Unveiling The Taxonomic Shifts in Indigenous Bacterial Communities During Textile Sludge Detoxification: A Bacterial Metabarcoding Approach

Legume cover crops are increasingly incorporated into sustainable production systems, yet their influence on rhizosphere microbial communities remains poorly characterized, particularly for underutilized warm-season species. In this study, we investigated rhizosphere bacterial communities associated with cowpea (Vigna unguiculata), tepary bean (Phaseolus acutifolius), and sunn hemp (Crotalaria juncea) in an organic production system using 16S rRNA amplicon sequencing and compared them with fallow soils. All legume species were associated with shifts in bacterial community composition relative to fallow soil, with increased relative abundance of copiotrophic taxa such as Proteobacteria, while fallow soils were dominated by oligotrophic groups within Actinobacteriota. Distinct species-specific recruitment patterns were observed: tepary bean rhizospheres showed higher relative abundance of Rhizobiales, associated with taxa involved in biological nitrogen fixation, whereas cowpea and sunn hemp supported bacterial groups linked to organic matter turnover and plant growth. Weighted UniFrac analyses indicated clear separation between cover-cropped and fallow soils, accounting for approximately 54% of community variation. Functional predictions using PICRUSt2 suggested representation of pathways related to central carbon metabolism, amino acid biosynthesis, and siderophore production under legume rhizospheres. Predicted pathways associated with nitrogen metabolism also tended to be more represented under cover crops, although no pathways remained significant after false discovery rate correction. Overall, these findings indicate that summer legume cover crops are associated with shifts in rhizosphere bacterial communities and predicted functional potential relative to fallow soils. These findings highlight the potential of species selection in shaping rhizosphere microbial communities in organic production systems and provide a foundation for future studies investigating microbial processes associated with cover cropping.

The mammalian gut harbors a complex and specialized microbiota, which includes all tree domains of life (Archaea, Bacteria, and Eukarya). Bacteria are the most abundant group within the gut system, and they take part in metabolic processes that expand the hosts metabolic potential. One of the most beneficial traits of this relationship is that bacteria help to degrade recalcitrant plant materials. In this study, the microbiome of three Eurasian beaver gut systems (male and female subadult, and male juvenile) were analysed by applying metagenomics using 16S rRNA gene marker-based and direct sequencing-based approaches, to gain insights into the diversity, structure and function of the gut-inhabiting bacterial communities and genes involved in cellulose breakdown. Metagenomic DNA was isolated from the entire gut system of three Eurasian beavers, covering different compartments (stomach, small intestine, cecum, and colon). The taxonomic compositions of the bacterial communities within these compartments were assessed using the hypervariable regions V3-V4 of the 16S rRNA gene, amplified from the isolated DNA by PCR. Subsequently, amplicon-based analysis of 2,599,870 high-quality paired end reads revealed 277 unique OTUs in the entire dataset. The bacterial diversity in the cecum and colon was higher in the male subadult beaver than in the female subadult and male juvenile beaver. The gut bacterial community was dominated by Firmicutes and Actinobacteria, followed by Proteobacteria, Verrucomicrobia, Fusobacteria, Bacteroidetes, and Tenericutes. A bacterial community shift from the juvenile to subadult beaver was indicated by the decrease of members of Bacteroidetes and an increase in Verrucomicrobia members. In addition, the presence and abundance of some phyla could be associated with sex, e.g. Fusobacteria, were detected in both male beavers but not in the female. However, further studies of Eurasian beaver gut microbial communities are necessary to confirm these trends. The presence of Clostridiaceae 1, Lachnospiraceae, and Ruminococcaceae in the cecum and colon of the beaver indicated that plant cell wall breakdown is mainly performed in these compartments. The predicted functional profiles showed an increased relative abundance in genes necessary for cellulose breakdown and uptake of degradation products, which is in accordance to the presence of potential cellulolytic bacterial species. The abundance of unclassified Clostridiaceae 1, Lachnospiraceae, and Ruminococcaceae in the cecum and colon of the beaver as well as unclassified Bacteroidaceae in juvenile beaver suggest the presence of novel species exhibiting cellulolytic activity. In comparison to its North American relative, the Eurasian beaver has a higher relative abundance of Actinobacteria and Verrucomicrobia, and a lower abundance of Bacteroidetes in the gut system. In addition, high relative abundances of Ruminococcaceae and Lachnospiraceae were detected in the cecum and colon compartments of the Eurasian North American beaver (NAGrun). In general, the bacterial community structure in the cecum was similar to that of the colon in both the Eurasian and North American beavers. In-depth analysis of the microbiome of the back cecum and lower colon of both subadult beavers was performed through direct metagenome sequencing. A total of 6,200,436 high-quality paired-end reads were obtained. Metagenome assembly resulted in a total of 101,060 contigs with the largest contig of 198,219 bp. The bacterial community structure derived from the metagenome sequencing differed to that based on amplicon sequencing. The relative abundance of Proteobacteria was higher in the metagenome sequences. However, Proteobacteria, Firmicutes, and Actinobacteria remained the dominant phyla. The functional analysis of the metagenomes indicates the metabolic ability of the Eurasian beaver gut microbiome to neutralize toxic compounds from plants and heavy metals, as well as resistance to pathogens and antibiotics. Functional analysis revealed a high diversity of CAZymes, especially glycoside hydrolases (GHs) for the degradation of polysaccharides. A high relative abundance of genes associated to the cellulolytic process, especially GH3 and GH5 family members, was detected in the metagenomes. In addition, the CAZyme family involved in lignin breakdown, AA2, and an annotated DyP-like protein responsible for lignin degradation were also present in the gut microbiome of the beaver. Through combination of marker gene community analysis and metagenome analysis, a novel cellulase from GH family 5 was identified and isolated. The beaver cellulase candidate 33 (BC33) was characterized and exhibit optimal catalytic activity at pH 4 and 60 °C, with high affinity towards barley glucan (Km 0.205 ± 0.022 µM/min, Vmax 0.732 ± 0.026 µM/min). Since Eurasian beaver gut system is mainly an anoxic environment, the anaerobic cellulolytic bacteria, e.g. Clostridia could also produce cellulosomes. Parts of the building block for cellulosomes such as dockerin and cohesin were present in the Eurasian beaver gut metagenomes. Further studies are needed to confirm the existence of cellulosome system and to identify which CAZymes families are bound to the cellulosome, thus, enabling a better understanding of plant material digestion in the Eurasian beaver gut.

In this study, we examined the responses by the indigenous bacterial communities in salt-marsh sediment microcosms in vitro following treatment with Mississippi Canyon Block 252 oil (MC252). Microcosms were constructed of sediment and seawater collected from Bayou La Batre located in coastal Alabama on the Gulf of Mexico. We used an amplicon pyrosequencing approach on microcosm sediment metagenome targeting the V3–V5 region of the 16S rRNA gene. Overall, we identified a shift in the bacterial community in three distinct groups. The first group was the early responders (orders Pseudomonadales and Oceanospirillales within class Gammaproteobacteria), which increased their relative abundance within 2 weeks and were maintained 3 weeks after oil treatment. The second group was identified as early, but transient responders (order Rhodobacterales within class Alphaproteobacteria; class Epsilonproteobacteria), which increased their population by 2 weeks, but returned to the basal level 3 weeks after oil treatment. The third group was the late responders (order Clostridiales within phylum Firmicutes; order Methylococcales within class Gammaproteobacteria; and phylum Tenericutes), which only increased 3 weeks after oil treatment. Furthermore, we identified oil-sensitive bacterial taxa (order Chromatiales within class Gammaproteobacteria; order Syntrophobacterales within class Deltaproteobacteria), which decreased in their population after 2 weeks of oil treatment. Detection of alkane (alkB), catechol (C2,3DO) and biphenyl (bph) biodegradation genes by PCR, particularly in oil-treated sediment metacommunity DNA, delineates proliferation of the hydrocarbon degrading bacterial community. Overall, the indigenous bacterial communities in our salt-marsh sediment in vitro microcosm study responded rapidly and shifted towards members of the taxonomic groups that are capable of surviving in an MC252 oil-contaminated environment.Electronic supplementary materialThe online version of this article (doi:10.1007/s13205-014-0233-x) contains supplementary material, which is available to authorized users.

Vertical, seasonal and geographical patterns in ocean microbial communities have been observed in many studies, but the resolution of community dynamics has been limited by the scope of data sets, which are seldom up to the task of illuminating the highly structured and rhythmic patterns of change found in ocean ecosystems. We studied vertical and temporal patterns in the microbial community composition in a set of 412 samples collected from the upper 300 m of the water column in the northwestern Sargasso Sea, on cruises between 1991 and 2004. The region sampled spans the extent of deep winter mixing and the transition between the euphotic and the upper mesopelagic zones, where most carbon fixation and reoxidation occurs. A bioinformatic pipeline was developed to de-noise, normalize and align terminal restriction fragment length polymorphism (T-RFLP) data from three restriction enzymes and link T-RFLP peaks to microbial clades. Non-metric multidimensional scaling statistics resolved three microbial communities with distinctive composition during seasonal stratification: a surface community in the region of lowest nutrients, a deep chlorophyll maximum community and an upper mesopelagic community. A fourth microbial community was associated with annual spring blooms of eukaryotic phytoplankton that occur in the northwestern Sargasso Sea as a consequence of winter convective mixing that entrains nutrients to the surface. Many bacterial clades bloomed in seasonal patterns that shifted with the progression of stratification. These richly detailed patterns of community change suggest that highly specialized adaptations and interactions govern the success of microbial populations in the oligotrophic ocean.

Summary During soil development, bacteria and fungi can be differentially affected by changes in soil biogeochemistry. Since the chemistry of parent material affects soil pH, nutrient availability, and indirectly litter quality, we hypothesize that parent material has an important influence on microbial community patterns during long‐term soil development. In this paper, we tested for the effect of parent material, as well as, soil and litter properties upon microbial community patterns in three c. 20 000‐year‐old semi‐arid chronosequences developed on sedimentary and volcanic (i.e. Andesitic and Dacitic) soils in the Dry Puna of Bolivia. We evaluated microbial patterns by analysing the terminal restriction fragment length polymorphism from amplified bacterial 16S rRNA genes, and the fungal internal transcribed spacer region, and quantitative real‐time polymerase chain reaction. Soil and litter characteristics differed significantly between the Sedimentary and volcanic chronosequences. In particular, soil pH was alkaline in all stages of the Sedimentary chronosequence; whereas it changed from alkaline to near neutral across stages in both volcanic chronosequences. Composition of bacterial communities changed across volcanic chronosequences, and this change was associated with a reduction in soil pH and increases in litter quality, whereas no differences were found in the Sedimentary chronosequence. Fungal community composition, in contrast, did not change across any chronosequence. Relative microbial abundance, expressed as the fungal:bacterial ratio, declined across stages of the Sedimentary chronosequence in association with decreases in TC and TP, whereas in the Andesitic chronosequence decreases in fungal:bacterial ratios were related with increases in litter quality and declines in soil pH. Synthesis. Our results show the importance of parent material in affecting bacterial and fungal communities during soil development. Further, in semi‐arid chronosequences, fungal:bacterial ratios tend to decline given that soil pH in young soils is rather alkaline. Our results also are consistent with the general framework that highlights the importance of above‐ground (i.e. litter quality) and below‐ground (i.e. soil properties) in affecting microbial relative abundance and community composition during soil development.

Microbial composition and function in reclaimed mine sites along a reclamation chronosequence become increasingly similar to undisturbed reference sites

Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.

Interactions between hosts and associated microbial communities can fundamentally shape the development and ecology of 'holobionts', from humans to marine habitat-forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large-scale drivers of host-associated microbial communities are largely unknown. Using 16S-rRNA gene sequencing, we characterized 260 seaweed-associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a 'core' microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale.

Microbial communities play crucial roles in ecosystem functioning, yet their diversity and assembly in urban turfgrass systems remain underexplored. In 2017, microbial communities within 48 samples from managed turfgrass (home lawns, golf course fairways, and putting greens) and an unmanaged grass mixture in Madison, WI, USA were analyzed across leaf, thatch, rhizoplane, and rhizosphere habitats Intensive management, particularly in nitrogen-rich, sand-based putting greens, reduced fungal richness and diversity, whereas bacterial diversity patterns varied. Beta diversity analyses revealed distinct clustering: fungal communities differed most in unmanaged systems, while bacterial communities clustered within managed systems. Functional profiling demonstrated that bacterial communities maintained metabolic stability despite taxonomic shifts, while fungal communities showed dynamic functional responses to management. Furthermore, management practices also impacted microbial community assembly. Bacterial communities were predominantly shaped by neutral, stochastic processes, while fungal communities were more sensitive to management, showing deterministic, niche-based assembly and compositional shifts. These findings underscore the contrasting impacts of management on microbial communities and highlight the importance of sustainable turfgrass practices that balance plant health with microbial ecosystem functions. By linking microbial assembly processes to functional outcomes, this study provides insights for optimizing urban landscapes to enhance soil health and ecosystem resilience.

Microbial community size is a potential predictor of nematode functional group in limed grasslands

Distribution characteristics of emerging contaminants and microbial communities in Bohai Sea sediments.

The geographic distribution patterns of soil microbial communities associated with cultivated Acanthopanax senticosus plants in Northeast China were investigated. High-throughput sequencing revealed that the diversity and community assembly of bacterial and fungal communities in the inter-root soil varied significantly with geographic location. The study found that bacterial communities were predominantly assembled through stochastic processes at most sites, while fungal communities showed greater variation, with both stochastic and deterministic processes involved. The complexity of bacterial-fungal co-occurrence networks also varied with longitude and latitude, demonstrating both positive and negative interactions. PICRUSt 2.0 and FUNGuild were used to predict the potential functions of soil bacterial and fungal microbiota, respectively, during different land use patterns. The average taxonomic distinctness (AVD) index indicated varying degrees of community stability across sites. Key microbial taxa contributing to community variability were identified through Random Forest modeling, with Bacteriap25 and Sutterellaceae standing out among bacteria, and Archaeorhizomyces and Clavaria among fungi. Soil chemical properties, including pH, TN, TP, EC, and SOC, significantly correlated with microbial diversity, composition, and co-occurrence networks. Structural equation modeling revealed that geographic distribution patterns directly and indirectly influenced soil chemical properties and microbial communities. Overall, the study provides insights into the geographic distribution patterns of soil microbial communities associated with A. senticosus and highlights the need for further research into the underlying mechanisms shaping these patterns.

Bioaugmentation of Hydrogenispora ethanolica LX-B affects hydrogen production through altering indigenous bacterial community structure

This study aimed to induce a shift in a bacterial community by adding substrate into a biofloc system to characterize this shift and estimate its benefits in improving water quality and aquatic animal growth. We compared the bacterial communities between two biofloc systems, either with (sB treatment) or without (nB treatment) the addition of substrate (elastic solid packing filler), and we also analyzed the effects of the shift on the water quality and growth performance of shrimp (Litopenaeus vannamei). Beta diversity analysis indicated that the bacterial communities in the two treatments were significantly different (Jaccard index 0.94 ± 0.01, pseudo-F = 3.96, p = 0.001). The addition of substrate showed significant positive effects on bacterial alpha diversity indices (Shannon, Heip, Pielou, and Simpson; p < 0.05) and the abundances of beneficial genera (e.g., Arenimonas, Arthrobacter, Exiguobacterium, Leadbetterella, Luteolibacter, Marinobacter, Nitratireductor, Novosphingobium, Thermomonas, Plesiocystis, and Rubrivivax; p < 0.05). In addition, the substrate also showed significant positive effects on water quality parameters (TAN, TSS, turbidity, biofloc volume, pH, and carbonate alkalinity; p < 0.05), and it also significantly improved shrimp zootechnical performance indices (survival rate, feed conversion ratio, and productivity; p < 0.05). Redundancy analysis revealed that 94.25–98.58% of the variation in the water quality and the shrimp growth performance between the two treatments could be attributed to the shift in bacterial composition and diversity induced by the addition of substrate. These findings characterize the shift in the microbial community in the biofloc system induced by the substrate, and demonstrate how this shift could be beneficial to the water quality and the growth performance of shrimp.

The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.