Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere

Dehalogenimonas Strain W from Estuarine Sediments Dechlorinates 1,2-Dichloroethane under Elevated Salinity

Organohalide-respiring bacteria (OHRB) have been found in various environments and play an indispensable role in the biogeochemical cycling and detoxification of halogenated organic compounds (HOCs). Currently, few ORHB have been reported to perform reductive dechlorination under high salinity conditions, indicating a knowledge gap on the diversity of OHRB and the survival strategy of OHRB in saline environments (e.g., estuarine, marine). This study reports the characterization of an enrichment culture dominated by a new Dehalogenimonas population strain W derived from estuarine sediments, which demonstrates the capability to dechlorinate 1,2-dichloroethane (1,2-DCA) to ethene under elevated salinity (≥5.1% NaCl, w/v). Metagenomic and proteomic analyses revealed that the distinctive high-salinity dechlorination of strain W is primarily attributed to a putative reductive dehalogenase (RDase) DdeA, which shares >91.4% amino acid identity with the dihaloeliminating RDase DcpA from other Dehalogenimonas strains. Additionally, ectoine biosynthesis enzymes (EctABC) contribute to the strain's salt tolerance. These findings underscore the potential of OHRB, particularly Dehalogenimonas, to detoxify HOCs in high-salinity environments, such as estuarine and marine ecosystems, by employing compatible solutes as an adaptive mechanism.

Survival strategies and assembly mechanisms of microbial communities in petroleum-contaminated soils

This study analyzed petroleum-contaminated soils from south and north locations in China to explore the structure, diversity, functional genes and assembly processes of microbial communities' . Compared with soils from south locations, soils from northern regions exhibited elevated pH, total nitrogen (TN), and total petroleum hydrocarbon (TPH) levels. Among these, TN and TPH were the most influential on the microbial community. The dominant phyla for bacteria, archaea, and fungi were Proteobacteria, Thaumarchaeota, and Ascomycota, respectively. Among them, Proteobacteria was strongly correlated with various functional genes including alkB and many aromatics degradation and denitrification genes (r > 0.9, p < 0.01), suggesting that Proteobacteria play an important role in petroleum-contaminated soils. Metabolism in northern regions was more active than that in southern regions. The northern regions showed a pronounced tendency for denitrification, while the southern regions were characterized by acetoclastic methanogenesis. The assembly of microbial communities exhibited regional patterns, the deterministic assembly was more prominent in the northern soils, while the stochastic assembly was evident in the southern soils. Overall, these findings provide a new conceptual framework to understand the biosphere in petroleum-contaminated soil, potentially guiding improved management practices in the environmental remediation.

Deep-sea in situ and laboratory multi-omics provide insights into the sulfur assimilation of a deep-sea Chloroflexota bacterium

Chloroflexota bacteria are abundant and globally distributed in various deep-sea ecosystems. It has been reported based on metagenomics data that two deep-sea Chloroflexota lineages (the SAR202 group and Dehalococcoidia class) have the potential to drive sulfur cycling. However, the absence of cultured Chloroflexota representatives is a significant bottleneck toward understanding their contribution to the deep-sea sulfur cycling. In this study, we find that Phototrophicus methaneseepsis ZRK33 isolated from deep-sea sediment has a heterotrophic lifestyle and can assimilate sulfate and thiosulfate. Using combined physiological, genomic, proteomic, and in situ transcriptomic methods, we find that strain ZRK33 can perform assimilatory sulfate reduction in both laboratory and deep-sea conditions. Metabolism of sulfate or thiosulfate by strain ZRK33 significantly promotes the transport and degradation of various macromolecules and thereby stimulates the energy production. In addition, metagenomic results show that genes associated with assimilatory and dissimilatory sulfate reduction are ubiquitously distributed in the metagenome-assembled genomes of Chloroflexota members derived from deep-sea sediments. Metatranscriptomic results also show that the expression levels of related genes are upregulated, strongly suggesting that Chloroflexota bacteria may play undocumented roles in deep-sea sulfur cycling.

IMPORTANCE

The cycling of sulfur is one of Earth's major biogeochemical processes and is closely related to the energy metabolism of microorganisms living in the deep-sea cold seep and hydrothermal vents. To date, some of the members of Chloroflexota are proposed to play a previously unrecognized role in sulfur cycling. However, the sulfur metabolic characteristics of deep-sea Chloroflexota bacteria have never been reported, and remain to be verified in cultured deep-sea representatives. Here, we show that the deep-sea Chloroflexota bacterium ZRK33 can perform sulfate assimilation in both laboratory and deep-sea conditions, which expands our knowledge of the sulfur metabolic potential of deep-sea Chloroflexota bacteria. We also show that the genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the deep-sea Chloroflexota members, providing hints to the roles of Chloroflexota bacteria in deep-sea sulfur biogeochemical cycling.

Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy)

Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.

Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts

Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.

Cultivation of marine bacteria of the SAR202 clade

Bacteria of the SAR202 clade, within the phylum Chloroflexota, are ubiquitously distributed in the ocean but have not yet been cultivated in the lab. It has been proposed that ancient expansions of catabolic enzyme paralogs broadened the spectrum of organic compounds that SAR202 bacteria could oxidize, leading to transformations of the Earth's carbon cycle. Here, we report the successful cultivation of SAR202 bacteria from surface seawater using dilution-to-extinction culturing. The growth of these strains is very slow (0.18-0.24 day-1) and is inhibited by exposure to light. The genomes, of ca. 3.08 Mbp, encode archaella (archaeal motility structures) and multiple sets of enzyme paralogs, including 80 genes coding for enolase superfamily enzymes and 44 genes encoding NAD(P)-dependent dehydrogenases. We propose that these enzyme paralogs participate in multiple parallel pathways for non-phosphorylative catabolism of sugars and sugar acids. Indeed, we demonstrate that SAR202 strains can utilize several substrates that are metabolized through the predicted pathways, such as sugars ʟ-fucose and ʟ-rhamnose, as well as their lactone and acid forms.

Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

BACKGROUND

When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles.

RESULTS

Our dataset represents 3635 metagenome-assembled genomes encompassing 511 novel and recently identified genera from deep-sea hydrothermal settings. Some of the novel bacterial (107) and archaeal genera (30) that were recently reported from the deep-sea Brothers volcano were also detected at the deep-sea hydrothermal vent fields, while 99 bacterial and 54 archaeal genera were endemic to the deep-sea Brothers volcano deposits. We report some of the first examples of medium- (≥ 50% complete, ≤ 10% contaminated) to high-quality (> 90% complete, < 5% contaminated) MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur, and hydrogen metabolic processes across all sites and illustrates sulfur and nitrogen metabolic "handoffs" in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment.

CONCLUSION

Our study of globally distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa. Video Abstract.

Grinding Beads Influence Microbial DNA Extraction from Organic-Rich Sub-Seafloor Sediment

Sub-seafloor sediment is the largest microbial habitat on Earth. The study of microbes in sub-seafloor sediment is largely limited by the technical challenge of acquiring ambient microbial DNA because of sediment heterogeneity. Changes in the extraction method, even just by one step, can affect the extraction yields for complicated sediment samples. In this work, sub-seafloor sediment samples from the Baltic Sea with high organic carbon content were used to evaluate the influence of different grinding beads on DNA extraction. We found that the grinding beads can affect the DNA extraction from the organic-matter- and biosiliceous-clay-rich samples. A mixture of 0.5-mm and 0.1-mm grinding beads exhibited higher DNA yields and recovered more unique taxa than other bead combinations, such as Stenotrophomonas from Gammaproteobacteria and Leptotrichia from Fusobacteria; therefore, these beads are more suitable than the others for DNA extraction from the samples used in this study. This advantage might be magnified in samples with high biomass. On the contrary, the use of only small beads might lead to underestimation for certain Gram-positive strains. Overall, the discovery of abundant widespread deep biosphere clades in our samples indicated that our optimized DNA extraction method successfully recovered the in situ microbial community.

Continuous plug-flow anammox system for mature landfill leachate treatment: Key zone for anammox pathway

This study established the one-stage partial nitrification coupled anammox and partial denitrification coupled anammox process in an anoxic/oxic continuous plug-flow system and operated for 465 days to treat mature landfill leachate. 97.9 %-98.1 % of inorganic nitrogen was removed when the nitrogen loading rate was maintained at 0.33-0.36 kg N/m³/d, and a high anammox contribution to nitrogen removal (89.8 %-92.4 %) was achieved. The long-term in-situ free ammonia (FA) anoxic treatment contributed to the stable performances of partial nitrification and in-situ fermentation. The employed integrated fixed-film activated sludge technology favored the enrichment of hzsA, hzsB, hdh, amoA, hao, narG, and napA functional genes. The oxic zone, particularly oxic biofilm, was the key zone for anammox pathway, where Candidatus_Kuenenia (from 1.6 % to 8.3 %) with high tolerance to FA and salinity stress outcompeted Candidatus_Brocadia (from 18.3 % to 0.1 %) as the dominant anammox bacteria. This study could provide guidance for anammox-mediated landfill leachate treatment in practical projects.

Antibiotic resistance genes correlate with metal resistances and accumulate in the deep water layers of the Black Sea

Seas and oceans are a global reservoir of antibiotic resistance genes (ARGs). Only a few studies investigated the dynamics of ARGs along the water column of the Black Sea, a unique environment, with a peculiar geology, biology and history of anthropogenic pollution. In this study, we analyzed metagenomic data from two sampling campaigns (2013 and 2019) collected across three different sites in the Western Black Sea at depths ranging from 5 to 2000 m. The data were processed to annotate ARGs, metal resistance genes (MRGs) and integron integrase genes. The ARG abundance was significantly higher in the deep water layers and depth was the main driver of beta-diversity both for ARGs and MRGs. Moreover, ARG and MRG abundances strongly correlated (r = 0.95). The integron integrase gene abundances and composition were not influenced by the water depth and did not correlate with ARGs. The analysis of the obtained MAGs showed that some of them harbored intI gene together with several ARGs and MRGs, suggesting the presence of multidrug resistant bacteria and that MRGs and integrons could be involved in the selection of ARGs. These results demonstrate that the Black Sea is not only an important reservoir of ARGs, but also that they accumulate in the deep water layers where co-selection with MRGs could be assumed as a relevant mechanism of their persistence.

Chemical fertilizer reduction combined with bio-organic fertilizers increases cauliflower yield via regulation of soil biochemical properties and bacterial communities in Northwest China

The continuous application of chemical fertilizers in vegetable cropping has led to deterioration of the soil environment and reduced yield and quality. The objective of this study was to evaluate the effect of combining chemical and bio-organic fertilizers on cauliflower yield, soil biochemical properties, and the bacterial community. Six treatments were established: no fertilizer (CK, control), chemical fertilizers (CF, conventional dosage for this region), balanced fertilization (BF, 30% reduction of chemical fertilizers), and balanced fertilization plus 3,000, 6,000, or 12,000 kg.ha-1 bio-organic fertilizer (Lvneng Ruiqi Biotechnology Co., Ltd., Gansu, China) (BF + OF1, BF + OF2, BF + OF3, respectively). A two-season field experiment with cauliflower was conducted under the different fertilizer treatments in irrigation districts along the Yellow River, Northwest China. The results indicate that the yield, soil organic matter, total potassium content, and enzyme activity under the bio-organic treatments were generally higher than those under the CF treatment. Compared with the CF treatment, the BF treatment increased soil organic matter content, enzyme activity and soil bacterial relative abundance. Moreover, the bacterial alpha-diversity were higher than those of conventional fertilization. The predominant phyla, including Proteobacteria, Actinobacteria, Gemmatimonadetes, and Chloroflexi, were the main contributors to the microbiome shift, as demonstrated by their remarkable enrichment in the soil under BF + OF2 and BF + OF3 treatments. Furthermore, Pearson correlation analyses show significant correlations among the soil organic matter, available P and K, electrical conductivity, and relative abundance of potentially beneficial microbial groups, such as the genera Massilia, Bacillus, Lysobacter, and Nitrosospira. Overall, this study suggests that balanced fertilization and the application of bio-organic fertilizers are essential to ensure soil fertility and long-term sustainable green productivity.

Deep mining decreases the microbial taxonomic and functional diversity of subsurface oil reservoirs

Microbes in subsurface oil reservoirs play important roles in elemental cycles and biogeochemical processes. However, the community assembly pattern of indigenous microbiome and their succession under long-term human activity remain poorly understood. Here we studied the microbial community assembly in underground sandstone cores from 190 to 2050 m in northeast China and their response to long-term oil recovery (10-50 years). Indigenous microbiome in subsurface petroleum reservoirs were dominated by Gammaproteobacteria, Firmicutes, Alphaproteobacteria, Bacteroidetes, and Actinobacteria, which exhibited a higher contribution of homogenizing dispersal assembly and different taxonomy distinct ecological modules when compared with perturbed samples. Specifically, the long-term oil recovery reduced the bacterial taxonomic- and functional-diversity, and increased the community co-occurrence associations in subsurface oil reservoirs. Moreover, distinguished from the perturbed samples, both variation partition analysis and structural equation model revealed that the contents of quartz, NO₃^- and Cl^- significantly structured the α- and β-diversity in indigenous subsurface bacterial communities. These findings first provide the holistic picture of microbiome in the deep oil reservoirs, which demonstrate the significant impact of human activity on microbiome in deep continental subsurface.

Bacterial, archaeal, and fungal community structure and interrelationships of deep-sea shrimp intestine and the surrounding sediment

Invertebrate shrimp are one of the dominant benthic macrofaunae in the deep-sea environment. The microbiota of shrimp intestine can contribute to the adaptation of their host. The impact of surrounding sediment on intestinal microbiota has been observed in cultured shrimp species, but needs to be further investigated in deep-sea shrimp. The characterization of bacterial, archaeal, and fungal community structure and their interrelationships is also limited. In this study, wild-type deep-sea shrimp and the surrounding sediment were sampled. Shrimp individuals incubated in a sediment-absent environment were also used in this study. Microbial community structure of the shrimp intestine and sediment was investigated through amplicon sequencing targeting bacterial 16S rRNA genes, archaeal 16S rRNA genes, and fungal ITS genes. The results demonstrate distinct differences in community structure between shrimp intestine and the surrounding sediment and between surface and deep (5 mbsf) sediment. The composition of the intestinal microbiota in shrimp living without sediment was different from that of wild-type shrimp, indicating that the presence or absence of sediment could influence the shrimp intestinal microbiota. Carbohydrate metabolism, energy metabolism (carbon fixation, methane metabolism, nitrogen metabolism, and sulfur metabolism), amino acid metabolism, and xenobiotic biodegradation were the most commonly predicted microbial functionalities and they interacted closely with one another. Overall, this study provided comprehensive insights into bacterial, archaeal, and fungal community structure of deep-sea shrimp intestine as well as potential ecological interactions with the surrounding sediment. This study could update our understanding of the microbiota characteristics in shrimp and sediment in deep-sea ecosystems.

Efficient nitrogen removal from mature landfill leachate in a step feed continuous plug-flow system based on one-stage anammox process

A continuous plug-flow multistage anoxic/oxic (A/O) system based on one-stage partial nitrification coupled anammox (PNA) process with integrated fixed-film activated sludge (IFAS) was established and operated over 400 days. A step feed strategy effectively controlled free ammonia concentration and alleviated impacts on ammonia oxidizing bacteria (AOB) and anammox bacteria (AnAOB). During day 301-405, 98.1% of total inorganic nitrogen was removed from mature landfill leachate, whereas chemical oxygen demand (COD) removal efficiency was 52.9%. With the enrichment of AnAOB in oxic biofilm, nitrogen removal via the anammox pathway reached 94.3%-95.0%. During system operation, the dominant anammox genus shifted from Candidatus_Brocadia to Candidatus_Kuenenia. Fluorescent in situ hybridization (FISH) indicated AnAOB encapsulated by AOB colonies were mainly distributed inside of the biofilm, which promoted nitrite utilization by the anammox process. This innovative system and the results are of great value to practical applications.

Long-Term Biocide Efficacy and Its Effect on a Souring Microbial Community

Reservoir souring, which is the production of H₂S mainly by sulfate-reducing microorganisms (SRM) in oil reservoirs, has been a long-standing issue for the oil industry. While biocides have been frequently applied to control biogenic souring, the effects of biocide treatment are usually temporary, and biocides eventually fail. The reasons for biocide failure and the long-term response of the microbial community remain poorly understood. In this study, one-time biocide treatments with glutaraldehyde (GA) and an aldehyde-releasing biocide (ARB) at low (100 ppm) and high (750 ppm) doses were individually applied to a complex SRM community, followed by 1 year of monitoring of the chemical responses and the microbial community succession. The chemical results showed that souring control failed after 7 days at a dose of 100 ppm regardless of the biocide type and lasting souring control for the entire 1-year period was achieved only with ARB at 750 ppm. Microbial community analyses suggested that the high-dose biocide treatments resulted in 1 order of magnitude lower average total microbial abundance and average SRM abundance, compared to the low-dose treatments. The recurrence of souring was associated with reduction of alpha diversity and with long-term microbial community structure changes; therefore, monitoring changes in microbial community metrics may provide early warnings of the failure of a biocide-based souring control program in the field. Furthermore, spore-forming sulfate reducers (Desulfotomaculum and Desulfurispora) were enriched and became dominant in both GA-treated groups, which could cause challenges for the design of long-lasting remedial souring control strategies.

IMPORTANCE Reservoir souring is a problem for the oil and gas industry, because H₂S corrodes the steel infrastructure, downgrades oil quality, and poses substantial risks to field personnel and the environment. Biocides have been widely applied to remedy souring, but the long-term performance of biocide treatments is hard to predict or to optimize due to limited understanding of the microbial ecology affected by biocide treatment. This study investigates the long-term biocide performance and associated changes in the abundance, diversity, and structure of the souring microbial community, thus advancing the knowledge toward a deeper understanding of the microbial ecology of biocide-treated systems and contributing to the improvement of current biocide-based souring control practices. The study showcases the potential application of incorporating microbial community analyses to forecast souring, and it highlights the long-term consequences of biocide treatment in the microbial communities, with relevance to both operators and regulators.

Highly decomposed organic carbon mediates the assembly of soil communities with traits for the biodegradation of chlorinated pollutants

To improve biodegradation strategies for chlorinated pollutants, the roles of soil organic matter and microbial function need to be clarified. It was hypothesised that microbial degradation of specific organic fractions in soils enhance community metabolic capability to degrade chlorinated pollutants. This field study used historic records of dieldrin concentrations since 1988 and established relationships between dieldrin dissipation and soil carbon fractions together with bacterial and fungal diversity in surface soils of Kurosol and Chromosol. Sparse partial least squares analysis linked dieldrin dissipation to metabolic activities associated with the highly decomposed carbon fraction. Dieldrin dissipation, after three decades of natural attenuation, was associated with increased bacterial species fitness for the decomposition of recalcitrant carbon substrates including synthetic chlorinated pollutants. These metabolic capabilities were linked to the decomposed carbon fraction, an important driver for the microbial community and function. Common bacterial traits among taxonomic groups enriched in samples with high dieldrin dissipation included their slow growth, large genome and complex metabolism which supported the notion that metabolic strategies for dieldrin degradation evolved in an energy-low soil environment. The findings provide new perspectives for bioremediation strategies and suggest that soil management should aim at stimulating metabolism at the decomposed, fine carbon fraction.

Exploring the abundance, metabolic potential and gene expression of subseafloor Chloroflexi in million-year-old oxic and anoxic abyssal clay

Chloroflexi are widespread in subsurface environments, and recent studies indicate that they represent a major fraction of the communities in subseafloor sediment. Here, we compare the abundance, diversity, metabolic potential and gene expression of Chloroflexi from three abyssal sediment cores from the western North Atlantic Gyre (water depth >5400 m) covering up to 15 million years of sediment deposition, where Chloroflexi were found to represent major components of the community at all sites. Chloroflexi communities die off in oxic red clay over 10-15 million years, and gene expression was below detection. In contrast, Chloroflexi abundance and gene expression at the anoxic abyssal clay site increase below the seafloor and peak in 2-3 million-year-old sediment, indicating a comparably higher activity. Metatranscriptomes from the anoxic site reveal increased expression of Chloroflexi genes involved in cell wall biogenesis, protein turnover, inorganic ion transport, defense mechanisms and prophages. Phylogenetic analysis shows that these Chloroflexi are closely related to homoacetogenic subseafloor clades and actively transcribe genes involved in sugar fermentations, gluconeogenesis and Wood-Ljungdahl pathway in the subseafloor. Concomitant expression of cell division genes indicates that these putative homoacetogenic Chloroflexi are actively growing in these million-year-old anoxic abyssal sediments.

Mainly on the Plane: Deep Subsurface Bacterial Proteins Bind and Alter Clathrate Structure

Gas clathrates are both a resource and a hindrance. They store massive quantities of natural gas but also can clog natural gas pipelines, with disastrous consequences. Eco-friendly technologies for controlling and modulating gas clathrate growth are needed. Type I Antifreeze Proteins (AFPs) from cold-water fish have been shown to bind to gas clathrates via repeating motifs of threonine and alanine. We tested whether proteins encoded in the genomes of bacteria native to natural gas clathrates bind to and alter clathrate morphology. We identified putative clathrate-binding proteins (CBPs) with multiple threonine/alanine motifs in a putative operon (cbp) in metagenomes from natural clathrate deposits. We recombinantly expressed and purified five CbpA proteins, four of which were stable, and experimentally confirmed that CbpAs bound to tetrahydrofuran (THF) clathrate, a low-pressure analogue for structure II gas clathrate. When grown in the presence of CbpAs, the THF clathrate was polycrystalline and platelike instead of forming single, octahedral crystals. Two CbpAs yielded branching clathrate crystals, similar to the effect of Type I AFP, while the other two produced hexagonal crystals parallel to the [1 1 1] plane, suggesting two distinct binding modes. Bacterial CBPs may find future utility in industry, such as maintaining a platelike structure during gas clathrate transportation.

Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia

Dehalococcoidia (Dia) class microorganisms are frequently found in various pristine and contaminated environments. Metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) studies have substantially improved the understanding of Dia microbial ecology and evolution; however, an updated thorough investigation on the genomic and evolutionary characteristics of Dia microorganisms distributed in geographically distinct environments has not been implemented. In this study, we analyzed available genomic data to unravel Dia evolutionary and metabolic traits. Based on the phylogeny of 16S rRNA genes retrieved from sixty-seven genomes, Dia microorganisms can be categorized into three groups, the terrestrial cluster that contains all Dehalococcoides and Dehalogenimonas strains, the marine cluster I, and the marine cluster II. These results reveal that a higher ratio of horizontally transferred genetic materials was found in the Dia marine clusters compared to that of the Dia terrestrial cluster. Pangenome analysis further suggests that Dia microorganisms have evolved cluster-specific enzymes (e.g., dehalogenase in terrestrial Dia, sulfite reductase in marine Dia) and biosynthesis capabilities (e.g., siroheme biosynthesis in marine Dia). Marine Dia microorganisms are likely adapted to versatile metabolisms for energy conservation besides organohalide respiration. The genomic differences between marine and terrestrial Dia may suggest distinct functions and roles in element cycling (e.g., carbon, sulfur, chlorine), which require interdisciplinary approaches to unravel the physiology and evolution of Dia in various environments.

Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics

Rare members of environmental microbial communities are often overlooked and unexplored, primarily due to the lack of techniques capable of acquiring their genomes. Chloroflexi belong to one of the most understudied phyla, even though many of its members are ubiquitous in the environment and some play important roles in biochemical cycles or biotechnological applications. We here used a targeted cell-sorting approach, which enables the selection of specific taxa by fluorescent labeling and is compatible with subsequent single-cell genomics, to enrich for rare Chloroflexi species from a wastewater-treatment plant and obtain their genomes. The combined workflow was able to retrieve a substantially higher number of novel Chloroflexi draft genomes with much greater phylogenetical diversity when compared to a metagenomics approach from the same sample. The method offers an opportunity to access genetic information from rare biosphere members which would have otherwise stayed hidden as microbial dark matter and can therefore serve as an essential complement to cultivation-based, metagenomics, and microbial community-focused research approaches.

Roles of Organohalide-Respiring Dehalococcoidia in Carbon Cycling

The class Dehalococcoidia within the Chloroflexi phylum comprises the obligate organohalide-respiring genera Dehalococcoides, Dehalogenimonas, and “Candidatus Dehalobium.” Knowledge of the unique ecophysiology and biochemistry of Dehalococcoidia has been largely derived from studies with enrichment cultures and isolates from sites impacted with chlorinated pollutants; however, culture-independent surveys found Dehalococcoidia sequences in marine, freshwater, and terrestrial biomes considered to be pristine (i.

The class Dehalococcoidia within the Chloroflexi phylum comprises the obligate organohalide-respiring genera Dehalococcoides, Dehalogenimonas, and “Candidatus Dehalobium.” Knowledge of the unique ecophysiology and biochemistry of Dehalococcoidia has been largely derived from studies with enrichment cultures and isolates from sites impacted with chlorinated pollutants; however, culture-independent surveys found Dehalococcoidia sequences in marine, freshwater, and terrestrial biomes considered to be pristine (i.e., not impacted with organohalogens of anthropogenic origin). The broad environmental distribution of Dehalococcoidia, as well as other organohalide-respiring bacteria, supports the concept of active halogen cycling and the natural formation of organohalogens in various ecosystems. Dechlorination reduces recalcitrance and renders organics susceptible to metabolic oxidation by diverse microbial taxa. During reductive dechlorination, hydrogenotrophic organohalide-respiring bacteria, in particular Dehalococcoidia, can consume hydrogen to low consumption threshold concentrations (<0.3 nM) and enable syntrophic oxidation processes. These functional attributes and the broad distribution imply that Dehalococcoidia play relevant roles in carbon cycling in anoxic ecosystems.

Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions

Uncultured members of the Chloroflexi phylum are highly enriched in numerous subseafloor environments. Their metabolic potential was evaluated by reconstructing 31 Chloroflexi genomes from six different subseafloor habitats. The near ubiquitous presence of enzymes of the Wood-Ljungdahl pathway, electron bifurcation, and ferredoxin-dependent transport-coupled phosphorylation indicated anaerobic acetogenesis was central to their catabolism. Most of the genomes simultaneously contained multiple degradation pathways for complex carbohydrates, detrital protein, aromatic compounds, and hydrogen, indicating the coupling of oxidation of chemically diverse organic substrates to ubiquitous CO₂ reduction. Such pathway combinations may confer a fitness advantage in subseafloor environments by enabling these Chloroflexi to act as primary fermenters and acetogens in one microorganism without the need for syntrophic H₂ consumption. While evidence for catabolic oxygen respiration was limited to two phylogenetic clusters, the presence of genes encoding putative reductive dehalogenases throughout the phylum expanded the phylogenetic boundary for potential organohalide respiration past the Dehalococcoidia class.

Gas seepage pockmark microbiomes suggest the presence of sedimentary coal seams in the Öxarfjörður graben of northeastern Iceland

Natural gas seepage pockmarks are found off- and onshore in the Öxarfjörður graben, Iceland. The bacterial communities of two onshore seepage sites were analysed by 16S rRNA gene amplicon sequencing; the geochemical characteristics, hydrocarbon content, and the carbon isotope composition of the sites were also determined. While one site was found to be characterised by biogenic origin of methane gas, with a carbon isotope ratio (δ¹³C (‰)) of -63.2, high contents of organic matter and complex hydrocarbons, the other site showed a mixed origin of the methane gas (δ¹³C (‰) = -26.6) with geothermal characteristics and lower organic matter content. While both sites harboured Proteobacteria as the most abundant bacterial phyla, the Deltaproteobacteria were more abundant at the geothermal site and the Alphaproteobacteria at the biogenic site. The Dehalococcoidia class of phylum Chloroflexi was abundant at the geothermal site while the Anaerolineae class was more abundant at the biogenic site. Bacterial strains from the seepage pockmarks were isolated on a variety of selective media targeting bacteria with bioremediation potential. A total of 106 strains were isolated and characterised, including representatives from the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. This article describes the first microbial study on gas seepage pockmarks in Iceland.

Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities

Recent experimental and bioinformatic advances enable the recovery of genomes belonging to yet-uncultured microbial lineages directly from environmental samples. Here, we report on the recovery and characterization of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) representing candidate phylum LCP-89, previously defined based on 16S rRNA gene sequences. Analysis of LCP-89 genomes recovered from Zodletone Spring, an anoxic spring in Oklahoma, predicts slow-growing, rod-shaped organisms. LCP-89 genomes contain genes for cell wall lipopolysaccharide (LPS) production but lack the entire machinery for peptidoglycan biosynthesis, suggesting an atypical cell wall structure. The genomes, however, encode S-layer homology domain-containing proteins, as well as machinery for the biosynthesis of CMP-legionaminate, inferring the possession of an S-layer glycoprotein. A nearly complete chemotaxis machinery coupled to the absence of flagellar synthesis and assembly genes argues for the utilization of alternative types of motility. A strict anaerobic lifestyle is predicted, with dual respiratory (nitrite ammonification) and fermentative capacities. Predicted substrates include a wide range of sugars and sugar alcohols and a few amino acids. The capability of rhamnose metabolism is confirmed by the identification of bacterial microcompartment genes to sequester the toxic intermediates generated. Comparative genomic analysis identified differences in oxygen sensitivities, respiratory capabilities, substrate utilization preferences, and fermentation end products between LCP-89 genomes and those belonging to its four sister phyla (Calditrichota, SM32-31, AABM5-125-24, and KSB1) within the broader FCB (Fibrobacteres-Chlorobi-Bacteroidetes) superphylum. Our results provide a detailed characterization of members of the candidate division LCP-89 and highlight the importance of reconciling 16S rRNA-based and genome-based phylogenies.IMPORTANCE Our understanding of the metabolic capacities, physiological preferences, and ecological roles of yet-uncultured microbial phyla is expanding rapidly. Two distinct approaches are currently being utilized for characterizing microbial communities in nature: amplicon-based 16S rRNA gene surveys for community characterization and metagenomics/single-cell genomics for detailed metabolic reconstruction. The occurrence of multiple yet-uncultured bacterial phyla has been documented using 16S rRNA surveys, and obtaining genome representatives of these yet-uncultured lineages is critical to our understanding of the role of yet-uncultured organisms in nature. This study provides a genomics-based analysis highlighting the structural features and metabolic capacities of a yet-uncultured bacterial phylum (LCP-89) previously identified in 16S rRNA surveys for which no prior genomes have been described. Our analysis identifies several interesting structural features for members of this phylum, e.g., lack of peptidoglycan biosynthetic machinery and the ability to form bacterial microcompartments. Predicted metabolic capabilities include degradation of a wide range of sugars, anaerobic respiratory capacity, and fermentative capacities. In addition to the detailed structural and metabolic analysis provided for candidate division LCP-89, this effort represents an additional step toward a unified scheme for microbial taxonomy by reconciling 16S rRNA gene-based and genomics-based taxonomic outlines.

Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept

The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due to liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till cropping culminated in a decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in the rhizosphere than in bulk soil, regardless of the time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense, while functions related to nucleic acids metabolism increased. Functions in the soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that the soybean root system selects microbial taxa via trade-offs, to maintain functional resilience in the rhizosphere microbiome over time.

Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi

A novel slow-growing, facultatively anaerobic, filamentous bacterium, strain MO-CFX2^T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediment collected off the Shimokita Peninsula of Japan. Cells were multicellular filamentous, non-motile and Gram-stain-negative. The filaments were generally more than 20 µm (up to approximately 200 µm) long and 0.5-0.6 µm wide. Cells possessed pili-like structures on the cell surface and a multilayer structure in the cytoplasm. Growth of the strain was observed at 20-37 °C (optimum, 30 °C), pH 5.5-8.0 (pH 6.5-7.0), and 0-30 g l^-1 NaCl (5 g l^-1 NaCl). Under optimum growth conditions, doubling time and maximum cell density were estimated to be approximately 19 days and ~10⁵ cells ml^-1, respectively. Strain MO-CFX2^T grew chemoorganotrophically on a limited range of organic substrates in anaerobic conditions. The major cellular fatty acids were saturated C16 : 0 (47.9 %) and C18 : 0 (36.9 %), and unsaturated C18 : 1ω9c (6.0 %) and C16 : 1ω7 (5.1 %). The G+C content of genomic DNA was 63.2 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-CFX2^T shares a notably low sequence identity with its closest relatives, which were Thermanaerothrix daxensis GNS-1^T and Thermomarinilinea lacunifontana SW7^T (both 85.8 % sequence identity). Based on these phenotypic and genomic properties, we propose the name Aggregatilinea lenta gen. nov., sp. nov. for strain MO-CFX2^T (=KCTC 15625^T, =JCM 32065^T). In addition, we also propose the associated family and order as Aggregatilineaceae fam. nov. and Aggregatilineales ord. nov., respectively.

Regulation of organohalide respiration

Organohalide respiration (OHR) is an anaerobic metabolism by which bacteria conserve energy with the use of halogenated compounds as terminal electron acceptors. Genes involved in OHR are organized in reductive dehalogenase (rdh) gene clusters and can be found in relatively high copy numbers in the genomes of organohalide-respiring bacteria (OHRB). The minimal rdh gene set is composed by rdhA and rdhB, encoding the catalytic enzyme involved in reductive dehalogenation and its putative membrane anchor, respectively. In this chapter, we present the major findings concerning the regulatory strategies developed by OHRB to control the expression of the rdh gene clusters. The first section focuses on the description of regulation patterns obtained from targeted transcriptional analyses, and from transcriptomic and proteomic studies, while the second section offers a detailed overview of the biochemically characterized OHR regulatory proteins identified so far. Depending on OHRB, transcriptional regulators belonging to three different protein families are found in the direct vicinity of rdh gene clusters, suggesting that they activate the transcription of their cognate gene cluster. In this chapter, strong emphasis was laid on the family of CRP/FNR-type RdhK regulators which belong to members of the genera Dehalobacter and Desulfitobacterium. Whereas only chlorophenols have been identified as effectors for RdhK regulators, the protein sequence diversity suggests a broader organohalide spectrum. Thus, effector identification of new regulators offers a promising alternative to elucidate the substrates of yet uncharacterized reductive dehalogenases. Future work investigating the possible cross-talk between OHR regulators and their possible use as biosensors is discussed.

Microbial communities associated with phosphogenic sediments and phosphoclast-associated DNA of the Benguela upwelling system

The processes that lead to the precipitation of authigenic calcium phosphate minerals in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating bacteria. These bacteria are believed to concentrate phosphate in sediment pore waters, creating supersaturated conditions with respect to apatite precursors. However, the relationship between microbes and phosphorite formation is not fully resolved. To further study this association, we examined microbial community data generated from two sources: sediment cores recovered from the shelf of the Benguela upwelling region where phosphorites are currently forming, and DNA preserved within phosphoclasts recovered from a phosphorite deposit along the Benguela shelf. iTag and clone library sequencing of the 16S rRNA gene showed that many of our sediment-hosted communities shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfate-reducing bacteria and sulfur-oxidizing bacteria were particularly abundant in our datasets, as were phylotypes that are known to carry out nitrification and the anaerobic oxidation of ammonium. The DNA extracted from phosphoclasts contained the signature of a distinct microbial community from those observed in the modern sediments. While some aspects of the modern and phosphoclast communities were similar, we observed both an enrichment of certain common microbial classes found in the modern phosphogenic sediments and a relative depletion of others. The phosphoclast-associated DNA could represent a relict signature of one or more microbial assemblages that were present when the apatite or its precursors precipitated. While these taxa may or may not have contributed to the precipitation of the apatite that now hosts their genetic remains, several groups represented in the phosphoclast extract dataset have the genetic potential to metabolize polyphosphate, and perhaps modulate phosphate concentrations in pore waters where carbonate fluorapatite (or its precursors) are known to be precipitating.

Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments

Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the microbial communities of marine sediments of the Ross Sea, Antarctica, and found candidate phylum Atribacteria JS1 lineage was the most abundant candidate phylum accounting for 9.8-40.8% of the bacterial communities with a single dominant operational taxonomic unit (OTU). To elucidate the metabolic potential and ecological function of this species, we applied a single-cell genomic approach and obtained 18 single-cell amplified genomes presumably from a single species that was consistent with the dominant OTU throughout the sediments. The composite genome constructed by co-assembly showed the highest genome completeness among available Atribacteria JS1 genomes. Metabolic reconstruction suggested fermentative potential using various substrates and syntrophic acetate oxidation coupled with hydrogen or formate scavenging methanogens. This metabolic potential supports the predominance of Atribacteria JS1 in anoxic environments expanding our knowledge of the ecological function of this uncultivated group.

Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment

Desulfatiglans-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized Desulfatiglans isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental Desulfatiglans-populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven Desulfatiglans-related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of Desulfatiglans-populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine Desulfatiglans populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.

Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics

Aplysina aerophoba is an emerging model marine sponge, with a well-characterized microbial community in terms of diversity and structure. However, little is known about the expressed functional capabilities of its associated microbes. Here, we present the first metaproteomics-based study of the microbiome of A. aerophoba. We found that transport and degradation of halogenated and chloroaromatic compounds are common active processes in the sponge microbiomes. Our data further reveal that the highest number of proteins were affiliated to a sponge-associated Tectomicrobium, presumably from the family Entotheonellaceae, as well as to the well-known symbiont "Candidatus Synechococcus spongiarium", suggesting a high metabolic activity of these two microorganisms in situ. Evidence for nitric oxide (NO) conversion to nitrous oxide was consistently observed for Tectomicrobia across replicates, by production of the NorQ protein. Moreover, we found a potential energy-yielding pathway through CO oxidation by putative Chloroflexi bacteria. Finally, we observed expression of enzymes that may be involved in the transformation of chitin, glycoproteins, glycolipids and glucans into smaller molecules, consistent with glycosyl hydrolases predicted from analyses of the genomes of Poribacteria sponge symbionts. Thus, this study provides crucial links between expressed proteins and specific members of the A. aerophoba microbiome.

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling

The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.

Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes

The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi.

The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments and provide evidence for a homacetogenic lifestyle of these abundant marine Chloroflexi. Moreover, genome signature and key metabolic genes indicate an evolutionary relationship between these deep-sea sediment microbes and terrestrial, reductively dehalogenating Dehalococcoides.

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.

Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank

Microbial communities living in deeply buried sediment may be adapted to long-term energy limitation as they are removed from new detrital energy inputs for thousands to millions of years. However, sediment layers near the underlying oceanic crust may receive inputs from below that influence microbial community structure and/or activity. As part of the Census of Deep Life, we used 16S rRNA gene tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement interface samples from the subsurface of the Juan de Fuca Ridge flank (collected on IODP Expedition 327) to examine this possible basement influence on deep sediment communities. This area experiences rapid sedimentation, with an underlying basaltic crust that hosts a dynamic flux of hydrothermal fluids that diffuse into the sediment. Chloroflexi sequences dominated tag libraries in all sediment samples, with variation in the abundance of other bacterial groups (e.g., Actinobacteria, Aerophobetes, Atribacteria, Planctomycetes, and Nitrospirae). These variations occur in relation to the type of sediment (clays versus carbonate-rich) and the depth of sample origin, and show no clear connection to the distance from the discharge outcrop or to basement fluid microbial communities. Actinobacteria-related sequences dominated the basalt libraries, but these should be viewed cautiously due to possibilities for imprinting from contamination. Our results indicate that proximity to basement or areas of seawater recharge is not a primary driver of microbial community composition in basal sediment, even though fluids diffusing from basement into sediment may stimulate microbial activity.