FEMS microbiology ecology最新文献

The adaptation of the phylum Chloroflexota to various geochemical conditions is thought to have originated in primitive microbial ecosystems, involving hydrogenotrophic energy conservation under ferruginous anoxia. Oligotrophic deep waters displaying anoxic ferruginous conditions, such as those of Lake Towuti, and their sediments may thus constitute a preferential ecological niche for investigating metabolic versatility in modern Chloroflexota. Combining pore water geochemistry, cell counts, sulfate reduction rates, and 16S rRNA genes with in-depth analysis of metagenome-assembled genomes, we show that Chloroflexota benefit from cross-feeding on metabolites derived from canonical respiration chains and fermentation. Detailing their genetic contents, we provide molecular evidence that Anaerolineae have metabolic potential to use unconventional electron acceptors, different cytochromes, and multiple redox metalloproteins to cope with oxygen fluctuations, and thereby effectively colonizing the ferruginous sediment-water interface. In sediments, Dehalococcoidia evolved to be acetogens, scavenging fatty acids, haloacids, and aromatic acids, apparently bypassing specific steps in carbon assimilation pathways to perform energy-conserving secondary fermentations combined with CO2 fixation via the Wood-Ljungdahl pathway. Our study highlights the partitioning of Chloroflexota populations according to alternative electron acceptors and donors available at the sediment-water interface and below. Chloroflexota would have developed analogous primeval features due to oxygen fluctuations in ancient ferruginous ecosystems.

Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations. The decrease from 10 to 0.1 µM oxygen (3.6 to 0.036 pO2% present atmospheric level, respectively) caused the upregulation of the transcription of genes involved in signal transduction mechanisms, energy production and conversion and secondary metabolites biosynthesis, transport, and catabolism based on clusters of orthologous group categories. Contrary to established observations for aerobic metabolism, key genes in oxidative stress response were significantly upregulated at lower oxygen concentrations, presumably due to an NADH/NAD+ redox ratio imbalance as the cells transitioned into nanoxia. Furthermore, A. capsulatum adapted to nanoxia by inducing a respiro-fermentative metabolism and rerouting fluxes of its central carbon and energy pathways to adapt to high NADH/NAD+ redox ratios. Our results reveal physiological features and metabolic capabilities that allowed A. capsulatum to adapt to oxygen-limited conditions, which could expand into other environmentally relevant soil strains.

While numerous environmental factors contribute to the spread of antibiotic resistance genes (ARGs), quantifying their relative contributions remains a fundamental challenge. Similarly, it is important to differentiate acute human health risks from environmental exposure, versus broader ecological risk of ARG evolution and spread across microbial taxa. Recent studies have proposed various methods for achieving such aims. Here, we introduce MetaCompare 2.0, which improves upon original MetaCompare pipeline by differentiating indicators of human health resistome risk (potential for human pathogens of acute resistance concern to acquire ARGs) from ecological resistome risk (overall mobility of ARGs and potential for pathogen acquisition). The updated pipeline's sensitivity was demonstrated by analyzing diverse publicly-available metagenomes from wastewater, surface water, soil, sediment, human gut, and synthetic microbial communities. MetaCompare 2.0 provided distinct rankings of the metagenomes according to both human health resistome risk and ecological resistome risk, with both scores trending higher when influenced by anthropogenic impact or other stress. We evaluated the robustness of the pipeline to sequence assembly methods, sequencing depth, contig count, and metagenomic library coverage bias. The risk scores were remarkably consistent despite variations in these technological aspects. We packaged the improved pipeline into a publicly-available web service (http://metacompare.cs.vt.edu/) that provides an easy-to-use interface for computing resistome risk scores and visualizing results.

Uptake hydrogenase (Hup) recycles H2 formed by nitrogenase during nitrogen fixation, thereby preserving energy. Among root nodule bacteria, most rhizobial strains examined are Hup-, while only one Hup-  Frankia inoculum had been identified. Previous analyses had led to the identification of two different [NiFe] hydrogenase syntons. We analysed the distribution of different types of [NiFe] hydrogenase in the genomes of different Frankia species. Our results show that Frankia strains can contain four different [NiFe] hydrogenase syntons representing groups 1f, 1h, 2a, and 3b according to Søndergaard, Pedersen, and Greening (HydDB: a web tool for hydrogenase classification and analysis. Sci Rep 2016;6:34212. https://doi.org/10.1038/srep34212.); no more than three types were found in any individual genome. The phylogeny of the structural proteins of groups 1f, 1h, and 2a follows Frankia phylogeny; the phylogeny of the accessory proteins does not consistently. An analysis of different [NiFe] hydrogenase types in Actinomycetia shows that under the most parsimonious assumption, all four types were present in the ancestral Frankia strain. Based on Hup activities analysed and the losses of syntons in different lineages of genome reduction, we can conclude that groups 1f and 2a are involved in recycling H2 formed by nitrogenase while group 1 h and group 3b are not.

Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.

Nematodes are common in most terrestrial environments, where populations are often known to undergo cycles of boom and bust. Useful in such scenarios, nematodes present developmental programs of diapause, giving rise to stress-resistant larvae and enabling dispersal in search of new resources. Best studied in Caenorhabditis elegans, stress resistant dauer larvae emerge under adverse conditions, primarily starvation, and migrate to new niches where they can resume development and reproduce. Caenorhabditis elegans is a bacterivore but has been shown to harbor a persistent and characteristic gut microbiome. While much is known about the gut microbiome of reproducing C. elegans, what dauers harbor is yet unknown. This is of interest, as dauers are those that would enable transmission of microbes between nematode generations and geographical sites, maintaining continuity of host-microbe interactions. Using culture-dependent as well as sequencing-based approaches, we examined the gut microbiomes of dauers emerging following population growth on ten different natural-like microbially diverse environments as well as on two defined communities of known gut commensals and found that dauers were largely devoid of gut bacteria. These results suggest that host gut-microbiome interactions in C. elegans are not continuous across successive generations and may reduce the likelihood of long-term worm-microbe coevolution.

Protist communities in the southern Pacific Ocean make a major contribution to global biogeochemical cycling, but remain understudied due to their remote location. We therefore have limited understanding of how large-scale physical gradients (e.g. temperature) and mesoscale oceanographic features (e.g. fronts) influence microeukaryote diversity in this region. We performed a high-resolution examination of protist communities along a latitudinal transect (>3000 km) at 150°W in the central southern Pacific Ocean that encompassed major frontal regions, including the subtropical front (STF), the subantarctic front (SAF), and the polar front (PF). We identified distinct microbial communities along the transect that were primarily delineated by the positions of the STF and PF. Some taxa were not constricted by these environmental boundaries and were able to span frontal regions, such as the colonial haptophyte Phaeocystis. Our findings also support the presence of a latitudinal diversity gradient (LDG) of decreasing diversity of the protist community with increasing latitude, although some individual taxa, notably the diatoms, do not adhere to this rule. Our findings show that oceanographic features and large-scale physical gradients have important impacts on marine protist communities in the southern Pacific Ocean that are likely to strongly influence their response to future environmental change.

Gut microbial diversity influences the health and vitality of the host, yet it is itself affected by internal and external factors, including land-use. The impact of land-use practices on wild rodents' gut microbiomes remains understudied, despite their abundance and potential as reservoirs for zoonotic pathogens. We examined the bacterial and fungal gut microbiomes of bank voles (Myodes glareolus) and common voles (Microtus arvalis) across grassland and forest habitats with varying land-use intensities and types. We collected rodents seasonally and used 16S rRNA and ITS amplicon sequencing for microbe identification. We found significant differences in alpha and beta diversities between the species, with M. arvalis exhibiting higher diversity. Seasonality emerged as a prominent factor influencing microbial diversity, with significant variations between sampling months. While land-use affects the gut microbiome, its impact is subordinate to seasonal variations. Differential abundance analysis underscores the dynamic nature of microbial composition, with seasonal changes playing a predominant role. Overall, our findings highlight the significant influence of seasonality on gut microbiome diversity and composition in wild rodents, reflecting dietary shifts associated with seasonal changes. Understanding the interplay between environmental factors and microbial communities in wild rodents enahnces our knowledge of ecosystem health and resilience, warranting further investigation.

Along the river-sea continuum, microorganisms are directionally dispersed by water flow while being exposed to strong environmental gradients. To compare the two assembly mechanisms that may strongly and differently influence metacommunity dynamics, namely homogenizing dispersal and heterogeneous selection, we characterized the total (16S rRNA gene) and putatively active (16S rRNA transcript) bacterial communities in the Pearl River-South China Sea Continuum, during the wet (summer) and dry (winter) seasons using high-throughput sequencing. Moreover, well-defined sampling was conducted by including freshwater, oligohaline, mesohaline, polyhaline, and marine habitats. We found that heterogeneous selection exceeded homogenizing dispersal in both the total and active fractions of bacterial communities in two seasons. However, homogeneous selection was prevalent (the dominant except in active bacterial communities during summer), which was primarily due to the bacterial communities' tremendous diversity (associated with high rarity) and our specific sampling design. In either summer or winter seasons, homogeneous and heterogeneous selection showed higher relative importance in total and active communities, respectively, implying that the active bacteria were more responsive to environmental gradients than were the total bacteria. In summary, our findings provide insight into the assembly of bacterial communities in natural ecosystems with high spatial connectivity and environmental heterogeneity.

Particle-attached bacterial (PAB) communities play pivotal roles in water organic matter decomposition, nutrient cycling, and the natural self-purification processes. However, we know little about their responses to seasonal environmental fluctuations, under eutrophication in reservoir ecosystems. In this study, we studied the shifts of PAB communities to seasonal environmental fluctuations in tropical China. Trophic state index (TSI) indicated that the studied reservoirs ranged from mesotrophic to eutrophic state with a gradual increase in TSI from 31 to 58. In eutrophic reservoirs, Cyanobacteria, especially Raphidiopsis raciborskii, significantly increased in its relative abundance from wet to dry season, but Synechococcales and Microcystaceae decreased. In contrast, the relative abundance of Clostridia, Bacilli, Coriobacteriia, Enterobacteriales, and Vibrionales were more susceptible to seasonal environmental fluctuations in mesotrophic than eutrophic reservoirs. PAB co-occurrence relationships in mesotrophic reservoirs varied more greatly in response to seasonal environmental fluctuations, compared with eutrophic reservoirs, in terms of topological properties of connectedness, average degree, robustness and vulnerability. Our results further demonstrated that the seasonal stability of PAB co-occurrence relationships was strongly correlative with TSI through mediating key bacterial taxa and community biodiversity. We proposed that eutrophication dramatically reduced the seasonal variation of PAB community compositions and co-occurring relationships in reservoir ecosystems.