More Than a Stick in the Mud: Eelgrass Leaf and Root Bacterial Communities Are Distinct From Those on Physical Mimics

We examine the role of physical structure versus biotic interactions in structuring host-associated microbial communities on a marine angiosperm, Zostera marina, eelgrass. Across several months and sites, we compared microbiomes on physical mimics of eelgrass roots and leaves to those on intact plants. We find large, consistent differences in the microbiome of mimics and plants, especially on roots, but also on leaves. Key taxa that are more abundant on leaves have been associated with microalgal and macroalgal disease and merit further investigation to determine their role in mediating plant-microalgal-pathogen interactions. Root associated taxa were associated with sulphur and nitrogen cycling, potentially ameliorating environmental stresses for the plant. Our work identifies targets for future work on the functional role of the seagrass microbiome in promoting the success of these angiosperms in the sea through identifying components of microbial communities that are specific to seagrasses.

Genome-resolved transcriptomics reveals novel PCE-dehalogenating bacteria from Aarhus Bay sediments

Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria, and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from tetrachloroethene respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 medium-quality bins with over 75% completeness and less than 5% contamination. Sixteen bins harbored RDase genes and were affiliated taxonomically to the class of Bacilli and phyla of Bacteroidota, Synergistota, and Spirochaetota, which have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically close to the genus Vulcanibacillus (phylum Firmicutes), contained an unprecedented 97 reductive dehalogenase (RDase) genes. Of these, 84 RDase genes of bin.26 were transcribed during tetrachloroethene dechlorination in addition to RDase genes from the members of Synergistales (bin.5 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested that the RDase genes were likely under the regulation of transcriptional regulators not previously associated with organohalide respiration, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to add to the current knowledge of the diversity, activity, and regulation of RDase genes.IMPORTANCEPristine marine environment is the major reservoir for naturally produced organohalides, in which reductive dehalogenation underneath plays an important role in the overall cycling of these compounds. Here, we obtain some novel OHRB genomes from Aarhus Bay marine sediments, which are phylogenetically distant to the well-documented OHRB and widely distributed across the bacterial phyla, such as Bacteroidota, Synergistota, and Spirochaetota. Furthermore, transcriptional profiles unravel that these RDase genes are induced differently, and their activity is controlled by diverse regulatory systems. Accordingly, elucidating the reductive dehalogenation of pristine marine environments substantially advances our understanding of the diversity, phylogeny, and regulatory variety of dehalogenating bacteria contributing to the global halogen cycle.

Growth on Hydrogen by the Sulfate-Reducing Oleidesulfovibrio alaskensis Induces Biofilm Dispersion and Detachment─Implications for Underground Hydrogen Storage

Hydrogen is a versatile energy carrier for human activity but is also a ubiquitous electron donor for subsurface microorganisms. During underground hydrogen storage operations, it is expected that microbial communities will use the injected hydrogen as electron donor for diverse metabolisms, and induce a variety of microbial-triggered risks. A significant concern is the formation of biofilm and induced bioclogging, which may reduce the hydrogen injectivity and storage operation efficiency by altering the subsurface hydrogen flow. This study investigates how different electron donors─specifically hydrogen and lactate─affect the growth dynamics of a sulfate-reducing bacterium (Oleidesulfovibrio alaskensis G20) and the associated biofilm formation in porous media. The pore-scale observations reveal that lactate promotes robust biofilms resulting in bioclogging, compared to hydrogen promoting increased microbial motility with less biomass production. Potential hydrogen chemotaxis leads to biofilm dispersal and detachment over time as the cells seemingly favor a planktonic lifestyle over biofilm formation. Multiple hydrogen injections enhanced biofilm detachment and reduced the risk of pore blockage associated with microbial growth. Three hydrogen injections resulted in 69% biofilm detachment, while nitrogen injection caused only 31% detachment over three cycles. The combination of increased cell motility and reduced biofilm attachment indicates that the risk of bioclogging during cyclic UHS operation might be low for this model bacterial strain.

Myxosortase: an intramembrane protease that sorts MYXO-CTERM proteins to the cell surface

Cell surface proteins determine how cells interact with their biotic and abiotic environments. In social myxobacteria, a C-terminal protein sorting tag called MYXO-CTERM is universally found within the Myxococcota phylum, where their genomes typically contain dozens of proteins with this motif. MYXO-CTERM harbors a tripartite architecture: a short signature motif containing an invariant cysteine, followed by a transmembrane helix and a short arginine-rich C-terminal region localized in the cytoplasm. In Myxococcus xanthus, MYXO-CTERM is predicted to be posttranslationally lipidated and cleaved for subsequent cell surface localization by the type II secretion system. Here, following our bioinformatic discovery, we experimentally show that myxosortase (MrtX, MXAN_2755) is responsible for the C-terminal cleavage and cell surface anchoring of TraA, a prototypic cell surface receptor. The cleavage by MrtX depends on conserved cysteines within the MYXO-CTERM motif of TraA. M. xanthus mutants lacking myxosortase are defective in TraA-mediated outer membrane exchange and exhibit cell envelope defects. In a heterologous Escherichia coli expression system, the MYXO-CTERM motif is cleaved when MrtX is co-expressed. Therefore, MrtX represents a new family of sorting enzyme that enables cell surface localization of MYXO-CTERM proteins.IMPORTANCEThe CPBP (CaaX protease and bacteriocin processing) protease family is widespread across the three domains of life. Despite considerable research on eukaryotic homologs, prokaryotic CPBP family members remain largely unexplored. In this study, we experimentally reveal the function of a novel CPBP protease called myxosortase. Our findings show that myxosortase is responsible for the C-terminal cleavage and cell surface anchoring of substrate proteins containing MYXO-CTERM motifs in Myxococcus xanthus. MYXO-CTERM cleavage also occurred in a heterologous Escherichia coli host when myxosortase is co-expressed. This is the first report that a CPBP protease is involved in protein sorting in prokaryotes. This work provides important insights into the biogenesis and anchoring of cell surface proteins in gram-negative bacteria.

Pressure up to 60 bar has no major effect on the overall hydrogen consumption of the sulfate reducer Oleidesulfovibrio alaskensis

AIMS

Subsurface environments found in geological aquifers or reservoirs are not sterile, but harbor diverse microbial communities for which hydrogen (H2) is a ubiquitous electron donor, especially for sulfate-reducing bacteria (SRB). Most studies investigating SRB have been conducted through consumption experiments at near-atmospheric pressure. However, pressures are significantly higher in subsurface formations. It remains a crucial question whether high H2 partial pressure influences microbial consumption. Therefore, we tested a relevant SRB under increased H2-pressure to investigate changes in H2-consumption behavior.

METHODS AND RESULTS

We cultured the H2-consuming SRB Oleidesulfovibrio alaskensis G20 under 1, 30, and 60 bar of H2 overpressure and quantified consumption over time. Data were compared to sterile incubations. After 16 days, the total amount of consumed H2, sulfate, and acetate was similar for all pressure conditions and pH ended over 9, which is beyond the described pH limit. While the maximum H2 consumption rate was found higher at atmospheric pressures (0.20 mmol per day) compared to 30 and 60 bar (0.13 and 0.11 mmol per day), the maximum rate per surface area was comparable (0.02, 0.03, 0.02 mmol per day per cm2). The total rate of H2 consumption per cm2 was higher with increasing pressure, which is probably related to the increased solubility of H2 in the brine phase due to pressure.

CONCLUSIONS

The data show that pressures up to 60 bar have no significant effect on the overall activity of O. alaskensis. The governing factor for the H2 consumption rate is contact area between brine and gas phase and the concentration of dissolved H2.

Microbial Fe(III) reduction across a pH gradient: The impacts on secondary mineralization and microbial community development

Fe(III) (hydr)oxides are prevalent in natural environments where they impact contaminant mobility, greenhouse gas release, and nutrient cycling. In anoxic conditions, dissimilatory iron reducing bacteria (DIRB) and other microbial groups primarily drive Fe(III) reduction. Dissimilatory iron reduction (DIR) results in the reductive dissolution of Fe(III) phases and subsequent secondary mineralization. These processes are highly sensitive to pH changes, since protons serve as reactants in DIR. However, there is limited understanding of how DIR impacts secondary mineralization and microbial community development under relevant pH gradients. This study investigated the impact of initial pH (6.3, 6.9, 7.3, 7.7, 9) and Fe(III) source (goethite, lepidocrocite) on DIR, using acetate as the electron donor. The rate and extent of Fe(III) reduction decreased with increasing pH and that lepidocrocite, with its relatively lower crystallinity compared to goethite, supported greater DIR activity. Solid phase analyses revealed predominant formation of siderite alongside lepidocrocite reduction in microcosms with initial pH at 6.3 and 6.9. Similarly, in microcosms with initial pH at 7.3 and 7.7, partial transformation to siderite occurred. In contrast, goethite-amended microcosms did not show clear mineralogical transformations, despite the observed Fe(II) production. Microbial community analysis using 16S rRNA sequencing indicated greater enrichment of DIRB at lower pH, with a decline in abundance as pH increased. Overall, pH influenced DIR more than Fe mineralogy, highlighting its critical role in DIR processes, secondary mineral formation, and DIRB community development. This study further provides insights for developing remediation strategies involving microbial Fe(III) reduction under varying pH conditions.

Convergence in Amino Acid Outsourcing Between Animals and Predatory Bacteria

All animals have outsourced about half of the 20 proteinogenic amino acids (AAs). We recently demonstrated that the loss of biosynthetic pathways for these outsourced AAs is driven by energy-saving selection. Paradoxically, these metabolic simplifications enabled animals to use costly AAs more frequently in their proteomes, allowing them to explore sequence space more freely. Based on these findings, we proposed that environmental AA availability and cellular respiration mode are the two primary factors determining the evolution of AA auxotrophies in animals. Remarkably, our recent analysis showed that bacterial AA auxotrophies are also governed by energy-related selection, thereby roughly converging with animals. However, bacterial AA auxotrophies are highly heterogeneous and scattered across the bacterial phylogeny, making direct ecological and physiological comparisons with the animal AA outsourcing model challenging. To better test the universality of our model, we focused on Bdellovibrionota and Myxococcota-two closely related bacterial phyla that, through aerobic respiration and a predatory lifestyle, best parallel animals. Here, we show that Bdellovibrionota, driven by energy-related selection, outsourced a highly similar set of AAs to those in animals. This sharply contrasts with Myxococcota, which exhibit far fewer AA auxotrophies and rarely show signatures of energy-driven selection. These differences are also reflected in Bdellovibrionota proteomes, which are substantially more expensive than those of Myxococcota. Finally, we found evidence that the expression of costly proteins plays a crucial role in the predatory phase of the Bdellovibrio life cycle. Together, our findings suggest that Bdellovibrionota, through their obligate predatory lifestyle, exhibit the closest analogy to the AA auxotrophy phenotype observed in animals. In contrast, facultative predation, as seen in Myxococcota, appears to substantially limit the evolution of AA auxotrophies. These cross-domain convergences strongly support the general validity of our AA outsourcing model.

Fungi promote cross-domain interactions even in deep anoxic mangrove sediments

BACKGROUND

Microbial communities in mangrove sediments play vital ecological roles that underpin the functioning of the overall mangrove ecosystem. Fungal communities, in particular, are known to play crucial roles across sediment systems, yet their roles in mangrove sediments, especially in deeper layers, remain poorly understood without a comprehensive inter-domain characterization. To better understand fungal roles in sediment horizons, 10 sediment cores extending down to a depth of 1 m were taken in three mangrove sites to characterise the archaeal, bacterial, and fungal communities at 10 cm depth intervals.

RESULTS

We demonstrate that sediment depth has distinct effects on the three microbial communities. While fungal community compositions were similar across sediment depths, bacterial and archaeal community compositions were stratified into three distinct layers, surface (10-30 cm), subsurface (40-60 cm), and deep (70-100 cm). Co-occurrence networks were then constructed to investigate the roles of fungi in these sediment layers, where fungi were consistently identified as keystone taxa in maintaining the microbial network topology, with co-domain interactions constituting more than half of all interactions. Even in the deepest layer, fungal nodes still retained high betweenness centralities, acting as network hubs to potentially augment microbial interactions vital for the functioning of the overall ecosystem.

CONCLUSIONS

Overall, our results emphasise the important role of fungi in mediating microbial interactions across sediment depths even in deep, anoxic sediment layers, and highlight the importance of cross-domain interactions as integral to a more holistic understanding of the mangrove microbiome.

Comparative analysis of crab growth performance, enzyme activity, and microbiota between rice-crab coculture and pond farming systems

Introduction

To support the sustainable development of rice and aquaculture industries, various rice-animal coculture systems have been developed. One such system, the rice-crab coculture system (RCC), has been practiced for decades in northern China. However, studies on the crab physiological status in RCC remain limited. Microorganisms play a crucial role in aquaculture by influencing animal nutrition, health, nutrient cycling, water quality, and environmental impact. Research on the gut and environmental microbiota in RCC is scarce.

Methods

This study compared the growth performance, immune and digestive enzyme activities of crabs between RCC and traditional pond farming system (PF). In addition, the microbiota in crab guts, water, and sediment from both systems was investigated using 16S rRNA gene sequencing.

Results

Crabs in RCC exhibited superior growth performance and higher enzymatic activities, including acid phosphatase (ACP), alkaline phosphatase (AKP), lipase (LPS), and trypsin (TRY). Significant differences were observed in microbiota composition across crab gut, water, and sediment samples, respectively. RCC crabs had a lower abundance of Bacteroidota and a higher abundance of Firmicutes in their gut microbiota. The RCC environment was enriched with beneficial bacteria such as Rhizobiales, Methylococcales, KD4-96, C39, Xanthomonadales, and Nitrosomonadaceae. Microbial function predictions confirmed enhanced methanotrophy and nitrogen fixation in the RCC.

Discussion

The RCC enhances the growth rate and immune capability of crabs. Crabs from RCC consume more animal-based nutrition, which results in distinct differences in gut microbiota composition and higher levels of LPS and TRY compared to those in PF. Additionally, RCC supports environmentally beneficial bacteria that contribute to greenhouse gas reduction, carbon and nitrogen fixation, organic matter decomposition, and ammonia oxidation, benefiting both the crabs and their ecosystem. These findings enhance our understanding of crab physiology and microbial communities in RCC and PF systems.

Substrate stiffness modulates collective colony expansion of the social bacterium Myxococcus xanthus

Many cellular functions depend on the physical properties of the cell's environment. Many bacteria have different types of surface appendages to enable adhesion and motion on various surfaces. Myxococcus xanthus is a social soil bacterium with two distinctly regulated modes of surface motility, termed the social motility mode, driven by type IV pili, and the adventurous motility mode, based on focal adhesion complexes. How bacteria sense different surfaces and subsequently coordinate their collective motion remains largely unclear. Using polyacrylamide hydrogels of tunable stiffness, we found that wild type M. xanthus spreads faster on stiffer substrates. Here, we show that using motility mutants that disrupt adventurous motility suppresses this substrate stiffness response, suggesting focal adhesion-based adventurous motility is substrate stiffness dependent. We also show that modifying surface adhesion by adding adhesive ligands, chitosan, increases the amount of M. xanthus flairs, a characteristic feature of adventurous motility. Taken together, we hypothesize a central role of M. xanthus adventurous motility as a driving mechanism for surface and surface stiffness sensing.

Seasonal variation of microbial community and diversity in the Taiwan Strait sediments

Human activities and ocean currents in the Taiwan Strait exhibit significant seasonal variation, yet the response of marine microbes to ocean changes under anthropogenic and climatic stress remains unclear. Using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics and functional variations of microbial communities in sediment samples. Our findings revealed distinct seasonal patterns in microbial diversity and composition. Proteobacteria, Desulfobacterota, and Crenarchaeota dominated at the phylum level, while Candidatus Nitrosopumilus, Woeseia, and Subgroup 10 were prevalent at the genus level. Iron concentrations, heavy metals and C/N ratio were primary factors influencing microbial communities during specific seasons, whereas sulfur content, temperature fluctuations, and heavy metals shaped the entire microbial structure and diversity. Core microbial groups, including Desulfobulbus, Subgroup 10, Unidentified Latescibacterota, and Sumerlaea, played essential roles in regulating community structure and functional transitions. Marker species, such as Aliidiomarina sanyensis, Spirulina platensis, Croceimarina litoralis and Sulfuriflexus mobilis, acted as seasonal indicators. Bacteria exhibited survival strategy akin to higher organisms, encompassing process of synthesis, growth, dormancy, and disease resistance throughout the seasonal cycle. Core microbial groups and marker species in specific seasons can serve as indicators for monitoring and assessing the health of the Taiwan Strait ecosystem.

Comparative analysis of novel Pseudobdellovibrionaceae genera and species yields insights into the genomics and evolution of bacterial predation mode

Bacteria of the family Pseudobdellovibrionaceae belong to a group of bacteria that kill and feed on other bacteria. The diversity of predation strategies, habitats, and genome characteristics of these bacteria are largely unexplored, despite their ecological and evolutionary importance in microbial communities. Therefore, we characterized new Pseudobdellovibrionaceae strains isolated from the direct environments of three animal hosts: the zebrafish ( Danio rerio ), the threespine stickleback fish ( Gasterosteus aculeatus ), and the nematode Caenorhabditis elegans . We used transmission electron microscopy (TEM) and genomic analyses to characterize the morphology and predation modes of our isolates. While most of our isolates exhibited periplasmic (i.e. endoparasitic) predation, one isolate clearly exhibited epibiotic (i.e. exoparasitic) predation and represents only the third confirmed epibiotic strain within its clade. Of our isolates, six are members of five new species in the genus Bdellovibrio and two strains likely represent new genera within the family Pseudobdellovibrionaceae . From metabarcoding data, we found indications that Pseudobdellovibrionaceae are widespread among our three animal hosts. Genomic analyses showed that epibiotic predators lack genes involved in host independence (i.e. prey-independent feeding) and peptidoglycan modification. However, genes unique to epibiotic predators may underlie this predation mode, particularly those involved in cell wall remodeling and recycling. With robust phylogenomic analyses, we show that our novel isolates cluster with previously described Pseudobdellovibrionaceae isolates according to predation mode. Further, by placing Pseudobdellovibrionaceae predators within a wider evolutionary history including other predatory and non-predatory bacteria, we postulate periplasmic predation as the ancestral mode, with more derived epibiotic predators exhibiting genome streamlining.

Distribution and Environmental Preference of Potential Mercury Methylators in Paddy Soils across China

The neurotoxin methylmercury (MeHg) is produced mainly from the transformation of inorganic Hg by microorganisms carrying the hgcAB gene pair. Paddy soils are known to harbor diverse microbial communities exhibiting varying abilities in methylating inorganic Hg, but their distribution and environmental drivers remain unknown at a large spatial scale. Using hgcA gene amplicon sequencing, this study examined Hg-methylating communities from major rice-producing paddy soils across a transect of ∼3600 km and an altitude of ∼1300 m in China. Results showed that hgcA+ OTU richness was higher in tropical and subtropical paddy soils compared to temperate zones. Geobacteraceae, Smithellaceae, and Methanoregulaceae were identified as the dominant hgcA+ families associated with MeHg production, collectively accounting for up to 77% of total hgcA+ sequences. Hierarchical partitioning analyses revealed that pH was the main driver of hgcA genes from Geobacteraceae (14.8%) and Methanoregulaceae (16.3%), while altitude accounted for 21.4% of hgcA genes from Smithellaceae. Based on these environmental preferences, a machine-learning algorithm was used to predict the spatial distribution of these dominant hgcA+ families, thereby providing novel insights into important microbial determinants for improved prediction of MeHg production in paddy soils across China.

Reducing methane emissions by developing low-fumarate high-ethanol eco-friendly rice

Methane in rice paddies is mainly produced by methanogenic communities feeding on carbon from root exudates and debris. However, the dominant root secretion governing methane emissions is not yet identified after decades of studies, even though secreted carbohydrates and organic acids have been shown to contribute to methane emissions. In this study, we discovered that fumarate and ethanol are two major rice-orchestrated secretions and play a key role in regulating methane emissions. Fumarate released in the rhizosphere is metabolized by microorganisms, supporting the growth of methanogenic archaea that produce methane as an end carbon product, while ethanol mitigates methane emissions through inhibition of methanogenic activity and growth as well as reducing fumarate synthesis in the rice root. Furthermore, we elucidated the route of fumarate metabolism in the anoxic rhizospheric zone. We found that fumarate in the rice root is produced from acetate via propionate and succinate, and when released into soil directly is oxidized to propionate before conversion via acetate into methane as the end product. The knowledge on fumarate and ethanol metabolism in rice was then used for hybrid breeding of new rice varieties with the property of low methane emission. Cultivation of these novel rice lines or employing our findings for rice cultivation managements showed up to 70% reductions in methane production from seven paddy field sites during 3 years of cultivation trials. Taken together, these findings offer great possibilities for effective mitigation of the global climatic impact of rice cultivation.

New insights in uranium bioremediation by cytochromes of the bacterium Geotalea uraniireducens

The bacterium Geotalea uraniireducens, commonly found in uranium-contaminated environments, plays a key role in bioremediation strategies by converting the soluble hexavalent form of uranium (U(VI)) into less soluble forms (e.g., U(IV)). While most of the reduction and concomitant precipitation of uranium occur outside the cells, there have been reports of important reduction processes taking place in the periplasm. In any case, the triheme periplasmic cytochromes are key players, either by ensuring an effective interface between the cell's interior and exterior or by directly participating in the reduction of the metal. Therefore, understanding the functional mechanism of the highly abundant triheme cytochromes in G. uraniireducens' is crucial for elucidating the respiratory pathways in this bacterium. In this work, a detailed functional characterization of the triheme cytochromes PpcA and PpcB from G. uraniireducens was conducted using NMR and visible spectroscopy techniques. Despite sharing high amino acid sequence identity and structural homology with their counterparts from Geobacter sulfurreducens, the results showed that the heme reduction potential values are less negative, the order of oxidation of the hemes is distinct, and the redox and redox-Bohr network of interactions revealed unprecedented functional mechanisms in the cytochromes of G. uraniireducens. In these cytochromes, the reduction potential values of the three heme groups are much more similar, resulting in a narrower range of values, that facilitates directional electron flow from the inner membrane, thereby optimizing the uranium reduction.

Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq)

Hydrothermal sediments host phylogenetically diverse and physiologically complex microbial communities. Previous studies of microbial community structure in hydrothermal sediments have typically used short-read sequencing approaches. To improve on these approaches, we use LoopSeq, a high-throughput synthetic long-read sequencing method that has yielded promising results in analyses of microbial ecosystems, such as the human gut microbiome. In this study, LoopSeq is used to obtain near-full length (approximately 1,400-1,500 nucleotides) bacterial 16S rRNA gene sequences from hydrothermal sediments in Guaymas Basin. Based on these sequences, high-quality alignments and phylogenetic analyses provided new insights into previously unrecognized taxonomic diversity of sulfur-cycling microorganisms and their distribution along a lateral hydrothermal gradient. Detailed phylogenies for free-living and syntrophic sulfur-cycling bacterial lineages identified well-supported monophyletic clusters that have implications for the taxonomic classification of these groups. Particularly, we identify clusters within Candidatus Desulfofervidus that represent unexplored physiological and genomic diversity. In general, LoopSeq-derived 16S rRNA gene sequences aligned consistently with reference sequences in GenBank; however, chimeras were prevalent in sequences as affiliated with the thermophilic Candidatus Desulfofervidus and Thermodesulfobacterium, and in smaller numbers within the sulfur-oxidizing family Beggiatoaceae. Our analysis of sediments along a well-documented thermal and geochemical gradient show how lineages affiliated with different sulfur-cycling taxonomic groups persist throughout surficial hydrothermal sediments in the Guaymas Basin.

Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification

Poorly understood microorganisms "short-circuit" the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory type strain T. lovleyi SZ. Here, we describe the identification of tightly regulated pathways for efficient nitrate foraging and respiration with acetate, an important intermediate of organic matter degradation that Geobacterales efficiently assimilate and oxidize. Challenging the established dogma that high carbon/nitrate ratios stimulate the reduction of nitrate to ammonium, T. lovleyi doubled rapidly across a wide range of ratios provided nitrate concentrations were low enough to prevent the accumulation of the toxic nitrite intermediate. Yet, excess electrons during hydrogenotrophic growth alleviated nitrite toxicity and stimulated the reduction of nitrate to ammonium even under conditions of severe acetate limitation. These findings underscore the importance of nitrite toxicity in the ammonification of nitrate by Geobacterales and provide much needed mechanistic understanding of microbial adaptations contributing to soil nitrogen conservation. This information is critical to enhance the predictive value of genomic-based traits in environmental surveys and to guide strategies for sustainable management of nitrogen fertilization as well as mitigation of green-house emissions and agrochemical leaching from agricultural lands.

Dynamic quinone repertoire accompanied the diversification of energy metabolism in Pseudomonadota

It is currently unclear how Pseudomonadota, a phylum that originated around the time of the Great Oxidation Event, became one of the most abundant and diverse bacterial phyla on Earth, with metabolically versatile members colonizing a wide range of environments with different O2 concentrations. Here, we address this question by studying isoprenoid quinones, which are central components of energy metabolism covering a wide range of redox potentials. We demonstrate that a dynamic repertoire of quinone biosynthetic pathways accompanied the diversification of Pseudomonadota. The low potential menaquinone (MK) was lost in an ancestor of Pseudomonadota while the high potential ubiquinone (UQ) emerged. We show that the O2-dependent and O2-independent UQ pathways were both present in the last common ancestor of Pseudomonadota, and transmitted vertically. The O2-independent pathway has a conserved genetic organization and displays signs of positive regulation by the master regulator "fumarate and nitrate reductase" (FNR), suggesting a conserved role for UQ in anaerobiosis across Pseudomonadota. The O2-independent pathway was lost in some lineages but maintained in others, where it favoured a secondary reacquisition of low potential quinones (MK or rhodoquinone), which promoted diversification towards aerobic facultative and anaerobic metabolisms. Our results support that the ecological success of Pseudomonadota is linked to the acquisition of the largest known repertoire of quinones, which allowed adaptation to oxic niches as O2 levels increased on Earth, and subsequent diversification into anoxic or O2-fluctuating environments.

Identifying the active microbes driving organosulfur cycling from taurine and methionine in marine sediment

Studies on microbial sulfur cycling in marine sediment have primarily centered on the cycling of inorganic sulfur. The microbial diversity underlying the cycling of organosulfur compounds is largely unexplored. In this study, we present the first quantification of dissolved organic sulfur (DOS) microbial assimilation in marine surface sediments using 13C-DOS quantitative DNA stable isotope probing (qSIP). We sampled marine sediment from 493 m water depth on the Puerto Rico continental slope, measured 13C-assimilation from two DOS substrates (13C-taurine and 13C-methionine), and compared the 13C-DOS assimilation to 13C-glucose uptake. Taurine utilization was confined to bacteria, whereas methionine was degraded by bacteria and archaea, including methanogenic Methanococcoides. Globally widespread uncultivated clades of Gammaproteobacteria and Deltaproteobacteria were the main drivers of DOS cycling and exhibited increased assimilation of carbon from taurine and methionine, compared to glucose. Only one operational taxonomic unit (OTU) affiliated with Neptuniibacter was found to assimilate taurine and methionine, but not glucose, implying that microbes exclusively utilizing both DOS substrates as a carbon source in marine sediments are rare. Still, a substantial number of bacterial taxa exhibited a higher assimilation of 13C from taurine or methionine, compared to glucose, indicating their preference for both DOS substrates over glucose as a carbon source in the sediment. These results represent the first quantitative assessment of organosulfur cycling from taurine and methionine by uncultivated microbes in a marine benthic environment.

Membrane fouling characteristics and cleaning strategies for rural decentralized nanofiltration drinking water station based on groundwater source

Groundwater is an important source of drinking water in rural areas. In this study, the performance of water purificat ion in a rural water station equipped with nanofiltration (NF) membranes based groundwater source was investigated, as well as the contamination morphology, foulant composition and distribution characteristics of NF membrane. Results showed that significant differences of membrane foulants were observed in different sections of NF membrane. The inlet and middle sections were dominated by organic foulants and exhibited a high abundance of microbial communities associated with organic matter metabolism, and the outlet section was dominated by inorganic foulants and showed an elevated abundance of microorganisms such as Dechloromonas, norank_f_Desulfuromonadaceae, Ferribacterium, Dietzia, Mycobacterium, and Bradyrhizobium. Inorganic fouling accounted for 39.32% of the total resistance and was the main factor contributing to the decrease in membrane flux. Based on the flux recovery after membrane cleaning, the flux recovery obtained by the combination of " acid followed by alkaline " is 1.59 times higher than the flux of the contaminated membrane. This study can support the operation and maintenance of NF drinking water stations to extend the service life of membranes.

Microbial Cycling of Sulfur and Other Redox-Sensitive Elements in Porewaters of San Clemente Basin, California, and Cocos Ridge, Costa Rica

The microbial recycling of organic matter in marine sediments depends upon electron acceptors that are utilized based on availability and energetic yield. Since sulfate is the most abundant oxidant once oxygen has been depleted, the sulfide produced after sulfate reduction becomes an important electron donor for autotrophic microbes. The ability of sulfide to be re-oxidized through multiple metabolic pathways and intermediates with variable oxidation states prompts investigation into which species are preferentially utilized and what are the factors that determine the fate of reduced sulfur species. Quantifying these sulfur intermediates in porewaters is a critical first step towards achieving a more complete understanding of the oxidative sulfur cycle, yet this has been accomplished in very few studies, none of which include oligotrophic sedimentary environments in the open ocean. Here we present profiles of porewater sulfur intermediates from sediments underlying oligotrophic regions of the ocean, which encompass about 75% of the ocean's surface and are characterized by low nutrient levels and productivity. Aiming at addressing uncertainties about if and how sulfide produced by the degradation of scarce sedimentary organic matter plays a role in carbon fixation in the sediment, we determine depth profiles of redox-sensitive metals and sulfate isotope compositions and integrate these datasets with 16S rRNA microbial community composition data and solid-phase sulfur concentrations. We did not find significant correlations between sulfur species or trace metals and specific sulfur cycling taxa, which suggests that microorganisms in pelagic and oxic sediments may be generalists utilizing flexible metabolisms to oxidize organic matter through different electron acceptors.

Microbial diversity of hot springs of the Kuril Islands

The Kuril Islands are located in the Far-East of Russia and enriched with shallow and terrestrial hot springs. Prokaryotic diversity of Kuril geothermal environments has been studied fragmentarily and mainly by culture-dependent methods. We performed the first large-scale investigation of microbial communities, inhabited more than 30 terrestrial hot springs of Kunashir and Iturup Islands, analyzed by 16S rRNA gene fragment amplicon sequencing, together with chemical analysis of thermal waters and sediments. The Circumneutral Bacterial group containing springs with pH 5.7-8.5 and temperature 40-79 °C possessed the highest biodiversity and consisted almost entirely of Bacteria. Cyanobacteriota (the Leptolyngbyaceae and Oculatellaceae families) and phototrophic Chloroflexota dominated in the microbial mats in hot springs with temperatures up to 60 °C. The higher temperature ones were dominated by Aquificota (Sulfurihydrogenibium and Hydrogenobacter species). The Acidic Bacterial group (pH 2.2-3.6, 41-64 °C) inhabited by the genera Acidithiobacillus, Hydrogenobaculum and Thiomonas. Archaea of Acidianus, Metallosphaera, Thermoplasma and Caldisphaera spp. as well as uncultivated lineages ('Ca. Marsarchaeales', 'Ca. Caldiarchaeum', BSLdp215) were abundant in the Acidic Archaeal group (pH 1.5-2.9, 50-94 °C). The microbial composition of the Kuril hot springs strongly correlated with pH and moderately correlated with water chemistry, while degree of correlation between the communities' compositions with temperature and location was low.

Comparative genomics of obligate predatory bacteria belonging to phylum Bdellovibrionota highlights distribution and predicted functions of lineage-specific protein families

Comparative genomics of predatory bacteria is important to understand their ecology and evolution and explore their potential to treat drug-resistant infections. We compared chromosomes of 18 obligate predators from phylum Bdellovibrionota (16 intraperiplasmic, two epibiotic) and 15 non-predatory bacteria. Phylogenetics of conserved single-copy genes and analysis of genome-wide average amino acid identity provide evidence for at least five Bdellovibrio species and support recent reclassifications of predatory taxa. To define shared and differential genome content, we grouped predicted protein sequences into gene clusters based on sequence similarity. Few gene clusters are shared by all 33 bacteria or all 18 predatory bacteria; however, we identified gene clusters conserved within lineages, such as intraperiplasmic Bdellovibrio, and not found in other bacteria. Many of these are predicted to function in cell envelope biogenesis, signal transduction, and other roles important for predatory lifestyles. Among intraperiplasmic Bdellovibrio, we detected high abundance of gene clusters predicted to encode transglycosylases, endopeptidases, and lysozymes, and we identified six gene clusters (amidase, L,D-transpeptidase, four transglycosylases) with evidence of recent gene duplication and gene family expansion. Focusing on peptidoglycan metabolism, we defined a suite of gene clusters that include peptidoglycan-degrading and -modifying enzymes and occur only in predatory bacteria, suggesting these proteins may have evolved activities specific to predation. Our analyses highlight key genome content differences between obligate predatory bacteria and non-predatory relatives and identify gene clusters that may encode enzymes adapted to predatory lifestyles. These lineage-specific proteins are strong candidates for functional characterization to clarify their role in predation.IMPORTANCEEvolution of predation as a bacterial lifestyle involves selective pressure on and adaptation of enzymes that contribute to killing and digestion of prey bacteria, in some cases from within the prey itself. Such enzymes are a hallmark of obligate predatory bacteria belonging to phylum Bdellovibrionota, which includes the well-studied predator Bdellovibrio. By comparing protein sequences of obligate predatory bacteria and their non-predatory relatives, we define key genome content differences that distinguish bacterial predators and identify lineage-specific enzymes that may have evolved unique activities due to selective pressures related to a predatory lifestyle. In addition to providing insights into the ecology and evolution of predatory bacteria, comparative genomics studies, like this, can inform efforts to develop predatory bacteria and/or their enzymes as potential biocontrol agents to combat drug-resistant bacterial infections.

Bacterial Community Structure and Environmental Driving Factors in the Surface Sediments of Six Mangrove Sites from Guangxi, China

Mangroves, as blue carbon reservoirs, provide a unique habitat for supporting a variety of microorganisms. Among these, bacteria play crucial roles in the biogeochemical processes of mangrove sediments. However, little is known about their community composition, spatial distribution patterns, and environmental driving factors, particularly across the large geographical scales of mangrove wetlands. In this study, the composition and spatial distribution of the bacterial community structure and its response to fifteen physicochemical parameters (including temperature, pH, salinity, moisture, clay, silt, sand, organic carbon (OC), total nitrogen (TN), total phosphorus (TP), inorganic phosphorus (IP), organic phosphorus (OP), δ13C, δ15N, and carbon/nitrogen ratio (C/N ratio)) were characterized in 32 sampling locations of six different mangrove habitats from Guangxi, China, applying 16S rRNA gene high-throughput sequencing technology and correlation analysis. Our results indicated that the spatial distribution patterns in bacterial communities were significantly different among the six different mangrove sites, as evidenced by NMDS (non-metric multidimensional scaling), ANOSIM (analysis of similarity), and LDA (linear discriminant analysis) analysis. Composition analysis of bacterial communities showed that overall, Chloroflexi (8.3-31.6%), Proteobacteria (13.6-30.1%), Bacteroidota (5.0-24.6%), and Desulfobacterota (3.8-24.0%) were the most abundant bacterial phyla in the mangrove surface sediments. Redundancy analysis (RDA) further highlighted that salinity, δ13C, temperature, δ15N, and silt were the most critical environmental variables influencing the composition of bacterial communities across the whole mangrove samples. Notably, Chloroflexi, one of the most abundant bacterial phyla in the mangrove wetlands, displayed a significantly positive correlation with OC and a negative correlation with δ13C, suggesting its essential role in the degradation of terrestrial-derived organic carbon. These findings support the current understanding of the roles of the bacterial communities and their interactions with environmental factors in diverse mangrove ecosystems.

Sulfate-Reducing Bacteria Isolated from an Oil Field in Kazakhstan and a Description of Pseudodesulfovibrio karagichevae sp. nov

Sulfidogenic bacteria cause numerous issues in the oil industry since they produce sulfide, corroding steel equipment, reducing oil quality, and worsening the environmental conditions in oil fields. The purpose of this work was to isolate and taxonomically identify the sulfidogenic bacteria responsible for the corrosion of steel equipment at the Karazhanbas oil field (Kazakhstan). In this study, we characterized five sulfidogenic strains of the genera Pseudodesulfovibrio, Oleidesulfovibrio, and Acetobacterium isolated from the formation water of the Karazhanbas oil field (Kazakhstan). Sulfate-reducing strain 9FUST revealed 98.9% similarity of the 16S rRNA gene sequence with the closely related strain 'Pseudodesulfovibrio methanolicus' 5S69T and was studied in detail to enhance the taxonomic resolution. Strain 9FUST grew optimally at 23-28 °C, pH 6.5, and 0-2% (w/v) NaCl. The strain used lactate, pyruvate, methanol, ethanol, fructose, ribose, and H2/CO2 (in the presence of acetate) as carbon and energy sources for sulfate reduction. Iso-C17:1 ω11, C15:0, iso-C15:0, and C16:0 were the predominant fatty acids. The genome is 4.20 Mbp with a G + C content of 64.0%. The average nucleotide identity and digital DNA-DNA hybridization values with Pseudodesulfovibrio spp. genomes were 72.5-91.6% (<95%) and 18.5-45.0% (<70%), respectively, and supported our conclusion that 9FUST (=VKM B-3654T = KCTC 25498T) belonged to a novel Pseudodesulfovibrio species, for which the name Pseudodesulfovibrio karagichevae sp. nov. is proposed. Pangenome analysis of sixteen Pseudodesulfovibrio species and functional annotation analysis of identified genes revealed complete modules of enzymes of the main metabolic pathways, characteristic of bacteria of this genus, and unique genes highlighting the adaptations of strain 9FUST in carbohydrate metabolism, nutrient uptake, and environmental stress response. Isolation of these strains expands our understanding of the diversity of sulfidogens in oil reservoirs and can be used to test the effectiveness of biocides used in an oil field.

Unveiling the bacterial diversity and potential of the Avicennia marina ecosystem for enhancing plant resilience to saline conditions

BACKGROUND

Avicennia marina ecosystems are critical for coastal protection, water quality enhancement, and biodiversity support. These unique ecosystems thrive in extreme saline conditions and host a diverse microbiome that significantly contributes to plant resilience and growth. Global food security is increasingly threatened by crop yield losses due to abiotic stresses, including saline soils. Traditional plant breeding for salt tolerance is both costly and time-consuming. This study explores the potential of bacteria from A. marina to enhance plant growth under saline conditions, emphasizing their ecological significance.

RESULTS

We analyzed the microbiome of A. marina from the Red Sea coast using high-throughput Illumina sequencing and culture-dependent methods across various compartments (bulk soil, rhizosphere, rhizoplane, roots, and leaves). Our findings revealed distinct compartment-specific microbial communities, with Proteobacteria being the dominant phylum. Functional predictions indicated diverse microbial roles in metal uptake and plant growth promotion (PGP). Remarkably, our culture-dependent methods allowed us to recover 56% of the bacterial diversity present in the microbiome, resulting in the isolation and characterization of 256 bacterial strains. These isolates were screened for PGP traits, including salt and heat tolerance, siderophore production, and pectinase activity. Out of the 77 bacterial isolates tested, 11 demonstrated a significant ability to enhance Arabidopsis growth under salt stress.

CONCLUSIONS

Our study highlights the ecological significance of mangrove microbiomes and the potential of culture collections in offering innovative solutions for ecological restoration and crop production in saline conditions. The unique collection of mangrove bacteria, particularly from the rhizosphere and endophytes, showcases significant PGP traits and stress tolerance capabilities. These findings emphasize the importance of functional traits, such as salt tolerance, in the recruitment of endophytic bacteria by plants over taxonomic affiliation. The identified bacterial strains hold potential not only for developing biofertilizers to improve crop productivity but also for ecological restoration projects aimed at rehabilitating saline-degraded lands, thereby contributing to overall ecosystem health and sustainability.

Phylogeny and evolution of dissimilatory sulfite reduction in prokaryotes

Sulfate is the second most common nonmetallic ion in modern oceans, as its concentration dramatically increased alongside tectonic activity and atmospheric oxidation in the Proterozoic. Microbial sulfate/sulfite metabolism, involving organic carbon or hydrogen oxidation, is linked to sulfur and carbon biogeochemical cycles. However, the coevolution of microbial sulfate/sulfite metabolism and Earth's history remains unclear. Here, we conducted a comprehensive phylogenetic analysis to explore the evolutionary history of the dissimilatory sulfite reduction (Dsr) pathway. The phylogenies of the Dsr-related genes presented similar branching patterns but also some incongruencies, indicating the complex origin and evolution of Dsr. Among these genes, dsrAB is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of dsrAB was shaped by vertical inheritance and multiple horizontal gene transfer events and that selection pressure varied across distinct lineages. Dated phylogenetic trees indicated that key evolutionary events of dissimilatory sulfur-metabolizing prokaryotes were related to the Great Oxygenation Event (2.4-2.0 Ga) and several geological events in the "Boring Billion" (1.8-0.8 Ga), including the fragmentation of the Columbia supercontinent (approximately 1.6 Ga), the rapid increase in marine sulfate (1.3-1.2 Ga), and the Neoproterozoic glaciation event (approximately 1.0 Ga). We also proposed that the voluminous iron formations (approximately 1.88 Ga) might have induced the metabolic innovation of iron reduction. In summary, our study provides new insights into Dsr evolution and a systematic view of the coevolution of dissimilatory sulfur-metabolizing prokaryotes and the Earth's environment.

From small water bodies to lakes: Exploring the diversity of freshwater bacteria in an Alpine Biosphere Reserve

Small water bodies, although supporting high biodiversity, are often understudied in the Alpine region. In this work, we characterized the planktic and benthic bacterial communities, as well as the water chemistry, of a wide physiographic range of 19 freshwater bodies within an Alpine Biosphere Reserve, including ponds, pasture ponds, peat bogs, shallow lakes, and lakes. We collected both water and surface sediment samples, followed by metabarcoding analysis based on the V3-V4 regions of the 16S rRNA gene. We investigated the changes in biodiversity and the distribution of unique and shared amplicon sequence variants (ASVs) between water (11,829 ASVs) and surface sediment (19,145 ASVs) habitats, as well as across different freshwater typologies. The majority of ASVs (78 %) were unique to a single sample, highlighting the variability and uniqueness of bacterial communities in such freshwater bodies. Most freshwater environments showed higher α-diversity in sediment samples (median, 1469 ASVs) compared to water (468 ASVs). We found that water and sediment habitats harboured unique bacterial communities with significant differences in their taxonomic compositions. Benthic bacteria were associated with several biogeochemical and degradative processes occurring in the sediments, with no notable differences among freshwater typologies and with phylogenetically and ecologically similar species. Conversely, planktic communities showed greater heterogeneity: small water bodies and peat bogs were characterized by higher relative abundances of Patescibacteria (up to 33 %), while lakes and shallow lakes were dominated by Actinobacteriota (up to 36 %). Cyanobacteria (426 ASVs) were generally distributed at low abundances in both water and sediment habitats. Overall, our results provided essential insights into the bacterial ecology of understudied environments such as ponds and pasture ponds and highlighted the importance of further exploring their rich pelagic and benthic bacterial biodiversity.

Bacteriovorax antarcticus sp. nov., a bacterial predator isolated from near Potter Cove on King George Island, Antarctica

A new species of bacterial predator (PP10T) was isolated from a biocrust sample taken from near Potter Cove, King George Island, Antarctica (62°14'15.62″S 58°43'15.65″W). The Bdellovibrio and like organism was vibrio-shaped and employed a single polar flagellum for motility. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that this isolate clustered within the genus Bacteriovorax in the family Bacteriovoracaceae. The 16S rRNA gene sequence similarities between isolate PP10T and the type strain (Bacteriovorax stolpii DSM 12778T) were only 97.14%. The draft genome of PP10T has a size of 4.243 Mbps, with 4148 genes and a G+C content of 38.49%. While the optimal temperature for its growth was 25 °C, PP10T was active at 4 °C, classifying it as psychrotolerant. The results of genetic and physiological tests indicated phenotypic differentiation of strain PP10T from the type strain Bx. stolpii DSM 12778T. Based on physiological and phylogenetic analyses, as well as the prey spectrum, isolate PP10 represents a novel species within the genus Bacteriovorax, for which the name Bacteriovorax antarcticus sp. nov. is proposed. The type strain is PP10T (= KCTC 8097T = DSM 116241T).

On the diversity, phylogeny and biogeography of cable bacteria

Cable bacteria have acquired a unique metabolism, which induces long-distance electron transport along their centimeter-long multicellular filaments. At present, cable bacteria are thought to form a monophyletic clade with two described genera. However, their diversity has not been systematically investigated. To investigate the phylogenetic relationships within the cable bacteria clade, 16S rRNA gene sequences were compiled from literature and public databases (SILVA 138 SSU and NCBI GenBank). These were complemented with novel sequences obtained from natural sediment enrichments across a wide range of salinities (2-34). To enable taxonomic resolution at the species level, we designed a procedure to attain full-length 16S rRNA gene sequences from individual cable bacterium filaments using an optimized nested PCR protocol and Sanger sequencing. The final database contained 1,876 long 16S rRNA gene sequences (≥800 bp) originating from 92 aquatic locations, ranging from polar to tropical regions and from intertidal to deep sea sediments. The resulting phylogenetic tree reveals 90 potential species-level clades (based on a delineation value of 98.7% 16S rRNA gene sequence identity) that reside within six genus-level clusters. Hence, the diversity of cable bacteria appears to be substantially larger than the two genera and 13 species that have been officially named up to now. Particularly brackish environments with strong salinity fluctuations, as well as sediments with low free sulfide concentrations and deep sea sediments harbor a large pool of novel and undescribed cable bacteria taxa.

Cascading sulfur cycling in simulated oil sands pit lake water cap mesocosms transitioning from oxic to euxinic conditions

Base Mine Lake (BML), the first full-scale demonstration of oil sands tailings pit lake reclamation technology, is experiencing expansive, episodic hypolimnetic euxinia resulting in greater sulfur biogeochemical cycling within the water cap. Here, Fluid Fine Tailings (FFT)-water mesocosm experiments simulating the in situ BML summer hypolimnetic oxic-euxinic transition determined sulfur biogeochemical processes and their controlling factors. While mesocosm water caps without FFT amendments experienced limited geochemical and microbial changes during the experimental period, FFT-amended mesocosm water caps evidenced three successive stages of S speciation in ∼30 days: (S1) rising expansion of water cap euxinia from FFT to water surface; enabling (S2) rapid sulfate (SO42-) reduction and sulfide production directly within the water column; fostering (S3) generation and subsequent consumption of sulfur oxidation intermediate compounds (SOI). Identified key SOI, elemental S and thiosulfate, support subsequent SOI oxidation, reduction, and/or disproportionation processes in the system. Dominant water cap microbes shifted from methanotrophs and denitrifying/iron-reducing bacteria to functionally versatile sulfur-reducing bacteria (SRB) comprising sulfate-reducing bacteria (Desulfovibrionales) and SOI-reducing/disproportionating bacteria (Campylobacterales and Desulfobulbales). The observed microbial shift is driven by decreasing [SO42-] and organic aromaticity, with putative hydrocarbon-degrading bacteria providing electron donors for SRB. Comparison between unsterile and sterile water treatments further underscores the biogeochemical readiness of the in situ water cap to enhance oxidant depletion, euxinia expansion and establishment of water cap SRB communities aided by FFT migration of anaerobes. Results here identify the collective influence of FFT and water cap microbial communities on water cap euxinia expansion associated with sequential S reactions that are controlled by concentrations of oxidants, labile organic substrates and S species. This emphasizes the necessity of understanding this complex S cycling in assessing BML water cap O2 persistence.

The microbiota of moon snail egg collars is shaped by host-specific factors

Moon snails (Family: Naticidae) lay eggs using a mixture of mucus and sediment to form an egg mass commonly referred to as an egg collar. These egg collars do not appear to experience micro-biofouling or predation, and this observation led us to hypothesize that the egg collars possess a chemically rich microbiota that protect the egg collars from pathogens. Herein, we sought to gain an understanding of the bacterial composition of egg collars laid by a single species of moon snails, Neverita delessertiana, by amplifying and sequencing the 16S rRNA gene from the egg collar and sediment samples collected at four distinct geographical regions in southwest Florida. Relative abundance and non-metric multidimensional scaling plots revealed distinct differences in the bacterial composition between the egg collar and sediment samples. In addition, the egg collars had a lower α-diversity than the sediment, with specific genera being significantly enriched in the egg collars. Analysis of microorganisms consistent across two seasons suggests that Flavobacteriaceae make up a large portion of the core microbiota (36%-58% of 16S sequences). We also investigated the natural product potential of the egg collar microbiota by sequencing a core biosynthetic gene, the adenylation domains (ADs), within the gene clusters of non-ribosomal peptide synthetase (NRPS). AD sequences matched multiple modules within known NRPS gene clusters, suggesting that these compounds might be produced within the egg collar system. This study lays the foundation for future studies into the ecological role of the moon snail egg collar microbiota.IMPORTANCEAnimals commonly partner with microorganisms to accomplish essential tasks, including chemically defending the animal host from predation and/or infections. Understanding animal-microbe partnerships and the molecules used by the microbe to defend the animals from pathogens or predation has the potential to lead to new pharmaceutical agents. However, very few of these systems have been investigated. A particularly interesting system is nutrient-rich marine egg collars, which often lack visible protections, and are hypothesized to harbor beneficial microbes that protect the eggs. In this study, we gained an understanding of the bacterial strains that form the core microbiota of moon snail egg collars and gained a preliminary understanding of their natural product potential. This work lays the foundation for future work to understand the ecological role of the core microbiota and to study the molecules involved in chemically defending the moon snail eggs.

Microbial community acclimation during anaerobic digestion of high-oil food waste

Anaerobic digestion is one of the most promising options for the disposal of biodegradable food waste. However, the relatively high content of oil in food waste inhibits the conversion efficiency of anaerobic digestion because of the accumulation of long-chain fatty acids (LCFAs). In this study, activated anaerobic sludge was acclimated to accommodate high-oil conditions. The methane yield of high-oil food waste digested by the acclimated sludge increased by 24.9% compared to that digested by the raw sludge. To determine the internal changes in the acclimated sludge, the shifts in the microbial communities during the acclimation period were investigated via high-throughput sequencing (HTS) based on the 16 S rRNA gene. The results indicated that Bacteroidetes, Firmicutes, Chloroflexi and Proteobacteria were the dominant bacteria at the phylum level. The acclimation time allows some functional bacterial taxa to proliferate, such as Clostridium and Longilinea, which are able to degrade LCFAs and turn them into small organic molecules that also have nutrient value for other bacteria. Among the archaeal communities, the hydrogenotrophic methanogen Methanobacterium nearly supplanted the acetotrophic methanogen Methanosaeta. The time profiles of volatile fatty acids (VFAs) and pH during this period provided additional evidence for the success of the acclimation. This study demonstrated the effectiveness of acclimation and the dynamic of microbial communities, which further contributed to the management and resource utilization of high-oil food waste.

A survey of the Desulfuromonadia "cytochromome" provides a glimpse of the unexplored diversity of multiheme cytochromes in nature

BACKGROUND

Multiheme cytochromes c (MHC) provide prokaryotes with a broad metabolic versatility that contributes to their role in the biogeochemical cycling of the elements and in energy production in bioelectrochemical systems. However, MHC have only been isolated and studied in detail from a limited number of species. Among these, Desulfuromonadia spp. are particularly MHC-rich. To obtain a broad view of the diversity of MHC, we employed bioinformatic tools to study the cytochromome encoded in the genomes of the Desulfuromonadia class.

RESULTS

We found that the distribution of the MHC families follows a different pattern between the two orders of the Desulfuromonadia class and that there is great diversity in the number of heme-binding motifs in MHC. However, the vast majority of MHC have up to 12 heme-binding motifs. MHC predicted to be extracellular are the least conserved and show high diversity, whereas inner membrane MHC are well conserved and show lower diversity. Although the most prevalent MHC have homologues already characterized, nearly half of the MHC families in the Desulforomonadia class have no known characterized homologues. AlphaFold2 was employed to predict their 3D structures. This provides an atlas of novel MHC, including examples with high beta-sheet content and nanowire MHC with unprecedented high numbers of putative heme cofactors per polypeptide.

CONCLUSIONS

This work illuminates for the first time the universe of experimentally uncharacterized cytochromes that are likely to contribute to the metabolic versatility and to the fitness of Desulfuromonadia in diverse environmental conditions and to drive biotechnological applications of these organisms.

Phenotypic and Genomic Characterization of a Sulfate-Reducing Bacterium Pseudodesulfovibrio methanolicus sp. nov. Isolated from a Petroleum Reservoir in Russia

The search for the microorganisms responsible for sulfide formation and corrosion of steel equipment in the oil fields of Tatarstan (Russia) resulted in the isolation of a new halotolerant strictly anaerobic sulfate-reducing bacterium, strain 5S69T. The cells were motile curved Gram-negative rods. Optimal growth was observed in the presence of 2.0-4.0% (w/v) NaCl, at pH 6.5, and at 23-28 °C under sulfate-reducing conditions. The isolate was capable of chemoorganotrophic growth with sulfate and other sulfoxides as electron acceptors, resulting in sulfide formation; and of pyruvate fermentation resulting in formation of H2 and acetate. The strain utilized lactate, pyruvate, ethanol, methanol, fumarate, and fructose, as well as H2/CO2/acetate for sulfate reduction. The genome size of the type strain 5S69T was 4.16 Mb with a G + C content of 63.0 mol%. On the basis of unique physiological properties and results of the 16S rRNA gene-based phylogenetic analysis, phylogenomic analysis of the 120 conserved single copy proteins and genomic indexes (ANI, AAI, and dDDH), assigning the type strain 5S69T ((VKM B-3653T = KCTC 25499T) to a new species within the genus Pseudodesulfovibrio, is suggested, with the proposed name Pseudodesulfovibrio methanolicus sp. nov. Genome analysis of the new isolate showed several genes involved in sulfate reduction and its sulfide-producing potential in oil fields with high saline formation water.

The Predatory Properties of Bradymonabacteria, the Representative of Facultative Prey-Dependent Predators

Bradymonabacteria, as the representative of the facultative prey-dependent predators, were re-classified from the preceding Deltaproteobacteria into the phylum Myxococcota and proposed as a novel class named Bradymonadia. However, it was ambiguous whether their predatory pattern and properties were similar to those of the other myxobacterial predators. Therefore, the physiologic features were compared to determine the similarities and differences during the process of group attack and kin discrimination. Comparative genomic analyses were performed to conclude the core genome encoded commonly by bradymonabacteria, Myxococcia, and Polyangia. In conclusion, we proposed that bradymonabacteria have a predation pattern similar to the that of the representative of opportunistic predators like Myxococcus xanthus but with some subtle differences. Their predation was predicted to be initiated by the needle-less T3SS*, and the S-motility mediated by T4P also participated in the process. Meanwhile, their group attacks relied on cell contact and cell destiny. Inter-species (strains) kin discriminations occurred without the existence of T6SS. However, no extracellular lethal substance was detected in the fermentation liquor culture of bradymonabacteria, and the death of prey cells could only be observed when touched by their cells. Moreover, the prey-selective predation was observed when the predator encountered certain prey from Bacillus (G+), Algoriphagus (G-), and Nocardioides (G+). Bradymonabacteria can be regarded as a potential consumer and decomposer, and preying on many sea-dwelling or human pathogenic bacteria allows this group a broad application prospect in marine culture and clinical disease control. Our study will provide more evidence for its exploitations and applications.

Two marine sulfur-reducing bacteria co-culture is essential for productive infection by a T4-like Escherichia coli-infecting phage

The control of microbiologically influenced corrosion (MIC) challenges the oil exploration sector. The MIC results from electrochemical reactions facilitated by microorganisms such as sulfate-reducing bacteria (SRB), which adhere to the surface of the ducts forming biofilms. SRB uses sulfate as the final electron acceptor, resulting in hydrogen sulfide as the final product, a highly reactive corrosive, and toxic compound. Due to the high diversity of the SRB group, this study evaluated the effect of an Escherichia coli phage, with biofilm degrading enzymes, in preventing biofilm formation by microbial consortium P48SEP and reducing H2S production in a complex SRB community. Three phage concentrations were evaluated (104, 108 and 1012 UFP/ml). High and medium phage concentrations prevented biofilm development, as evidenced by scanning electron microscopy, chemical analysis, and cell counts. In addition, the virus altered the expression pattern of some bacterial genes and the relative abundance of proteins related to biofilm formation and cell stress response. Using a complex culture formed mainly by SRB, it was possible to observe the bacterial growth, H2S, and metabolic activity reduction after the phage was added. This study shows for the first time the ability of an E. coli-infecting phage to prevent the biofilm formation of an SRB consortium and infect and replicate at high concentrations on the non-specific host. This new finding turns the use of non-specific phages a promising alternative for the control of biocorrosion in oil and gas installations, on the other side, alert to the use of large concentration of phages and the influence on bacterial groups with geological importance, opening a research field in phage biology.

Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete

The deterioration of fibre-reinforced sprayed concrete was studied in the Oslofjord subsea tunnel (Norway). At sites with intrusion of saline groundwater resulting in biofilm growth, the concrete exhibited significant concrete deterioration and steel fibre corrosion. Using amplicon sequencing and shotgun metagenomics, the microbial taxa and surveyed potential microbial mechanisms of concrete degradation at two sites over five years were identified. The concrete beneath the biofilm was investigated with polarised light microscopy, scanning electron microscopy and X-ray diffraction. The oxic environment in the tunnel favoured aerobic oxidation processes in nitrogen, sulfur and metal biogeochemical cycling as evidenced by large abundances of metagenome-assembled genomes (MAGs) with potential for oxidation of nitrogen, sulfur, manganese and iron, observed mild acidification of the concrete, and the presence of manganese- and iron oxides. These results suggest that autotrophic microbial populations involved in the cycling of several elements contributed to the corrosion of steel fibres and acidification causing concrete deterioration.

Microbiome as an endocrine organ and its relationship with eye diseases: Effective factors and new targeted approaches

Microbiome is an endocrine organ that refers to both the complicated biological system of microbial species that colonize our bodies and their genomes and surroundings. Recent studies confirm the connection between the microbiome and eye diseases, which are involved in the pathogenesis of eye diseases, including age-related macular disorders, diabetic retinopathy, glaucoma, retinitis pigmentosa, dry eye, and uveitis. The aim of this review is to investigate the microbiome in relation to eye health. First, a brief introduction of the characteristics of the gut microorganisms terms of composition and work, the role of dysbiosis, the gut microbiome and the eye microbiome in the progression of eye illnesses are highlighted, then the relationship among the microbiome and the function of the immune system and eye diseases, the role of inflammation and aging and the immune system, It has been reviewed and finally, the control and treatment goals of microbiome and eye diseases, the role of food factors and supplements, biotherapy and antibiotics in relation to microbiome and eye health have been reviewed.

Seasonal mouse cadaver microbial study: rupture time and postmortem interval estimation model construction

The estimation of postmortem interval (PMI) has long been a focal point in the field of forensic science. Following the death of an organism, microorganisms exhibit a clock-like proliferation pattern during the course of cadaver decomposition, forming the foundation for utilizing microbiology in PMI estimation. The establishment of PMI estimation models based on datasets from different seasons is of great practical significance. In this experiment, we conducted microbiota sequencing and analysis on gravesoil and mouse intestinal contents collected during both the winter and summer seasons and constructed a PMI estimation model using the Random Forest algorithm. The results showed that the MAE of the gut microbiota model in summer was 0.47 ± 0.26 d, R2 = 0.991, and the MAE of the gravesoil model in winter was 1.04 ± 0.22 d, R2 = 0.998. We propose that, in practical applications, it is advantageous to selectively build PMI estimation models based on seasonal variations. Additionally, through a combination of morphological observations, gravesoil microbiota sequencing results, and soil physicochemical data, we identified the time of cadaveric rupture for mouse cadavers, occurring at around days 24-27 in winter and days 6-9 in summer. This study not only confirms previous research findings but also introduces novel insights, contributing to the foundational knowledge necessary to advance the utilization of microbiota for PMI estimation.

What is the Difference between Conventional Drinking Water, Potable Reuse Water, and Nonpotable Reuse Water? A Microbiome Perspective

As water reuse applications expand, there is a need for more comprehensive means to assess water quality. Microbiome analysis could provide the ability to supplement fecal indicators and pathogen profiling toward defining a "healthy" drinking water microbiota while also providing insight into the impact of treatment and distribution. Here, we utilized 16S rRNA gene amplicon sequencing to identify signature features in the composition of microbiota across a wide spectrum of water types (potable conventional, potable reuse, and nonpotable reuse). A clear distinction was found in the composition of microbiota as a function of intended water use (e.g., potable vs nonpotable) across a very broad range of U.S. water systems at both the point of compliance (Betadisper p > 0.01; ANOSIM p < 0.01, r-stat = 0.71) and point of use (Betadisper p > 0.01; ANOSIM p < 0.01, r-stat = 0.41). Core and discriminatory analysis further served in identifying distinct differences between potable and nonpotable water microbiomes. Taxa were identified at both the phylum (Desulfobacterota, Patescibacteria, and Myxococcota) and genus (Aeromonas and NS11.12_marine_group) levels that effectively discriminated between potable and nonpotable waters, with the most discriminatory taxa being core/abundant in nonpotable waters (with few exceptions, such as Ralstonia being abundant in potable conventional waters). The approach and findings open the door to the possibility of microbial community signature profiling as a water quality monitoring approach for assessing efficacy of treatments and suitability of water for intended use/reuse application.

Age and environment are the main drivers shaping the wild common sole (Solea solea) microbiota

Microbiota plays an essential role in fish growth and health and may be influenced by the changing environmental conditions. Here, we explored the microbiota of wild common sole, one of the most important fishery resources in the Mediterranean Sea, collected from different areas in the North Adriatic Sea. Our results show that the sole microbiota differs from that of the surrounding environment and among the different body sites (gill, skin and gut). Gut microbiota composition showed to be strongly related to fish age, rather than maturity, sex or sampling site. Age-related shifts in gut microbial communities were identified, with increased abundances of Bacteroidia and Desulfobacteria, unveiling potential microbial proxies for age estimation crucial for fisheries management. Our results expand the limited knowledge of the wild common sole microbiota, also in the light of the potential usefulness of the fish microbiota as a tool for future stock identification and connectivity studies.

Characterization of bacterial communities associated with seabed sediments in offshore and nearshore sites to improve Microbiologically Influenced Corrosion mitigation on marine infrastructures

Microbiologically Influenced Corrosion (MIC) is one of the main threats for marine infrastructures, leading to severe safety and environmental risks associated with structural failures and/or leakages of dangerous fluids, together with potential huge economic losses and reputational damage for the involved parts. For a safe design and a proper installation of infrastructure systems in contact with the seabed, a deep knowledge of the site-specific microbial community of the sediments should be beneficial. Therefore, in addition to the simple detection or the sole quantification of Sulphate-Reducing Bacteria (SRB), the whole characterization of the microbial members involved in MIC phenomena is desirable. In this study, 16S rRNA-based comparison between bacterial communities thriving in offshore and nearshore marine sediments was performed, with a focus on the main bacterial groups putatively responsible for MIC. The nearshore sediments were significantly enriched in bacterial members associated with human and organic compounds contamination belonging to the Bacteroidota, Desulfobacterota, and Firmicutes phyla, while the offshore sediments hosted Alphaproteobacteria, Nitrospinota, and Nitrospirota members, representative of a low anthropogenic impact. Quantitative PCR targeting the dsrA gene and detailed community analyses revealed that the nearshore sediments were significantly enriched in SRB mainly affiliated to the Desulfobulbus and Desulfosarcina genera potentially involved in biocorrosion, compared to the offshore ones. These results suggest that the bacterial community associated with the high concentration of organic compounds derived by an elevated anthropogenic impact is likely to favour MIC. Such observations highlight the importance of microbiological investigations as prevention strategy against MIC processes, aiming both at characterizing sites for the establishment of new infrastructures and at monitoring those already installed.

The dynamic history of prokaryotic phyla: discovery, diversity and division

Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.

Methanogenesis coupled hydrocarbon biodegradation enhanced by ferric and sulphate ions

Bioremediation provides an environmentally sound solution for hydrocarbon removal. Although bioremediation under anoxic conditions is slow, it can be coupled with methanogenesis and is suitable for energy recovery. By altering conditions and supplementing alternative terminal electron acceptors to the system to induce syntrophic partners of the methanogens, this process can be enhanced. In this study, we investigated a hydrocarbon-degrading microbial community derived from chronically contaminated soil. Various hydrocarbon mixtures were used during our experiments in the presence of different electron acceptors. In addition, we performed whole metagenome sequencing to identify the main actors of hydrocarbon biodegradation in the samples. Our results showed that the addition of ferric ions or sulphate increased the methane yield. Furthermore, the addition of CO2, ferric ion or sulphate enhanced the biodegradation of alkanes. A significant increase in biodegradation was observed in the presence of ferric ions or sulphate in the case of all aromatic components, while naphthalene and phenanthrene degradation was also enhanced by CO2. Metagenome analysis revealed that Cellulomonas sp. is the most abundant in the presence of alkanes, while Ruminococcus and Faecalibacterium spp. are prevalent in aromatics-supplemented samples. From the recovery of 25 genomes, it was concluded that the main pathway of hydrocarbon activation was fumarate addition in both Cellulomonas, Ruminococcus and Faecalibacterium. Chloroflexota bacteria can utilise the central metabolites of aromatics biodegradation via ATP-independent benzoyl-CoA reduction. KEY POINTS: • Methanogenesis and hydrocarbon biodegradation were enhanced by Fe3+ or SO42- • Cellulomonas, Ruminococcus and Faecalibacterium can be candidates for the main hydrocarbon degraders • Chloroflexota bacteria can utilise the central metabolites of aromatics degradation.

Alteration of ascending colon mucosal microbiota in patients after cholecystectomy

BACKGROUND

Cholecystectomy is a successful treatment option for gallstones, although the incidence of colorectal cancer (CRC) has notably increased in post-cholecystectomy (PC) patients. However, it remains uncertain whether the altered mucosal microbiota in the ascending colon is related.

AIM

To investigate the potential correlation between gut microbiota and the surgical procedure of cholecystectomy.

METHODS

In total, 30 PC patients and 28 healthy controls underwent colonoscopies to collect mucosal biopsy samples. PC patients were divided based on their clinical features. Then, 16S-rRNA gene sequencing was used to analyze the amplicon, alpha diversity, beta diversity, and composition of the bacterial communities. Additionally, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) database, sourced from the Kyoto Encyclopedia of Genes and Genomes, was used to predict the functional capabilities of the bacteria.

RESULTS

PC patients were comparable with healthy controls. However, PC patients older than 60 years had a distinct composition compared to those under 60 years old. Bacteroidetes richness was considerably higher at the phylum level in PC patients. Bacteroides, Parabacteroides, and Bilophila were more abundant in the PC group than in the control group. Furthermore, PC patients exhibited greater enrichment in metabolic pathways, specifically those related to lipopolysaccharide biosynthesis and vancomycin group antibiotic production, than controls.

CONCLUSION

This study indicated that the mucosal microbiota in PC patients was altered, perhaps offering new perspectives on the treatment possibilities for CRC and diarrhea following cholecystectomy.

Flagellar stator genes control a trophic shift from obligate to facultative predation and biofilm formation in a bacterial predator

The bacterial predator Bdellovibrio bacteriovorus is considered to be obligatorily prey (host)-dependent (H-D), and thus unable to form biofilms. However, spontaneous host-independent (H-I) variants grow axenically and can form robust biofilms. A screen of 350 H-I mutants revealed that single mutations in stator genes fliL or motA were sufficient to generate flagellar motility-defective H-I strains able to adhere to surfaces but unable to develop biofilms. The variants showed large transcriptional shifts in genes related to flagella, prey-invasion, and cyclic-di-GMP (CdG), as well as large changes in CdG cellular concentration relative to the H-D parent. The introduction of the parental fliL allele resulted in a full reversion to the H-D phenotype, but we propose that specific interactions between stator proteins prevented functional complementation by fliL paralogs. In contrast, specific mutations in a pilus-associated protein (Bd0108) mutant background were necessary for biofilm formation, including secretion of extracellular DNA (eDNA), proteins, and polysaccharides matrix components. Remarkably, fliL disruption strongly reduced biofilm development. All H-I variants grew similarly without prey, showed a strain-specific reduction in predatory ability in prey suspensions, but maintained similar high efficiency in prey biofilms. Population-wide allele sequencing suggested additional routes to host independence. Thus, stator and invasion pole-dependent signaling control the H-D and the H-I biofilm-forming phenotypes, with single mutations overriding prey requirements, and enabling shifts from obligate to facultative predation, with potential consequences on community dynamics. Our findings on the facility and variety of changes leading to facultative predation also challenge the concept of Bdellovibrio and like organisms being obligate predators.

IMPORTANCE

The ability of bacteria to form biofilms is a central research theme in biology, medicine, and the environment. We show that cultures of the obligate (host-dependent) "solitary" predatory bacterium Bdellovibrio bacteriovorus, which cannot replicate without prey, can use various genetic routes to spontaneously yield host-independent (H-I) variants that grow axenically (as a single species, in the absence of prey) and exhibit various surface attachment phenotypes, including biofilm formation. These routes include single mutations in flagellar stator genes that affect biofilm formation, provoke motor instability and large motility defects, and disrupt cyclic-di-GMP intracellular signaling. H-I strains also exhibit reduced predatory efficiency in suspension but high efficiency in prey biofilms. These changes override the requirements for prey, enabling a shift from obligate to facultative predation, with potential consequences on community dynamics.

Eddy-driven diazotroph distribution in the subtropical North Atlantic: horizontal variability prevails over particle sinking speed

Mesoscale eddies influence the distribution of diazotrophic (nitrogen-fixing) cyanobacteria, impacting marine productivity and carbon export. Non-cyanobacterial diazotrophs (NCDs) are emerging as potential contributors to marine nitrogen fixation, relying on organic matter particles for resources, impacting nitrogen and carbon cycling. However, their diversity and biogeochemical importance remain poorly understood. In the subtropical North Atlantic along a single transect, this study explored the horizontal and vertical spatial variability of NCDs associated with suspended, slow-sinking, and fast-sinking particles collected with a marine snow catcher. The investigation combined amplicon sequencing with hydrographic and biogeochemical data. Cyanobacterial diazotrophs and NCDs were equally abundant, and their diversity was explained by the structure of the eddy. The unicellular symbiotic cyanobacterium UCYN-A was widespread across the eddy, whereas Trichodesmium and Crocosphaera accumulated at outer fronts. The diversity of particle-associated NCDs varied more horizontally than vertically. NCDs constituted most reads in the fast-sinking fractions, mainly comprising Alphaproteobacteria, whose abundance significantly differed from the suspended and slow-sinking fractions. Horizontally, Gammaproteobacteria and Betaproteobacteria exhibited inverse distributions, influenced by physicochemical characteristics of water intrusions at the eddy periphery. Niche differentiations across the anticyclonic eddy underscored NCD-particle associations and mesoscale dynamics, deepening our understanding of their ecological role and impact on ocean biogeochemistry.

Unraveling interspecies cross-feeding during anaerobic lignin degradation for bioenergy applications

Lignin, a major component of plant biomass, remains underutilized for renewable biofuels due to its complex and heterogeneous structure. Although investigations into depolymerizing lignin using fungi are well-established, studies of microbial pathways that enable anaerobic lignin breakdown linked with methanogenesis are limited. Through an enrichment cultivation approach with inoculation of freshwater sediment, we enriched a microbial community capable of producing methane during anaerobic lignin degradation. We reconstructed the near-complete population genomes of key lignin degraders and methanogens using metagenome-assembled genomes finally selected in this study (MAGs; 92 bacterial and 4 archaeal MAGs affiliated into 45 and 2 taxonomic groups, respectively). This study provides genetic evidence of microbial interdependence in conversion of lignin to methane in a syntrophic community. Metagenomic analysis revealed metabolic linkages, with lignin-hydrolyzing and/or fermentative bacteria such as the genera Alkalibaculum and Propionispora transforming lignin breakdown products into compounds such as acetate to feed methanogens (two archaeal MAGs classified into the genus Methanosarcina or UBA6 of the family Methanomassiliicoccaceae). Understanding the synergistic relationships between microbes that convert lignin could inform strategies for producing renewable bioenergy and treating aromatic-contaminated environments through anaerobic biodegradation processes. Overall, this study offers fundamental insights into complex community-level anaerobic lignin metabolism, highlighting hitherto unknown players, interactions, and pathways in this biotechnologically valuable process.

The fatal case of "Pigmentibacter" bacteremia following aspiration pneumonia in elderly patient

"Pigmentibacter ruber" was first reported in 2021, a novel bacterium of the family Silvanigrellaceae, isolated from human blood of the patient with aspiration pneumonia after the drowning accident in Republic of China. However, until now, there is only one report describing "P. ruber" infection, and no case of isolation from natural environment has been reported so far. Thus, the infectivity and pathogenicity of "Pigmentibacter" spp. has not been clearly understood. In this report, we described the fatal case of "Pigmentibacter" bacteremia subsequently occurred after aspiration pneumonia probably due to accidental ingestion of irrigation water in the elderly patient. Despite administration of broad-spectrum antibiotic, the patient dramatically deteriorated and eventually deceased. Whole-genome sequencing showed the strain isolated from the patient was identified as "Pigmentibacter" sp. (designated as strain Takaoka) and antimicrobial sensitivity testing showed it displayed high minimum inhibitory concentrations against various antibiotics including β-lactam. Further studies are needed to clarify the clinical characteristics of "Pigmentibacter" and its relative's infections and their antimicrobial sensitivity; however, the present case supported the clinical characteristics of "Pigmentibacter" infection, which can lead to bacteremia following aspiration pneumonia caused by mis-swallowing contaminated water, and poor outcome potentially due to multidrug resistances.