Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria

Choline degradation in Paracoccus denitrificans: identification of sources of formaldehyde

Paracoccus denitrificans is a facultative methylotroph that can grow on methanol and methylamine as sole sources of carbon and energy. Both are oxidized to formaldehyde and then to formate, so growth on C1 substrates induces the expression of genes encoding enzymes required for the oxidation of formaldehyde and formate. This induction involves a histidine kinase response regulator pair (FlhSR) that is likely triggered by formaldehyde. Catabolism of some complex organic substrates (e.g., choline and L-proline betaine) also generates formaldehyde. Thus, flhS and flhR mutants that fail to induce expression of the formaldehyde catabolic enzymes cannot grow on methanol, methylamine, and choline. Choline is oxidized to glycine via glycine betaine, dimethylglycine, and sarcosine. By exploring flhSR growth phenotypes and the activities of a promoter and enzyme known to be upregulated by formaldehyde, we identify the oxidative demethylations of glycine betaine, dimethylglycine, and sarcosine as sources of formaldehyde. Growth on glycine betaine, dimethylglycine, and sarcosine is accompanied by the production of up to three, two, and one equivalents of formaldehyde, respectively. Genetic evidence implicates two orthologous monooxygenases in the oxidation of glycine betaine. Interestingly, one of these appears to be a bifunctional enzyme that also oxidizes L-proline betaine (stachydrine). We present preliminary evidence to suggest that growth on L-proline betaine induces expression of a formaldehyde dehydrogenase distinct from the enzyme induced during growth on other formaldehyde-generating substrates.IMPORTANCEThe bacterial degradation of one-carbon compounds (methanol and methylamine) and some complex multi-carbon compounds (e.g., choline) generates formaldehyde. Formaldehyde is toxic and must be removed, which can be done by oxidation to formate and then to carbon dioxide. These oxidations provide a source of energy; in some species, the CO2 thus generated can be assimilated into biomass. Using the Gram-negative bacterium Paracoccus denitrificans as the experimental model, we infer that oxidation of choline to glycine generates up to three equivalents of formaldehyde, and we identify the three steps in the catabolic pathway that are responsible. Our work sheds further light on metabolic pathways that are likely important in a variety of environmental contexts.

Isolation and characteristics of two heterotrophic nitrifying and aerobic denitrifying bacteria, Achromobacter sp. strain HNDS-1 and Enterobacter sp. strain HNDS-6

In order to solve nitrogen pollution in environmental water, two heterotrophic nitrifying and aerobic denitrifying strains isolated from acid paddy soil were identified as Achromobacter sp. strain HNDS-1 and Enterobacter sp. strain HNDS-6 respectively. Strain HNDS-1 and strain HNDS-6 exhibited amazing ability to nitrogen removal. When (NH₄)₂SO₄, KNO₃, NaNO₂ were used as nitrogen resource respectively, the NH₄⁺-N, NO₃^--N, NO₂^--N removal efficiencies of strain HNDS-1 were 93.31%, 89.47%, and 100% respectively, while those of strain HNDS-6 were 82.39%, 96.92%, and 100%. And both of them could remove mixed nitrogen effectively in low C/N (C/N = 5). Strain HNDS-1 could remove 76.86% NH₄⁺-N and 75.13% NO₃^--N. And strain HNDS-6 can remove 65.07% NH₄⁺-N and 78.21% NO₃^--N. A putative ammonia monooxygenase, nitrite reductase, nitrate reductase, assimilatory nitrate reductase, nitrate/nitrite transport protein and nitric oxide reductase of strain HNDS-1, while hydroxylamine reductase, nitrite reductase, nitrate reductase, assimilatory nitrate reductase, nitrate/nitrite transport protein, and nitric oxide reductase of strain HNDS-6 were identified by genomic analysis. DNA-SIP analysis showed that genes Nxr, narG, nirK, norB, nosZ were involved in nitrogen removal pathway, which indicates that the denitrification pathway of strain HNDS-1 and strain HNDS-6 was NO₃^-→NO₂^-→NO→N₂O→N₂ during NH₄⁺-N removal process. And the nitrification pathway of strain HNDS-1 and strain HNDS-6 was NO₂^-→NO₃^-, but the nitrification pathway of NH₄⁺→ NO₂^- needs further studies.

Depth wide distribution and metabolic potential of chemolithoautotrophic microorganisms reactivated from deep continental granitic crust underneath the Deccan Traps at Koyna, India

Characterization of inorganic carbon (C) utilizing microorganisms from deep crystalline rocks is of major scientific interest owing to their crucial role in global carbon and other elemental cycles. In this study we investigate the microbial populations from the deep [up to 2,908 meters below surface (mbs)] granitic rocks within the Koyna seismogenic zone, reactivated (enriched) under anaerobic, high temperature (50°C), chemolithoautotrophic conditions. Subsurface rock samples from six different depths (1,679-2,908 mbs) are incubated (180 days) with CO₂ (+H₂) or HCO₃ ^- as the sole C source. Estimation of total protein, ATP, utilization of NO₃ ^- and SO₄ ^2- and 16S rRNA gene qPCR suggests considerable microbial growth within the chemolithotrophic conditions. We note a better response of rock hosted community towards CO₂ (+H₂) over HCO₃ ^-. 16S rRNA gene amplicon sequencing shows a depth-wide distribution of diverse chemolithotrophic (and a few fermentative) Bacteria and Archaea. Comamonas, Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, Klebsiella, unclassified Burkholderiaceae and Enterobacteriaceae are reactivated as dominant organisms from the enrichments of the deeper rocks (2335-2,908 mbs) with both CO₂ and HCO₃ ^-. For the rock samples from shallower depths, organisms of varied taxa are enriched under CO₂ (+H₂) and HCO₃ ^-. Pseudomonas, Rhodanobacter, Methyloversatilis, and Thaumarchaeota are major CO₂ (+H₂) utilizers, while Nocardioides, Sphingomonas, Aeromonas, respond towards HCO₃ ^-. H₂ oxidizing Cupriavidus, Hydrogenophilus, Hydrogenophaga, CO₂ fixing Cyanobacteria Rhodobacter, Clostridium, Desulfovibrio and methanogenic archaea are also enriched. Enriched chemolithoautotrophic members show good correlation with CO₂, CH₄ and H₂ concentrations of the native rock environments, while the organisms from upper horizons correlate more to NO₃ ^-, SO₄ ^2- _, Fe and TIC levels of the rocks. Co-occurrence networks suggest close interaction between chemolithoautotrophic and chemoorganotrophic/fermentative organisms. Carbon fixing 3-HP and DC/HB cycles, hydrogen, sulfur oxidation, CH₄ and acetate metabolisms are predicted in the enriched communities. Our study elucidates the presence of live, C and H₂ utilizing Bacteria and Archaea in deep subsurface granitic rocks, which are enriched successfully. Significant impact of depth and geochemical controls on relative distribution of various chemolithotrophic species enriched and their C and H₂ metabolism are highlighted. These endolithic microorganisms show great potential for answering the fundamental questions of deep life and their exploitation in CO₂ capture and conversion to useful products.

Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone-aquifer sediments

AIMS

This study attempted to demonstrate the vertical shift in bacterial, archaeal and fungal communities along the vadose zone-aquifer sediments and their respective responses to environmental factors.

METHODS AND RESULTS

We collected samples from the vadose zone and three aquifer sediments along a 42·5 m bore of a typical agricultural land. The results showed that the bacterial community shifted greatly with depth. The classes of Actinobacteria (19·5%) and NC10 (11·0%) were abundant in the vadose zone while Alphaproteobacteria (22·3%) and Gammaproteobacteria (20·1%) were enriched in the aquifer. Archaeal and fungal communities were relatively more homogeneous with no significant trend as a function of depth. Process analyses further indicated that selection dominated in the bacterial community, whereas stochastic processes governed archaeal and fungal communities. Moreover environment-bacteria interaction analysis showed that metal(loid)s, especially alkali metal, had a closer correlation with the bacterial community than physicochemical variables.

CONCLUSIONS

Depth strongly affected bacterial rather than archaeal and fungal communities. Metal(loid)s prevailed over physicochemical variables in shaping the bacterial community in the vadose zone-aquifer continuum.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study provides a new perspective on the structure of microbial communities from the vadose zone to the deep aquifers.

Diversity and extracellular enzyme activities of heterotrophic bacteria from sediments of the Central Indian Ocean Basin

Sedimentary bacteria play a role in polymetallic nodule formation and growth. There are, however, limited reports on bacterial diversity in nodule-rich areas of the Central Indian Ocean Basin (CIOB). In this study, bacterial abundance in thirteen sediment cores collected from the CIOB was enumerated, followed by phylogenetic characterisation and, screening of select heterotrophic bacteria for extracellular enzyme activities. Total bacterial counts (TBC) were in the order of 10⁷ cells g^-1; there was a significant difference (p > 0.05) among the cores but not within the sub-sections of the cores. The retrievable heterotrophic counts ranged from non-detectable to 5.33 × 10⁵ g^-1; the heterotrophic bacteria clustered within the phyla Firmicutes, Proteobacteria and Actinobacteria. Bacillus was the most abundant genus. The extracellular enzyme activities were in the order: amylase > lipase > protease > phosphatase > Dnase > urease. Major findings are compared with previous studies from the CIOB and other areas.

Cytosine Methylation Within Marine Sediment Microbial Communities: Potential Epigenetic Adaptation to the Environment

Marine sediments harbor a vast amount of Earth's microbial biomass, yet little is understood regarding how cells subsist in this low-energy, presumably slow-growth environment. Cells in marine sediments may require additional methods for genetic regulation, such as epigenetic modification via DNA methylation. We investigated this potential phenomenon within a shallow estuary sediment core spanning 100 years of age. Here, we provide evidence of dynamic community m5-cytosine methylation within estuarine sediment metagenomes. The methylation states of individual CpG sites were reconstructed and quantified across three depths within the sediment core. A total of 6,254 CpG sites were aligned for direct comparison of methylation states between samples, and 4,235 of these sites mapped to taxa and genes. Our results demonstrate the presence of differential methylation within environmental CpG sites across an age gradient of sediment. We show that epigenetic modification can be detected via Illumina sequencing within complex environmental communities. The change in methylation state of environmentally relevant genes across depths may indicate a dynamic role of DNA methylation in regulation of biogeochemical processes.

Survival of the fewest: Microbial dormancy and maintenance in marine sediments through deep time

Microorganisms buried in marine sediments are known to endure starvation over geologic timescales. However, the mechanisms of how these microorganisms cope with prolonged energy limitation is unknown and therefore yet to be captured in a quantitative framework. Here, we present a novel mathematical model that considers (a) the physiological transitions between the active and dormant states of microorganisms, (b) the varying requirement for maintenance power between these phases, and (c) flexibility in the provenance (i.e., source) of energy from exogenous and endogenous catabolism. The model is applied to sediments underlying the oligotrophic South Pacific Gyre where microorganisms endure ultra-low fluxes of energy for tens of millions of years. Good fits between model simulations and measurements of cellular carbon and organic carbon concentrations are obtained and are interpreted as follows: (a) the unfavourable microbial habitat in South Pacific Gyre sediments triggers rapid mortality and a transition to dormancy; (b) there is minimal biomass growth, and organic carbon consumption is dominated by catabolism to support maintenance activities rather than new biomass synthesis; (c) the amount of organic carbon that microorganisms consume for maintenance activities is equivalent to approximately 2% of their carbon biomass per year; and (d) microorganisms must rely solely on exogenous rather than endogenous catabolism to persist in South Pacific Gyre sediments over long timescales. This leads us to the conclusion that under oligotrophic conditions, the fitness of an organism is determined by its ability to simply stay alive, rather than to grow. This modelling framework is designed to be flexible for application to other sites and habitats, and thus serves as a new quantitative tool for determining the habitability of and an ultimate limit for life in any environment.

Environmental and Genetic Determinants of Biofilm Formation in Paracoccus denitrificans

The bacterium Paracoccus denitrificans is a model for the process of denitrification, by which nitrate is reduced to dinitrogen during anaerobic growth. Denitrification is important for soil fertility and greenhouse gas emission and in waste and water treatment processes. The ability of bacteria to grow as a biofilm attached to a solid surface is important in many different contexts. In this paper, we report that attached growth of P. denitrificans is stimulated by nitric oxide, an intermediate in the denitrification pathway. We also show that calcium ions stimulate attached growth, and we identify a large calcium binding protein that is required for growth on a polystyrene surface. We identify components of a signaling pathway through which nitric oxide may regulate biofilm formation. Our results point to an intimate link between metabolic processes and the ability of P. denitrificans to grow attached to a surface.

The genome of the denitrifying bacterium Paracoccus denitrificans predicts the expression of a small heme-containing nitric oxide (NO) binding protein, H-NOX. The genome organization and prior work in other bacteria suggest that H-NOX interacts with a diguanylate cyclase that cyclizes GTP to make cyclic di-GMP (cdGMP). Since cdGMP frequently regulates attached growth as a biofilm, we first established conditions for biofilm development by P. denitrificans. We found that adhesion to a polystyrene surface is strongly stimulated by the addition of 10 mM Ca²⁺ to rich media. The genome encodes at least 11 repeats-in-toxin family proteins that are predicted to be secreted by the type I secretion system (TISS). We deleted the genes encoding the TISS and found that the mutant is almost completely deficient for attached growth. Adjacent to the TISS genes there is a potential open reading frame encoding a 2,211-residue protein with 891 Asp-Ala repeats. This protein is also predicted to bind calcium and to be a TISS substrate, and a mutant specifically lacking this protein is deficient in biofilm formation. By analysis of mutants and promoter reporter fusions, we show that biofilm formation is stimulated by NO generated endogenously by the respiratory reduction of nitrite. A mutant lacking both predicted diguanylate cyclases encoded in the genome overproduces biofilm, implying that cdGMP is a negative regulator of attached growth. Our data are consistent with a model in which there are H-NOX-dependent and -independent pathways by which NO stimulates biofilm formation.

IMPORTANCE The bacterium Paracoccus denitrificans is a model for the process of denitrification, by which nitrate is reduced to dinitrogen during anaerobic growth. Denitrification is important for soil fertility and greenhouse gas emission and in waste and water treatment processes. The ability of bacteria to grow as a biofilm attached to a solid surface is important in many different contexts. In this paper, we report that attached growth of P. denitrificans is stimulated by nitric oxide, an intermediate in the denitrification pathway. We also show that calcium ions stimulate attached growth, and we identify a large calcium binding protein that is required for growth on a polystyrene surface. We identify components of a signaling pathway through which nitric oxide may regulate biofilm formation. Our results point to an intimate link between metabolic processes and the ability of P. denitrificans to grow attached to a surface.

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation

Metagenomics-based studies of mixed microbial communities are impacting biotechnology, life sciences and medicine. Computational binning of metagenomic data is a powerful approach for the culture-independent recovery of population-resolved genomic sequences, i.e. from individual or closely related, constituent microorganisms. Existing binning solutions often require a priori characterized reference genomes and/or dedicated compute resources. Extending currently available reference-independent binning tools, we developed the BusyBee Web server for the automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies). A reversible compression step as well as bootstrapped supervised binning enable quick turnaround times. The binning results are represented in interactive 2D scatterplots. Moreover, bin quality estimates, taxonomic annotations and annotations of antibiotic resistance genes are computed and visualized. Ground truth-based benchmarks of BusyBee Web demonstrate comparably high performance to state-of-the-art binning solutions for assembled contigs and markedly improved performance for long reads (median F1 scores: 70.02-95.21%). Furthermore, the applicability to real-world metagenomic datasets is shown. In conclusion, our reference-independent approach automatically bins assembled contigs or long reads, exhibits high sensitivity and precision, enables intuitive inspection of the results, and only requires FASTA-formatted input. The web-based application is freely accessible at: https://ccb-microbe.cs.uni-saarland.de/busybee.

Complete Genome Sequence of Bacillus subtilis Strain 29R7-12, a Piezophilic Bacterium Isolated from Coal-Bearing Sediment 2.4 Kilometers below the Seafloor

Here, we report the genome sequence of Bacillus subtilis strain 29R7-12, a piezophilic bacterium isolated from coal-bearing sediment down to ~2.4 km below the ocean floor in the northwestern Pacific. The strain is a Gram-positive spore-forming bacterium, closely related to Bacillus subtilis within the phylum Firmicutes. This is the first complete genome sequence of a Bacillus subtilis strain from the deep biosphere. The genome sequence will provide a valuable resource for comparative studies of microorganisms from the surface and subsurface environments.

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor

Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ. In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan. Analysis of 16S rRNA gene-tagged sequences showed that members of spore-forming bacteria within Firmicutes and Actinobacteria were predominantly detected in all enrichment cultures from ~1.5 to 2.4 km-deep sediment samples, followed by members of Proteobacteria, Acidobacteria, and Bacteroidetes according to the sequence frequency. To further study the physiology of the deep subseafloor sedimentary piezophilic bacteria, we isolated and characterized two bacterial strains, 19R1-5 and 29R7-12, from 1.9 and 2.4 km-deep sediment samples, respectively. The isolates were both low G+C content, gram-positive, endospore-forming and facultative anaerobic piezophilic bacteria, closely related to Virgibacillus pantothenticus and Bacillus subtilis within the phylum Firmicutes, respectively. The optimal pressure and temperature conditions for growth were 20 MPa and 42°C for strain 19R1-5, and 10 MPa and 43°C for strain 29R7-12. Bacterial (endo)spores were observed in both the enrichment and pure cultures examined, suggesting that these piezophilic members were derived from microbial communities buried in the ~20 million-year-old coal-bearing sediments after the long-term survival as spores and that the deep biosphere may host more abundant gram-positive spore-forming bacteria and their spores than hitherto recognized.