Groundwater chromate removal by autotrophic sulfur disproportionation.

Chromate [Cr(VI)] contamination in groundwater is a global environmental challenge. Traditional elemental sulfur-based biotechnologies for Cr(VI) removal depend heavily on the synthesis of dissolved organic carbon to fuel heterotrophic Cr(VI) reduction, a bottleneck in the remediation process. Here we show an alternative approach by leveraging sulfur-disproportionating bacteria (SDB) inherent to groundwater ecosystems, offering a novel and efficient Cr(VI) removal strategy. We implemented SDB within a sulfur-packed bed reactor for treating Cr(VI)-contaminated groundwater, achieving a notable removal rate of 6.19 mg L-1 h-1 under oligotrophic conditions. We identified the chemical reduction of Cr(VI) via sulfide, produced through sulfur disproportionation, as a key mechanism, alongside microbial Cr(VI) reduction within the sulfur-based biosystem. Genome-centric metagenomic analysis revealed a symbiotic relationship among SDB, sulfur-oxidizing, and chromate-reducing bacteria within the reactor, suggesting that Cr(VI) detoxification by these microbial communities enhances the sulfur-disproportionation process. This research highlights the significance of sulfur disproportionation in the cryptic sulfur cycle in Cr(VI)-contaminated groundwater and proposes its practical application in groundwater remediation efforts.

Exploring contribution of phytoplankton cell death to settleable particulate organic carbon in the East China Sea in spring.

Phytoplankton's death contributes to marine settleable particulate organic matter (POM). In this study, we used laboratory cultivation of different algal species to identify a positive correlation between the cumulative number of dead algal cells and POC>75 (carbon content of the settleable POM). The contribution coefficient of cell death to POC>75 varied among different algal species. Additionally, the field survey and incubation experiment were conducted in the East China Sea (ECS) to explore the spatial-temporal correlation between phytoplankton death and POC>75. The results concluded that phytoplankton death was the main factor controlling POC>75. In the ECS, the relationship between the surface cumulative mass of POC>75 and the cumulative number of dead cells followed: Cumulative mass of POC>75(mg) = 0.487 × Cumulative number of dead cells (/104) + 0.069. This study provided a methodology to quantitatively explain the relationship between phytoplankton death and settleable POM.

Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles.

Marine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. Recent studies using metagenomic techniques have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) from the bacterial phylum Armatimonadota in the Guaymas Basin, Gulf of California, and the Bohai Sea, China. These MAGs comprise two previously undescribed classes within Armatimonadota, which we propose naming Hebobacteria and Zipacnadia. They are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of metagenomic raw reads). The classes described here also have unique metabolic capabilities, possessing pathways to reduce carbon dioxide to acetate via the Wood-Ljungdahl pathway (WLP) and generating energy through the oxidative branch of glycolysis using carbon dioxide as an electron sink, maintaining the redox balance using the WLP. Hebobacteria may also be autotrophic, not previously identified in Armatimonadota. Furthermore, these Armatimonadota may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. Description of these MAGs enhances our understanding of diversity and metabolic potential within anoxic habitats worldwide.

Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling.

BACKGROUND: Sulfate-reducing bacteria (SRB) drive the ocean sulfur and carbon cycling. They constitute a diverse phylogenetic and physiological group and are widely distributed in anoxic marine environments. From a physiological viewpoint, SRB's can be categorized as complete or incomplete oxidizers, meaning that they either oxidize their carbon substrate completely to CO2 or to a stoichiometric mix of CO2 and acetate. Members of Desulfofabaceae family are incomplete oxidizers, and within that family, Desulfofaba is the only genus with three isolates that are classified into three species. Previous physiological experiments revealed their capability of respiring oxygen. RESULTS: Here, we sequenced the genomes of three isolates in Desulfofaba genus and reported on a genomic comparison of the three species to reveal their metabolic potentials. Based on their genomic contents, they all could oxidize propionate to acetate and CO2. We confirmed their phylogenetic position as incomplete oxidizers based on dissimilatory sulfate reductase (DsrAB) phylogeny. We found the complete pathway for dissimilatory sulfate reduction, but also different key genes for nitrogen cycling, including nitrogen fixation, assimilatory nitrate/nitrite reduction, and hydroxylamine reduction to nitrous oxide. Their genomes also contain genes that allow them to cope with oxygen and oxidative stress. They have genes that encode for diverse central metabolisms for utilizing different substrates with the potential for more strains to be isolated in the future, yet their distribution is limited. CONCLUSIONS: Results based on marker gene search and curated metagenome assembled genomes search suggest a limited environmental distribution of this genus. Our results reveal a large metabolic versatility within the Desulfofaba genus which establishes their importance in biogeochemical cycling of carbon in their respective habitats, as well as in the support of the entire microbial community through releasing easily degraded organic matters.

New globally distributed bacterial phyla within the FCB superphylum.

Microbes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.

Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments.

Marine microbial communities assemble along a sediment depth gradient and are responsible for processing organic matter. Composition of the microbial community along the depth is affected by various biotic and abiotic factors, e.g., the change of redox gradient, the availability of organic matter, and the interactions of different taxa. The community structure is also subjected to some random changes caused by stochastic processes of birth, death, immigration and emigration. However, the high-resolution shifts of microbial community and mechanisms of the vertical assembly processes in marine sediments remain poorly described. Archaeal and bacterial communities were analyzed based on 16S rRNA gene amplicon sequencing and metagenomes in the Bohai Sea sediment samples. The archaeal community was dominated by Thaumarchaeota with increased alpha diversity along depth. Proteobacteria was the dominant bacterial group with decreased alpha diversity as depth increased. Sampling sites and depths collectively affected the beta-diversity for both archaeal and bacterial communities. The dominant mechanism determining archaeal community assembly was determinism, which was mostly contributed by homogeneous selection, i.e., consistent selection pressures in different locations or depths. In contrast, bacterial community assembly was dominated by stochasticity. Co-occurrence networks among different taxa and key functional genes revealed a tight community with low modularity in the bottom sediment, and disproportionately more interactions among low abundant ASVs. This suggests a significant contribution to community stabilization by rare taxa, and suggests that the bottom layer, rather than surface sediments may represent a hotspot for benthic microbial interactions.

Genome-centric metagenomics analysis revealed the metabolic function of abundant microbial communities in thermal hydrolysis-assisted thermophilic anaerobic digesters under propionate stress.

The ecological roles of microbial communities and how they interact with each other in thermal hydrolysis process (THP) assisted thermophilic anaerobic digestion (THP-AD) reactors remain largely unknown, especially under propionate stress. Two thermophilic THP-AD reactors had methane yield of 240-248 mL/g VSadded, but accumulated approximately 2000 mg/L propionate. Genome-centric metagenomics analysis showed that 68 metagenome-assembled genomes (MAGs) were recovered, 32 MAGs of which were substantially enriched. Firmicutes spp. dominated the enriched microbial community, including hydrolytic/fermentative bacteria and syntrophs. Methanogenic activities were mainly mediated by Methanosarcina sp. and Methanothermobacter spp. In addition to hydrogenotrophic methanogens, Thermodesulfovibrio sp. could also be a vital H2 scavenger, contributing to maintaining low H2 partial pressure in the bioreactors. The remarkable accumulation of propionate could be likely attributed to the weak syntrophic propionate-oxidizing activity or its absence. These findings advanced our knowledge about the mutualistic symbiosis of carbon metabolism in thermophilic THP-AD reactors.

Responses of mesophilic anaerobic sludge microbiota to thermophilic conditions: Implications for start-up and operation of thermophilic THP-AD systems.

Anaerobic digestion (AD) has been widely employed for wastewater and organic waste treatment, in which methanogenesis is highly driven by close microbial interactions among intricate microbial communities. However, the ecological processes underpinning the community assembly that support methanogenesis in such engineered ecosystems remain largely unknown, especially when exposed to challenging circumstances (e.g., high temperature, ammonium content). Here, eight AD bioreactors were seeded with four different inocula (two from full-scale mesophilic AD systems and the other two from lab-scale mesophilic AD systems), and were operated under thermophilic conditions (55 °C) for treating thermal hydrolysis process (THP) pre-treated waste activated sludge to investigate how mesophilic community responds to thermophilic conditions during the long-term cultivation. Results showed that the inocula collected from the full-scale systems were more resilient than that from the lab-scale systems, which may be primarily attributed to indigenous robust methanogens. As a result, the former efficiently generated methane which was predominantly contributed by Methanothermobacter and Methanosarcina (healthy AD ecosystem), while methanogenic activity was remarkably prohibited in the latter (dysfunctional AD ecosystem). Thermophilic environment was a strong selection force, resulting in the convergence of microbial communities in both the healthy and dysfunctional AD ecosystems. Deterministic processes predominated the community assembly regardless of AD ecosystem function, but stronger influences of stochastic processes were observed in dysfunctional AD ecosystems, which was likely attributable from the stronger effect of immigrants from the feedstock. As indicated by molecular ecological network analysis, the microbial network structures in the healthy AD ecosystems were more stable than those in the dysfunctional AD ecosystems. Although keystone taxa were different among the bioreactors, most of which played vital roles in organic hydrolysis/fermentation. To sum up, this study greatly improved our understanding of the relationships between microbiological traits and AD ecosystem function under thermophilic conditions, which could provide useful information to guide thermophilic AD (e.g., THP-AD) start-up and health diagnosis during operation.

Disproportionate responses between free-living and particle-attached bacteria during the transition to oxygen-deficient zones in the Bohai Seawater.

The Bohai Sea has recently suffered several seasonal oxygen-deficiency, even hypoxia events during the summer. To better understand effects of dissolved oxygen (DO) concentration on the bacterial composition in particle attached (PA) and free living (FL) fractions during the transition from oxic water to low oxygen conditions, the bacterial communities under three different oxygen levels, i.e., high oxygen (HO, close to 100% O2 saturation), medium oxygen (MO, close to 75% O2 saturation), and low oxygen (LO, close to 50% O2 saturation) in the Bohai Sea were investigated using 16S rRNA amplicon sequencing. Fourteen water samples from 5 stations were collected during a cruise from August to September in 2018. The results showed that the sequences of Proteobacteria and Actinobacteriota jointly accounted for up to 74% across all 14 samples. The Shannon index in HO samples were significantly higher than in LO samples (P < 0.05), especially in PA communities. The composition of bacterial communities varied by oxygen concentration in all samples, and the effect was more pronounced in the PA fraction, which indicates that the PA fraction was more sensitive to the change in oxygen concentration, possibly due to the tighter interactions in this community than in the FL fraction. This study provides novel insights into the distribution of bacterial communities, and clues for understanding the responses of bacterial communities in the Bohai Sea during the transition from the oxic to oxygen-deficient zones.

Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea.

DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 3,197 genomes including 569 newly reconstructed genomes. Protein family content clearly separates the final set of 390 DPANN genomes from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.

Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system.

Thermal hydrolysis process (THP) is an effective pre-treatment method to reduce solids volume and improve biogas production during anaerobic digestion (AD) via increasing the biodegradability of waste activated sludge (WAS). However, the effects of THP pre-treated sludge on microbial diversity, interspecies interactions, and metabolism in AD systems remain largely unknown. We therefore setup and operated an anaerobic digester during a long-term period to shed light on the effect of THP pre-treatment on AD microbial ecology in comparison to conventional AD via Illumina based 16S rRNA gene amplicon sequencing and genome-centric metagenomics analysis. Results showed THP sludge significantly reduced the microbial diversity, shaped the microbial community structure, and resulted in more intense microbial interactions. Compared to WAS as the feed sludge, THP sludge shaped the core functional groups, but functional redundancy ensured the system's stability. The metabolic interactions between methanogens and syntrophic bacteria as well as the specific metabolic pathways were further elucidated. Hydrogenotrophic methanogens, Methanospirillum sp. and Methanolinea sp., were the primary contributors for methane production when treating THP and WAS, respectively, which also have potential for acetate oxidation to methane. Collectively, this study provides in-depth information on the interspecies interactions to better understand how THP pre-treatment influences AD microbial community.

New Microbial Biodiversity in Marine Sediments.

Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.

Influences of Seasonal Monsoons on the Taxonomic Composition and Diversity of Bacterial Community in the Eastern Tropical Indian Ocean.

The Indian Ocean is characterized by its complex physical systems and strong seasonal monsoons. To better understand effects of seasonal monsoon-driven circulation on the bacterioplanktonic community structure in surface waters and the bacterial distribution response to vertical stratification, patterns of seasonal, and vertical distribution of bacterial communities in the Eastern Tropical Indian Ocean were investigated using 16S rRNA gene profiling. Water samples were collected during the Southwest monsoon (from June to August), the fall inter-monsoon (from October and November) and the Northeast monsoon (from December to January), respectively, onboard during three cruises from July 2016 to January 2018. Surface bacterioplankton communities in these three seasons and in the upper water (3-300 m with six depths) during the Northeast monsoon contained a diverse group of taxa, mainly Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi. Redundancy discriminant analysis (RDA) uncovered that temperature, salinity, and dissolved oxygen (DO) were crucial environmental parameters that affected the structure of bacterial community in overall surface samples. However, significant differences in the composition of the bacterial community are likely due to changes in concentrations of salinity during the fall inter-monsoon, while phosphate for both the Southwest monsoon and the Northeast monsoon. Pearson's analysis revealed that the seasonal variation rather than the vertical variation of environmental factors had a more significant impact on the composition of bacterial community. In addition, a clear seasonal pattern of bacterial co-occurrence showed that inter-taxa associations during the fall inter-monsoon were closer than during the Northeast monsoon and the Southwest monsoon. Overall, our results implied clear differences in the composition of bacterial community, with more pronounced seasonal variation compared to the vertical variation in response to environmental changes.

Gene expression of terminal oxidases in two marine bacterial strains exposed to nanomolar oxygen concentrations.

The final step of aerobic respiration is carried out by a terminal oxidase transporting electrons to oxygen (O2). Prokaryotes harbor diverse terminal oxidases that differ in phylogenetic origin, structure, biochemical function, and affinity for O2. Here we report on the expression of high-affinity (cytochrome cbb3 oxidase), low-affinity (cytochrome aa3 oxidase), and putative low-affinity (cyanide-insensitive oxidase (CIO)) terminal oxidases in the marine bacteria Idiomarina loihiensis L2-TR and Marinobacter daepoensis SW-156 upon transition to very low O2 concentrations (<200 nM), measured by RT-qPCR. In both strains, high-affinity cytochrome cbb3 oxidase showed the highest expression levels and was significantly up-regulated upon transition to low O2 concentrations. Low-affinity cytochrome aa3 oxidase showed very low transcription levels throughout the incubation. Surprisingly, however, it was also up-regulated upon transition to low O2 concentrations. In contrast, putative low-affinity CIO had much lower expression levels and markedly different regulation patterns between the two strains. These results demonstrate that exposure to low O2 concentrations regulates the gene expression of different types of terminal oxidases, but also that the type and magnitude of transcriptional response is species-dependent. Therefore, in situ transcriptome data cannot, without detailed knowledge of the transcriptional regulation of the species involved, be translated into relative respiratory activity.

High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond.

Strain S3-2T, isolated from sediment of a frozen freshwater pond, shares 99% 16S rRNA gene sequence identity with strains of the genus Janthinobacterium. Strain S3-2T is a facultative anaerobe that lacks the ability to produce violacein but shows antibiotic resistance, psychrotolerance, incomplete denitrification, and fermentation. The draft genome of strain S3-2T has a size of ~5.8 Mbp and contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties of the strain, the low in silico DNA-DNA hybridization (DDH) values with related genomes (<35%), and the low whole genome-based average nucleotide identity (ANI) (<86%) with other strains within the genus Janthinobacterium, we propose that strain S3-2T is the type strain (= DSM 102223 = LMG 29653) of a new species within this genus. We propose the name Janthinobacterium psychrotolerans sp. nov. to emphasize the capability of the strain to grow at low temperatures.

Respiratory Kinetics of Marine Bacteria Exposed to Decreasing Oxygen Concentrations.

During aerobic respiration, microorganisms consume oxygen (O2) through the use of different types of terminal oxidases which have a wide range of affinities for O2. The Km values for O2 of these enzymes have been determined to be in the range of 3 to 200 nmol liter(-1). In this study, we examined the time course of development of aerobic respiratory kinetics of four marine bacterial species (Dinoroseobacter shibae, Roseobacter denitrificans, Idiomarina loihiensis, and Marinobacter daepoensis) during exposure to decreasing O2 concentrations. The genomes of all four species have genes for both high-affinity and low-affinity terminal oxidases. The respiration rate of the bacteria was measured by the use of extremely sensitive optical trace O2 sensors (range, 1 to 1,000 nmol liter(-1)). Three of the four isolates exhibited apparent Km values of 30 to 60 nmol liter(-1) when exposed to submicromolar O2 concentrations, but a decrease to values below 10 nmol liter(-1) was observed when the respiration rate per cell was lowered and the cell size was decreased due to starvation. The fourth isolate did not reach a low respiration rate per cell during starvation and exhibited apparent Km values of about 20 nmol liter(-1) throughout the experiment. The results clearly demonstrate not only that enzyme kinetics may limit O2 uptake but also that even individual cells may be diffusion limited and that this diffusion limitation is the most pronounced at high respiration rates. A decrease in cell size by starvation, due to limiting organic carbon, and thereby more efficient diffusion uptake may also contribute to lower apparent Km values.