2,6-dibromophenol and sponge extracts. Strain AA1 appears to have the ability to synthesize cobalamin, the key cofactor of most characterized reductive dehalogenase enzymes. The genome contains genes involved in cobalamin synthesis and uptake and can grow without cobalamin supplementation. Identification of this target gene associated with debromination lays the foundation for understanding how dehalogenating bacteria control the fate of organohalide compounds in sponges and their role in a symbiotic organobromine cycle. In the sponge environment, D. spongiiphila strain AA1 may thus take advantage of both brominated compounds and sulfate as electron acceptors for respiration.

Forensic Analysis of Polychlorinated Dibenzo-p-Dioxin and Furan Fingerprints to Elucidate Dechlorination Pathways

Polychlorinated dibenzo-p-dioxins and -furans (PCDD/Fs) are persistent organic pollutants whose main removal process in the environment is due to biodegradation, and particularly anaerobic reductive dechlorination. Since PCDD/F congeners that are substituted in the lateral 2, 3, 7, and 8 positions are the most toxic, removal of these chlorines is advantageous, but previous studies have only demonstrated their removal under laboratory conditions. We evaluated a concentration data set of PCDD/F congeners with four or more chlorines along with all 209 polychlorinated biphenyl (PCB) congeners in surface water, treated and untreated wastewater, landfill leachate, and biosolids (NY CARP data set) to determine whether peri and peri/lateral dechlorination of PCDD/Fs occurs in these environments. Positive Matrix Factorization (PMF) applied to the data set revealed a factor indicative of the microbial dechlorination of PCBs, and this factor also contained a variety of non-2,3,7,8 substituted PCDD/F congeners. These results suggest that dechlorination of PCDD/Fs at the lateral positions is facile if not preferred in these environments. The relative lack of tetra- and penta-chlorinated PCDD/Fs suggested that dechlorination proceeds to PCDD/F congeners with less than four chlorines. The PMF results were confirmed by examining three samples that contained >90% PCB dechlorination products from the Fresh Kills Landfill and the Hudson River. Even without factor analysis, these samples demonstrated almost identical PCDD/F congener patterns. This study suggests that PCDD/Fs are reductively dechlorinated to nontoxic non-2,3,7,8 PCDD/F congeners in sewers and landfills as well as in the sediment of the Upper Hudson River.

Profiling bacterial communities by MinION sequencing of ribosomal operons

BACKGROUND

An approach utilizing the long-read capability of the Oxford Nanopore MinION to rapidly sequence bacterial ribosomal operons of complex natural communities was developed. Microbial fingerprinting employs domain-specific forward primers (16S rRNA subunit), reverse primers (23S rRNA subunit), and a high-fidelity Taq polymerase with proofreading capabilities. Amplicons contained both ribosomal subunits for broad-based phylogenetic assignment (~ 3900 bp of sequence), plus the intergenic spacer (ITS) region (~ 300 bp) for potential strain-specific identification.

RESULTS

To test the approach, bacterial rRNA operons (~ 4200 bp) were amplified from six DNA samples employing a mixture of farm soil and bioreactor DNA in known concentrations. Each DNA sample mixture was barcoded, sequenced in quadruplicate (n = 24), on two separate 6-h runs using the MinION system (R7.3 flow cell; MAP005 and 006 chemistry). From nearly 90,000 MinION reads, roughly 33,000 forward and reverse sequences were obtained. This yielded over 10,000 2D sequences which were analyzed using a simplified data analysis pipeline based on NCBI Blast and assembly with Geneious software. The method could detect over 1000 operational taxonomic units in the sample sets in a quantitative manner. Global sequence coverage for the various rRNA operons ranged from 1 to 1951x. An iterative assembly scheme was developed to reconstruct those rRNA operons with > 35x coverage from a set of 30 operational taxonomic units (OTUs) among the Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, and Gemmatimonadetes. Phylogenetic analysis of the 16S rRNA and 23S rRNA genes from each operon demonstrated similar tree topologies with species/strain-level resolution.

CONCLUSIONS

This sequencing method represents a cost-effective way to profile microbial communities. Because the MinION is small, portable, and runs on a laptop, the possibility of microbiota characterization in the field or on robotic platforms becomes realistic.

Bacterial communities in the small intestine respond differently to those in the caecum and colon in mice fed low- and high-fat diets

Bacterial communities in the mouse caecum and faeces are known to be altered by changes in dietary fat. The microbiota of the mouse small intestine, by contrast, has not been extensively profiled and it is unclear whether small intestinal bacterial communities shift with dietary fat levels. We compared the microbiota in the small intestine, caecum and colon in mice fed a low-fat (LF) or high-fat (HF) diet using 16S rRNA gene sequencing. The relative abundance of major phyla in the small intestine, Bacteriodetes, Firmicutes and Proteobacteria, was similar to that in the caecum and colon; the relative abundance of Verrucomicrobia was significantly reduced in the small intestine compared to the large intestine. Several genera were uniquely detected in the small intestine and included the aerotolerant anaerobe, Lactobacillus spp. The most abundant genera in the small intestine were accounted for by anaerobic bacteria and were identical to those identified in the large intestine. An HF diet was associated with significant weight gain and adiposity and with changes in the bacterial communities throughout the intestine, with changes in the small intestine differing from those in the caecum and colon. Prominent Gram-negative bacteria including genera of the phylum Bacteroidetes and a genus of Proteobacteria significantly changed in the large intestine. The mechanistic links between these changes and the development of obesity, perhaps involving metabolic endotoxemia, remain to be determined.

Impact of estuarine gradients on reductive dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin in river sediment enrichment cultures

Polychlorinated dibenzo-p-dioxins (PCDDs) are among the most persistent organic pollutants. Although the total input of PCDDs into the environment has decreased substantially over the past four decades, their input via non-point sources is still increasing, especially in estuarine metropolitan areas. Here we report on the microbially mediated reductive dechlorination of PCDDs in anaerobic enrichment cultures established from sediments collected from five locations along the Hackensack River, NJ and investigate the impacts of sediment physicochemical characteristics on dechlorination activity. Dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) and abundance of Dehalococcoides spp. negatively correlated with salinity and sulfate concentration in sediments used to establish the cultures. 1,2,3,4-TeCDD was dechlorinated to a lesser extent in cultures established from sediments from the tidally influenced estuarine mouth of the river. In cultures established from low salinity sediments, 1,2,3,4-TeCDD was reductively dechlorinated with the accumulation of 2-monochlorodibenzo-p-dioxin as the major product. Sulfate concentrations above 2 mM inhibited 1,2,3,4-TecDD dechlorination activity. Consecutive lateral- and peri- dechlorination took place in enrichment cultures with a minimal accumulation of 2,3-dichlorodibenzo-p-dioxin in active cultures. A Dehalococcoides spp. community was enriched and accounted for up to 64% of Chloroflexi detected in these sediment cultures.

High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment

Sedimenticola selenatireducens strain AK4OH1^T (= DSM 17993^T = ATCC BAA-1233^T) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1^T was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions. The draft genome comprises 4,588,530 bp and 4276 predicted protein-coding genes including genes for the anaerobic degradation of 4-hydroxybenzoate and benzoate. Here we report the main features of the genome of S. selenatireducens strain AK4OH1^T.

Reductive dehalogenation activity of indigenous microorganism in sediments of the Hackensack River, New Jersey

Organohalogen pollutants are of concern in many river and estuarine environments, such as the New York-New Jersey Harbor estuary and its tributaries. The Hackensack River is contaminated with various metals, hydrocarbons and halogenated organics, including polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins. In order to examine the potential for microbial reductive dechlorination by indigenous microorganisms, sediment samples were collected from five different estuarine locations along the Hackensack River. Hexachlorobenzene (HCB), hexabromobenzene (HBB), and pentachloroaniline (PCA) were selected as model organohalogen pollutants to assess anaerobic dehalogenating potential. Dechlorinating activity of HCB and PCA was observed in sediment microcosms for all sampling sites. HCB was dechlorinated via pentachlorobenzene (PeCB) and trichlorobenzene (TriCB) to dichlorobenzene (DCB). PCA was dechlorinated via tetrachloroaniline (TeCA), trichloroanilines (TriCA), and dichloroanilines (DCA) to monochloroaniline (MCA). No HBB debromination was observed over 12 months of incubation. However, with HCB as a co-substrate slow HBB debromination was observed with production of tetrabromobenzene (TeBB) and tribromobenzene (TriBB). Chloroflexi specific 16S rRNA gene PCR-DGGE followed by sequence analysis detected Dehalococcoides species in sediments of the freshwater location, but not in the estuarine site. Analysis targeting 12 putative reductive dehalogenase (rdh) genes showed that these were enriched concomitant with HCB or PCA dechlorination in freshwater sediment microcosms.

The subzero microbiome: microbial activity in frozen and thawing soils

Most of the Earth's biosphere is characterized by low temperatures (<5°C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and, in particular, thawing of frozen soils are not yet well understood, although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change.

The Effect of Diet and Exercise on Intestinal Integrity and Microbial Diversity in Mice

BACKGROUND

The gut microbiota is now known to play an important role contributing to inflammatory-based chronic diseases. This study examined intestinal integrity/inflammation and the gut microbial communities in sedentary and exercising mice presented with a normal or high-fat diet.

METHODS

Thirty-six, 6-week old C57BL/6NTac male mice were fed a normal or high-fat diet for 12-weeks and randomly assigned to exercise or sedentary groups. After 12 weeks animals were sacrificed and duodenum/ileum tissues were fixed for immunohistochemistry for occludin, E-cadherin, and cyclooxygenase-2 (COX-2). The bacterial communities were assayed in fecal samples using terminal restriction fragment length polymorphism (TRFLP) analysis and pyrosequencing of 16S rRNA gene amplicons.

RESULTS

Lean sedentary (LS) mice presented normal histologic villi while obese sedentary (OS) mice had similar villi height with more than twice the width of the LS animals. Both lean (LX) and obese exercise (OX) mice duodenum and ileum were histologically normal. COX-2 expression was the greatest in the OS group, followed by LS, LX and OX. The TRFLP and pyrosequencing indicated that members of the Clostridiales order were predominant in all diet groups. Specific phylotypes were observed with exercise, including Faecalibacterium prausnitzi, Clostridium spp., and Allobaculum spp.

CONCLUSION

These data suggest that exercise has a strong influence on gut integrity and host microbiome which points to the necessity for more mechanistic studies of the interactions between specific bacteria in the gut and its host.

Identification of a Ruminococcaceae Species as the Methyl tert-Butyl Ether (MTBE) Degrading Bacterium in a Methanogenic Consortium

The widespread use of methyl tert-butyl ether (MTBE) has caused major contamination of groundwater sources and is a concern due to its taste and odor problems, as well as its toxicity. MTBE can be degraded anaerobically which makes bioremediation of contaminated aquifers a potential solution. Nevertheless, the organisms and mechanisms that are responsible for anaerobic MTBE degradation are still unknown. The aim of our research was to identify the organisms actively degrading MTBE. For this purpose we characterized an anaerobic methanogenic culture enriched with MTBE as the sole carbon source from the New Jersey Arthur Kill intertidal strait sediment. The cultures were analyzed using stable isotope probing (SIP) combined with terminal restriction fragment length polymorphism (T-RFLP), high-throughput sequencing and clone library analysis of bacterial 16S rRNA genes. The sequence data indicated that phylotypes belonging to the Ruminococcaceae in the Firmicutes were predominant in the methanogenic cultures. SIP experiments also showed sequential incorporation of the (13)C labeled MTBE by the bacterial community with a bacterium most closely related to Saccharofermentans acetigenes identified as the bacterium active in O-demethylation of MTBE. Identification of the microorganisms responsible for the activity will help us better understand anaerobic MTBE degradation processes in the field and determine biomarkers for monitoring natural attenuation.

Identification of Anaerobic Aniline-Degrading Bacteria at a Contaminated Industrial Site

Anaerobic aniline biodegradation was investigated under different electron-accepting conditions using contaminated canal and groundwater aquifer sediments from an industrial site. Aniline loss was observed in nitrate- and sulfate-amended microcosms and in microcosms established to promote methanogenic conditions. Lag times of 37 days (sulfate amended) to more than 100 days (methanogenic) were observed prior to activity. Time-series DNA-stable isotope probing (SIP) was used to identify bacteria that incorporated (13)C-labeled aniline in the microcosms established to promote methanogenic conditions. In microcosms from heavily contaminated aquifer sediments, a phylotype with 92.7% sequence similarity to Ignavibacterium album was identified as a dominant aniline degrader as indicated by incorporation of (13)C-aniline into its DNA. In microcosms from contaminated canal sediments, a bacterial phylotype within the family Anaerolineaceae, but without a match to any known genus, demonstrated the assimilation of (13)C-aniline. Acidovorax spp. were also identified as putative aniline degraders in both of these two treatments, indicating that these species were present and active in both the canal and aquifer sediments. There were multiple bacterial phylotypes associated with anaerobic degradation of aniline at this complex industrial site, which suggests that anaerobic transformation of aniline is an important process at the site. Furthermore, the aniline degrading phylotypes identified in the current study are not related to any known aniline-degrading bacteria. The identification of novel putative aniline degraders expands current knowledge regarding the potential fate of aniline under anaerobic conditions.

Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site

The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminal electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.

Effect of temperature on the reductive dechlorination of 1,2,3,4-tetrachlorodibenzofuran in anaerobic PCDD/F-contaminated sediments

The effect of temperature on the reductive dechlorination in sediments of the PCDD/F-contaminated Kymijoki River, Finland was assessed with 1,2,3,4-tetrachlorodibenzofuran (1,2,3,4-TeCDF) at various temperatures and with co-amendment of 2,3,4,6-tetrachlorophenol (2,3,4,6-TeCP) in laboratory microcosms. The dechlorination rate of 1,2,3,4-TeCDF increased with incubation temperature, with TeCDF half-lives of 2.1 y at 21°C, 3.9 y at 15°C, and 19.0 y at 4°C. Co-amendment with 2,3,4,6-TeCP reduced the TeCDF half-life to 1.8 y at 21°C. 1,2,3,4-TeCDF was dechlorinated mainly in the lateral position to 1,3,4-TrCDF and then to 1,3-DiCDF over 29 months, but incubation temperature affected the relative molar ratios of the dechlorination products. The abundance of the Dehalococcoides-like Chloroflexi community did not substantially change in microcosms over 24 months incubation at the different temperatures. The dechlorination activity of 1,2,3,4-TeCDF was significantly limited at lower temperatures, which should be considered in predicting the environmental fate of aged PCDD/Fs in sediments of the Kymijoki River.

Complete genome sequence of Granulicella tundricola type strain MP5ACTX9(T), an Acidobacteria from tundra soil

Granulicella tundricola strain MP5ACTX9(T) is a novel species of the genus Granulicella in subdivision 1 Acidobacteria. G. tundricola is a predominant member of soil bacterial communities, active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. The organism is a cold-adapted acidophile and a versatile heterotroph that hydrolyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates, including gene modules encoding for the carbohydrate-active enzyme (CAZy) families for the breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides such as plant based carbon polymers. The genome of G. tundricola strain MP5ACTX9(T) consists of 4,309,151 bp of a circular chromosome and five mega plasmids with a total genome content of 5,503,984 bp. The genome comprises 4,705 protein-coding genes and 52 RNA genes.

Most influential FEMS publications

A selection of influential FEMS publications to celebrate the 40th anniversary of FEMS.