Genome analysis of the candidate phylum MBNT15 bacterium from a boreal peatland predicted its respiratory versatility and dissimilatory iron metabolism

Nitrogen, sulfur, iron, and microbial communities co-shape the seasonal biogeochemical behaviors of As and Sb in coastal tidal flat wetlands associated with rivers

Arsenic (As) and antimony (Sb) are affected by complex biogeochemical processes in coastal ecosystems. However, the influence of N, S, Fe, and microbial communities on the biogeochemistry of As and Sb in coastal tidal flat wetlands remain uncertain, particularly when rivers flow into these areas. This study combined diffusive gradients in the thin-film technique with high-throughput sequencing to investigate the release and vertical distribution of As and Sb in river and coastal tidal flat wetland sediments. The results indicated a distinct stratification phenomenon in the As release at depths ranging from 20 mm to -150 mm. At river sites, the release of As occurred in the upper layer (above -40 mm), with peak values of 4.3 and 9.3 μg/L at HS and SY sites in summer, respectively, likely due to anaerobic ammonium oxidation. In the lower layer (below -40 mm), both As and Sb were released, and this was possibly due to Fe reduction. However, at the coastal tidal flat sites, the release of As and Sb may have been driven by anaerobic ammonium oxidation, dissimilatory nitrate reduction to ammonium, sulfate reduction, and Fe reduction. At the river sites, As exhibited increased activity during the summer, and the residual forms were converted more easily into mobile forms. Sb remained relatively stable during both winter and summer. Conversely, both As and Sb primarily existed in residual forms and exhibited higher stability during summer in the coastal tidal flat sites. The microbial phyla Nitrospirota (3.6-7.0 %) and Acidobacteriota (9.5-10.2 %) were more prevalent at the river sites, whereas Desulfobacterota (8.8-12.0 %) and Firmicutes (0.13-27.9 %) were more prevalent at the coastal tidal flat sites. The bacterial genera involved in the N, S, and Fe transformation processes differed between the two sites, and they were primarily Thiobacillus, Limnobacter, and Sulfurovum at the river sites and Sva1033, Anaeromyxobacter, and Sva0485 at the coastal tidal flat sites. In this study, the microorganisms that mediated N, S, and Fe complex processes at various depths in the sediment-water interface were decoupled to elucidate the effect of these processes on the biogeochemical behavior of As and Sb as they move from rivers to coastal tidal flat wetlands.

Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities

Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.

Vertical distribution characteristics of microplastics and bacterial communities in the sediment columns of Jianhu lake in China

Microorganisms change the properties of microplastics, at the same time, microplastics can also affect the distribution of microorganisms. To investigate this issue, we chose to study Jianhu Lake, a plateau lake in southwestern China, by collecting data at three sampling locations. The microplastics and bacterial communities in the sediment columns of Jianhu Lake were sampled within a 0 to 60 cm profile, and the basic characteristics of microplastic abundance, shape, color, size, and polymer type were determined accordingly, via their collection, separation, extraction, and identification. The bacterial community in the sediment samples were identified using 16S rRNA high-throughput sequencing, and we assessed whether those microplastic characteristics influenced the community composition and structure. We found the abundance of microplastics ranged from 624 to 3050 particles/kg (dw [dry weight]) in the three sediment columns. Line microplastics accounted for the largest proportion and these were found distributed in each layer. The polymer types present in the largest proportions were rayon (RY), polyester terephthalate (PET) and low-density styrene-butadiene-styrene (SBS). Among the bacterial communities in the sediment columns, the dominant phyla were Chloroflexi, Sva0485, Acidobacteriota, etc. The co-occurrence network analysis between the bacterial community and microplastic features in the sediment columns of Jianhu Lake revealed that there was a correlation between them, and the network were more complex at a depth of 20-40 cm. Our results demonstrate that microplastics can affect the diversity and structural characteristics of microbial communities in a lake ecosystem.

Foliar spraying of carbon dots reduces cadmium accumulation in rice by regulating rhizosphere immobilization, root development, and subcellular distribution

Cadmium (Cd) is a toxic heavy metal widespread in rice paddies and threatens food safety and human health. Foliar exposure represents a cost-effective, simple, and time-independent approach to enhance rice resistance and minimize Cd accumulation. Herein, foliar spraying of carbon dots (CDs) was found to significantly reduce Cd accumulation in rice roots and shoots by 31.51 % and 17.93 %, respectively. Gene expression and mineral nutrient analyses indicated that CDs exposure inhibited Cd uptake by suppressing OsNramp1 and increasing competition of Fe and Mn with Cd for OsNramp5. Besides, CDs exposure down-regulated OsHMA2 for Cd transport from roots to aerial parts and up-regulated OsHMA3 for Cd vacuole sequestration. Additionally, CDs treatment promoted rice root development by increasing root biomass, cell walls, and mechanical resistance, which helped to anchor rice plants and impede Cd uptake. Furthermore, CDs spraying increased the organic carbon content and altered the microbial communities in the rice rhizosphere by increasing root exudation. This process facilitated the binding of dissolved Cd in pore water to organic matter and iron‑manganese oxides, ultimately reducing the bioavailability of Cd. This study underscores the effectiveness and mechanism of simple foliar spraying of CDs to mitigate Cd accumulation in rice.

Evaluation of biofilm assembly and microbial diversity on a freshwater, ferrous-hulled shipwreck

Abandoned shipwrecks are sitting at the bottom of oceans, lakes, and rivers around the world. Over time, microbial-comprised biofilms can help protect wrecks against chemical corrosion or contribute to their deterioration through microbiologically influenced corrosion (MIC) by organisms including iron-oxidizing bacteria (FeOB) and sulfate-reducing bacteria (SRB). Assessing the community assembly of these biofilms will give us a better understanding of the role these microbes play in MIC and the factors that influence it. Here, we determine if microbial community composition differs across a shallow freshwater ferrous-hulled shipwreck environment. Results suggest that there was a statistically significant difference among the sample types indicating the wreck environments around Accomac influenced the community composition. This is consistent with previous observations within an estuarine, shallow-water wreck environment. Bacteroidota, Chloroflexota, and Cyanobacteriota were the primary taxa responsible for differences among these wreck environments. Interestingly, port-side biofilm communities were significantly different than those on the starboard side suggesting physical factors of the environment drove niche partitioning on each side of the wreck. Similarly, FeOB enrichments and known FeOB taxa were found across the entire wreck but were primarily found in samples associated with the port side of the wreck. Amplicon sequencing identified both known FeOB and SRB taxa with a higher proportion of FeOB than SRB. Overall, these results indicate that there is niche partitioning of the microbial communities as well as with corrosion-causing taxa within a shallow freshwater wreck site which may lead to variation in how microbes may contribute to the protection or deterioration of these ferrous-hulled wrecks.

IMPORTANCE

The overall structure, abundance, and diversity of microbial communities on shipwrecks have recently been studied in marine aquatic environments. While previous studies have looked at the microbial communities associated with shallow-water ferrous-hulled wrecks in marine environments, studies focusing on freshwater wreck systems are limited. The purpose of this study was to determine microbial community diversity and composition trends across the Accomac shipwreck environment. Furthermore, shipwrecks are colonized by corrosion-causing taxa, such as iron-oxidizing bacteria and sulfate-reducing bacteria which have been shown to influence the biocorrosion of ferrous-hulled structures. Identification of various microbes in biofilms, as well as corrosion-causing microbes, can help researchers identify the role they play in aquatic ecosystem development and persistence as well as artificial reef integrity. Understanding how microbes assemble on wrecks will provide insight into preservation strategies to prevent deterioration of these wrecks over time, as well as limiting biocorrosion of similar structures.

Enhancing Photosynthetic Carbon Transport in Rice Plant Optimizes Rhizosphere Bacterial Community in Saline Soil

Saline soils exert persistent salt stress on plants that inhibits their ability to carry out photosynthesis and leads to photosynthetic carbon (C) scarcity in plant roots and the rhizosphere. However, it remains unclear how a rhizosphere environment is shaped by photosynthetic C partitioning under saline conditions. Given that sucrose is the primary form of photosynthetic C transport, we, respectively, created sucrose transport distorted (STD) and enhanced (STE) rice lines through targeted mutation and overexpression of the sucrose transporter gene OsSUT5. This approach allowed us to investigate different scenarios of photosynthate partitioning to the rhizosphere. Compared to the non-saline soil, we found a significant decrease in soil dissolved organic carbon (DOC) in the rhizosphere, associated with a reduction in bacterial diversity when rice plants were grown under moderate saline conditions. These phenomena were sharpened with STD plants but were largely alleviated in the rhizosphere of STE plants, in which the rhizosphere DOC, and the diversity and abundances of dominant bacterial phyla were measured at comparable levels to the wildtype plants under non-saline conditions. The complexity of bacteria showed a greater level in the rhizosphere of STE plants grown under saline conditions. Several salt-tolerant genera, such as Halobacteroidaceae and Zixibacteria, were found to colonize the rhizosphere of STE plants that could contribute to improved rice growth under persistent saline stresses, due to an increase in C deposition.

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.

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.

Vanadium nitride decorated carbon cloth anode promotes aniline degradation and electricity generation of MFCs by efficiently enriching electroactive bacteria and promoting extracellular electron transfer

To increase the colonization of electroactive bacteria and accelerate the rate of extracellular electron transfer, a simple coated anode of microbial fuel cell was designed. Here, we took advantage of vanadium nitride (VN) particles to modify the carbon cloth (VN@CC). Compared with bare carbon cloth, the designed VN@CC bioanodes exhibited a larger electrochemically active area, better biocompatibility, and smaller charge transfer impedance. The MFC with VN@CC bioanodes achieved the maximum power density of 3.89 W m-2 and chemical oxygen demand removal rate of 84% when 1000 mg L-1 aniline was degraded, which were about 1.88 and 2.8 times that of CC. The morphology of biofilm and 16s rRNA gene sequence analysis proved that the VN@CC bioanodes facilitated the enrichment of electroactive bacteria (99.02%) and increased the ratio of fast electron transfer in the extracellular electron transfer, thus enhancing the MFC performance of aniline degradation and power output. This work disclosed that it was feasible to increase the overall performance of MFC by enhancing the EET efficiency and presented valuable insights for future work.

Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America

As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.