Rare Operational Taxonomic Units Research Articles

Metabarcoding expands knowledge on diversity and ecology of rare actinobacteria in the Brazilian Cerrado.

Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.

Dissecting the role of soybean rhizosphere-enriched bacterial taxa in modulating nitrogen-cycling functions

Crop roots selectively recruit certain microbial taxa that are essential for supporting their growth. Within the recruited microbes, some taxa are consistently enriched in the rhizosphere across various locations and crop genotypes, while others are unique to specific planting sites or genotypes. Whether these differentially enriched taxa are different in community composition and how they interact with nutrient cycling need further investigation. Here, we sampled bulk soil and the rhizosphere soil of five soybean varieties grown in Shijiazhuang and Xuzhou, categorized the rhizosphere-enriched microbes into shared, site-specific, and variety-specific taxa, and analyzed their correlation with the diazotrophic communities and microbial genes involved in nitrogen (N) cycling. The shared taxa were dominated by Actinobacteria and Thaumarchaeota, the site-specific taxa were dominated by Actinobacteria in Shijiazhuang and by Nitrospirae in Xuzhou, while the variety-specific taxa were more evenly distributed in several phyla and contained many rare operational taxonomic units (OTUs). The rhizosphere-enriched taxa correlated with most diazotroph orders negatively but with eight orders including Rhizobiales positively. Each group within the shared, site-specific, and variety-specific taxa negatively correlated with bacterial amoA and narG in Shijiazhuang and positively correlated with archaeal amoA in Xuzhou. These results revealed that the shared, site-specific, and variety-specific taxa are distinct in community compositions but similar in associations with rhizosphere N-cycling functions. They exhibited potential in regulating the soybean roots’ selection for high-efficiency diazotrophs and the ammonia-oxidizing and denitrification processes. This study provides new insights into soybean rhizosphere-enriched microbes and their association with N cycling.Key points• Soybean rhizosphere affected diazotroph community and enriched nifH, amoA, and nosZ.• Shared and site- and variety-specific taxa were dominated by different phyla.• Rhizosphere-enriched taxa were similarly associated with N-cycle functions.

Tea Plantation Intercropping Legume Improves Soil Ecosystem Multifunctionality and Tea Quality by Regulating Rare Bacterial Taxa

Microorganisms play essential roles in soil-ecosystem multifunctionality. However, the contribution of their community assembly processes, composition, diversity, and keystone species to ecosystem multifunctionality is unclear, especially in tea-plantation ecosystems. In order to assess the effects of various intercropping patterns (tea-plant monoculture and tea plants, respectively, intercropped with soybean, soybean—milk vetch, soybean—red clover, and soybean—smooth vetch) on soil rare and abundant taxa, a field experiment was carried out. We found that tea plantation intercropping with legumes improved the soil-ecosystem multifunctionality by altering the soil environment, and ultimately benefited nutrient absorption and quality improvement of tea leaves. Whether it was in bacteria or fungi, rare taxa had a higher proportion of deterministic processes in community assembly than abundant taxa. Additionally, intercropping practices changed the soil environment, and rare bacterial taxa were assembled and shifted from variable selection to homogeneous dispersal. Intercropping practices significantly changed the bacterial and fungal communities’ composition, and rare taxa had higher α-diversity than abundant taxa. Increasing legume species in intercropping practice enhanced community dissimilarity to the tea monoculture by affecting soil pH, ammonium nitrogen, and nitrate nitrogen. Rare bacterial and fungal β-diversity exhibited stronger positive relationships with ecosystem multifunctionality (both average and multi-threshold approaches) compared to the corresponding abundant taxa. Furthermore, ecosystem multifunctionality under different intercropping practices was closely related to the keystone rare operational taxonomic units, especially rare bacterial species of Chloroflexi. Our results emphasize the disparate feedbacks of rare and abundant taxa to diverse intercropping practices, as well as the important connection between rare bacterial taxa and ecosystem multifunctionality.

Fjords of the western and northern regions of Svalbard harbour distinct bacterioplankton community structures.

Fjords are highly dynamic ecosystems that are known to be sentinels to climate change due to increased glaciomarine interactions. The convergence and mixing of warm Atlantic water (AtW) and cold Arctic water (ArW) is known to influence the hydrodynamics and ecology of the Arctic fjords. However, most past studies were limited to single-fjord ecosystems, determining the baseline knowledge of inter-fjord comparison on bacterioplankton diversity and distribution patterns. In the present study, we investigated the bacterial diversity and community composition across three Arctic fjords located in the western and northern regions of Svalbard. Our observations show that the bacterial community structure varied significantly among the fjords, while abundant Operational Taxonomic Units (OTUs) were widespread (n = 100) between all the samples and rare OTUs (n = 2221) mainly contributed to these differences. Phylogenetic classification revealed that Alpha (27.3-55%) and Gamma-proteobacteria (16-51.3%), followed by Bacteroidota (17-35.7%) were dominant in the St.Jonsfjorden and Magdalenefjorden, while Verrucomicrobiota (up to 84.19%) and Actinobacteriota (up to 76.5%) were predominant in the Raudfjorden. Temperature, dissolved inorganic phosphate (DIP) and depth were found to significantly influence the community composition of abundant bacterial groups, whereas the rare bacterial groups were affected by temperature, DIP, dissolved inorganic nitrate (DIN), ammonium and depth. A comparative meta-analysis along with Kongsfjorden and Krossfjorden also showed that each fjord had a significantly different bacterioplankton community structure.

Abundant culturable diazotrophs within Actinomycetia rather than rare taxa are underlying inoculants for nitrogen promotion in desert soil

Desert soil may harbor various culturable diazotrophs that can endure multiple environmental stresses and promote ecological restoration. To explore nitrogen-fixing microorganisms that can be potential inoculants for nutrition improvement in nitrogen-limited ecosystems and disclose whether rare taxa contribute to the nitrogen incorporation process, we collected soil from the Mu Us Desert and combined 16S rRNA high-throughput sequencing, functional gene arrays (GeoChip) method, and culture-dependent approaches to observe the composition and key groups of culturable diazotrophs. Proteobacteria was the most dominant phylum, accounting for 73.07 % of the 823 operational taxonomic units (OTUs), grown in nitrogen-free media. Among all the valid assigned putative nitrogen-fixing OTUs, 53.21 % were identified as rare taxa in the soil. Among all the rare OTUs that could be effectively enriched as abundant taxa in the medium, over 58 % were also affiliated with Proteobacteria. Despite the predominance of Proteobacteria, the ordinary least squares regression model implied that less abundant Actinomycetia was significantly related to the nifH gene signal intensity generated by GeoChip, while rare culturable diazotrophic categories had no relationship with the nifH gene. The random forest analyses further confirmed that the most important indicator of the nitrogen-fixing process was Actinomycetia. The two stably generated pure cultures, classified as Streptomyces sp. (Actinomycetia) and Bacillus pumilus (Firmicutes) by Sanger sequencing and BLAST were inoculated into sterilized desert soil. Available nitrogen, total dissolved nitrogen (TDN), and total nitrogen (TN) were measured, and the two strains significantly increased the soil ammonium content, nitrate content, and TDN content. Our findings provide genomic and solid evidence that rare taxa within Proteobacteria maintain the biodiversity of culturable nitrogen fixers, whereas abundant Actinomycetia possess potential value as nitrogen-fixing inoculants in drylands.

Abundant and Rare Microbial Communities Respectively Contribute to an Aquaculture Pond Ecosystem

Unraveling the assembly mechanism is a core research topic of microbial ecology. Abundant and rare microbial communities are crucial for diversity, function and host health in a given ecosystem, but few studies focused on their assembly strategies. Here, we explored the microbial diversity of abundant and rare communities of water, shrimp intestine and sediment habitats in the shrimp cultural ponds. Our results found that the numbers of rare operational taxonomic units (OTUs) (6,003, 4,566 and 8,237 OTUs of water, intestine and sediment) was dozens of times more than abundant ones (only 199, 157 and 122 OTUs of water, intestine and sediment). The community diversity of abundant and rare microbial taxa was markedly different, as well as their taxonomic composition. Despite different diversity, similar abundance-occupancy relationship and biogeographic patterns between the abundant and rare microbial communities were observed, with much stronger obvious distance-decay relationships for rare community than abundant community. Furthermore, stochastic processes dominated the community assemblies of both abundant and rare microbial taxa, and deterministic process contributed more microbial community variation to rare taxa than abundant taxa. All the findings advance our understanding on the community assembly strategies of abundant and rare microbial taxa and prompt the contributions of abundant and rare microbial community to the aquatic ecosystems, which will improve aquaculture management strategy.

Rare microbial populations as sensitive indicators of bacterial community dissimilarity under different agricultural management practices

ABSTRACT Revealing the composition and role of rare and abundant microbial groups is crucial to understand ecosystem processes and function. In 2018, we characterized soil bacterial community, abundant (AMPs) and rare microbial populations (RMPs) with mineral fertilizer and mineral fertilizer combined with straw return under continuous maize (Zea mays L.) and soybean (Glycine max Merr.)-maize rotation systems in a Mollisol in Northeast China. The results showed that the effects of fertilization on total bacterial community, AMPs and RMPs were greater than cropping systems. The cropping systems had a stronger effect on α diversity of bacterial community than fertilization. The RMPs accounted for 50.1% of the relative abundance and contributed 64.3% to the community dissimilarity. The RMPs accounted for 96.7% of the amount of operational taxonomic units (OTUs), thus became the most important contributors to community diversity. The OTUs with lower relative abundance had a narrower niche range, indicating that rare OTUs were more easily affected by habitat uniqueness. The RMPs were important contributors to chemoheterotrophs and were more closely correlated with variations in soil functions than AMPs. Our results provided deep insight into the ecological role of RMPs, which is useful for rational management and improving agricultural ecosystem sustainability.

Effects of influent immigration and environmental factors on bacterial assembly of activated sludge microbial communities

The functional mechanism of microbial assembly of activated sludge (AS) in urban wastewater treatment plants (UWTPs) remains unclear. A comprehensive quantitative evaluation of the contribution of influent immigration and environmental factors to AS community composition requires investigation. In this study, the microbial characteristics of six full-scale UWTPs with different influent compositions and environmental factors (altitude, temperature, dissolved oxygen (DO), pH, chemical oxygen demand (COD), total nitrogen (TN), ammonia nitrogen (NH4+-N), and total phosphorus (TP)) were analyzed to determine the main forces affecting the bacterial assembly of AS microbial communities. Abundant and core taxa were screened out based on the abundance and frequency of operational taxonomic units (OTUs) occurrence in all samples. Abundant OTUs (18.7% occurrence) accounted for 87.7% of the total 16S rRNA sequences, while rare OTUs (71.7% occurrence) accounted for only 7.8% of the total 16S rRNA sequences. A total of 135 OTUs were identified as core taxa, accounting for 14.6–26.2% of the total reads, of which 83 OTUs belonged to abundant taxa. The richness and uniformity of the influent community were significantly lower than those of the AS system. The community composition in influent varied from that in AS. Moreover, about 89.7% (86.5% of 16S rRNA sequences) OTUs in AS samples showed positive growth rates, indicating that immigration of influent communities had a limited effect on the microbial composition of AS. Redundancy analysis (RDA) combined with co-occurrence network showed that the bacterial assembly of microbial communities was significantly correlated with altitude, pH, and TN (P < 0.05), and these three parameters could explain 23.3%, 21.1%, and 17.7% of the bacterial assembly of AS microbial communities in UWTPs, respectively.

Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake.

Lake Baikal is the deepest (~1.6 km) and most voluminous freshwater reservoir on Earth. Compared to plankton, its benthos remains poorly explored. Here, we ask whether latitude and/or depth determine benthic microbial community structure and how Baikal communities compare to those of other freshwater, brackish and marine sediments. To answer, we collected sediment upper layers (0-1 cm) across a ~600 km North-South transect covering the three basins of the lake and from littoral to bathybenthic depths (0.5-1450 m). Analysis of 16S and 18S rRNA gene amplicon sequences revealed communities with high richness and evenness where rare operational taxonomic units (OTUs) collectively dominated. Archaea represented up to 25% or prokaryotic sequences. Baikal sediments harbored typically marine eukaryotic and prokaryotic OTUs recently identified in some lakes (diplonemids, Bolidophyceae, Mamiellales, SAR202, marine-like Synechococcus, Pelagibacterales) but also SAR324, Syndiniales and Radiolaria. We hypothesize that, beyond the salinity barrier, adaptation to oligotrophy explains the presence of these otherwise typically marine lineages. Baikal core benthic communities were relatively stable across sites and seemed not determined by depth or latitude. Comparative analyses with other freshwater, brackish and marine prokaryotic sediment communities confirmed the distinctness of Baikal benthos, which include elements of similarity to marine and hydrothermally influenced systems.

Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns.

Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.

Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives.

Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus Musa as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs–primarily Lasiodiplodia, Fusarium, and Aspergillus–while a large variety of rare OTUs from across the Ascomycota were isolated only once. Fusarium species were notably abundant–of significance in light of Fusarium wilt, a disease threatening global banana crops–and so were targeted for additional sequencing with the marker EF1α in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.

A vertically and temporally diverse bacterial community in a shallow lake-water sediment site of a eutrophic lake

ABSTRACT Aquatic sediment accumulates organic matter and provides microenvironments for the growth of a diverse microbial community with key roles in the biogeochemical nutrient cycling of the lacustrine ecosystem. We investigated vertical and temporal variations of the sedimentary bacterial community composition in a shallow coastal site of eutrophic Lake Pamvotis (northwestern Greece) across 3 horizons between the surface and 5 cm below lake floor (cmblf) during transition to the cold period of the year (Oct–Dec). For this analysis we used Illumina sequencing of the V3–V4 hypervariable regions of the 16S rRNA gene. Bacterial community composition was dominated by Proteobacteria, Bacteroidetes, and Chloroflexi. Rare operational taxonomic units (OTUs) represented 96.09% (standard deviation 0.61%) of richness per sample, contributing significantly to diversity, and only a few became abundant during the study. Abundant OTUs represented <0.005% of richness but accounted for 20–33% of reads in different samples, mainly associated with anaerobic/microaerobic taxa common in polluted aquatic systems, sludge digesters, or wastewater (e.g., Thiolamprovum pedioforme, Candidatus Competibacter, Petrimonas). About 50% of OTUs found at the surface persisted with depth while shared OTUs between any 2 months were always >70% of richness. Overall, sediment bacterial community composition was diverse but remained largely homogeneous in the sediment of this human-impacted ecosystem at the temporal and vertical scale studied here. The study revealed the potential of specific bacterial taxa (e.g., Anaerolineae, Bellilinea) to serve as monitors of specific pollutants (e.g., polycyclic aromatic hydrocarbons) as well as the need to investigate the role of the rare biosphere in ecosystem functioning.

Subgingival microbiota of dogs with healthy gingiva or early periodontal disease from different geographical locations

BackgroundPeriodontal disease is the most common oral disease of dogs worldwide and results from a complex interplay between plaque bacteria, the host and environmental factors. Recent studies have enhanced our understanding of the associations between the plaque microbiota and canine periodontal disease. These studies, however, were limited in their geographical reach. Thus associations between the canine oral microbiota and geographical location were investigated by determining the composition of subgingival plaque samples from 587 dogs residing in the United Kingdom (UK), United States of America (USA), China and Thailand using 454-pyrosequencing.ResultsAfter quality filtering 6,944,757 sequence reads were obtained and clustering of these at ≥98% sequence resulted in 280 operational taxonomic units (OTUs) following exclusion of rare OTUs (present at < 0.05% in all four countries). The subgingival plaque from dog populations located in the UK, USA, China and Thailand had a similar composition although the abundance of certain taxa varied significantly among geographical locations. Exploration of the effect of clinical status and age revealed a marked similarity among the bacteria associated with increased age and those associated with gingivitis: Young dogs and those with no gingivitis were dominated by taxa from the phyla Bacteroidetes and Proteobacteria whereas older dogs and those with moderate gingivitis were dominated by members of the Firmicutes. The plaque microbiota of small breed dogs was found to significantly differ to medium and large breeds and was dominated by species belonging to the Firmicutes.ConclusionsThe bacterial associations with health, gingivitis and periodontitis were conserved across dogs from the UK, USA, China and Thailand. These bacterial signatures of periodontal health and disease have potential as biomarkers for disease detection.

Stochasticity versus determinism: Microbial community assembly patterns under specific conditions in petrochemical activated sludge

The pattern of microbial community assembly in petrochemical sludge is not well-explained. In this study, three kinds of petrochemical activated sludge (AS) from the same seed sludge were investigated to determine their microbial assembly pattern for long-term adaptation. Beta Nearest Taxon Index analysis revealed that the assembly strategies of the abundant and rare operational taxonomic unit (OTU) sub-communities are different for archaeal and bacterial communities. Abundant OTUs preferred deterministic processes, whereas rare OTUs randomly formed due to weak selection. Canonical correspondence analysis/variation partition analysis and Mantel testing results revealed that ammonium, petroleum, and chromium (Cr (VI)) mainly structured the abundant sub-communities. On the other hand, environmental variables, including ammonium, petroleum, and heavy metals, shaped the rare sub-communities. The PICRUSt2 tool was used to predict the functions. Results indicated a greater abundance of microbes harboring the hydrocarbon degradation pathway and heavy-metal-resistant enzymes. Cross-treatment experiments using one type of AS to treat the other two kinds of wastewater were conducted. The results of the cross-treatment experiments and qPCR both suggest the functional adaptation of the microbial community. We revealed selection strategies for the adaptation of bacteria and archaea in AS during environmental changes, providing a theoretical basis for petrochemical wastewater treatment.

Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability.

Despite the recognition of streams and rivers as sources of methane (CH4) to the atmosphere, the role of CH4 oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH4 oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream- and porewater CH4 concentrations. Michealis–Menten kinetic parameter of MOX, maximum reaction velocity (Vmax), and CH4 concentration at half Vmax (KS) increased with CH4 supply. KS values in the micromolar range matched the CH4 concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH4 oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.

Significant Bacterial Distance-Decay Relationship in Continuous, Well-Connected Southern Ocean Surface Water.

Recently, an increasing number of studies have focused on the biogeographic distribution of marine microorganisms. However, the extent to which geographic distance can affect marine microbial communities is still unclear, especially for the microbial communities in well-connected surface seawaters. In this study, the bacterial community compositions of 21 surface seawater samples, that were distributed over a distance of 7800km, were surveyed to investigate how bacterial community similarity changes with increasing geographical distance. Proteobacteria and Bacteroidetes were the dominant bacterial phyla, with Proteobacteria accounting for 52.6-92.5% and Bacteroidetes comprising 3.5-46.9% of the bacterial communities. A significant bacterial distance-decay relationship was observed in the well-connected Southern Ocean surface seawater. The number of pairwise shared operational taxonomic units (OTUs), and community similarities tended to decrease with increasing geographic distance. Calculation of the similarity indices with all, abundant or rare OTUs did not affect the observed distance-decay relationship. Spatial distance can largely explain the observed bacterial community variation. This study shows that even in well-connected surface waters, bacterial distance-decay patterns can be found as long as the geographical distance is great enough. The biogeographic patterns should then be present for marine microorganisms considering the large size and complexity of the marine ecosystem.

Estimation of Fungal Diversity and Identification of Major Abiotic Drivers Influencing Fungal Richness and Communities in Northern Temperate and Boreal Quebec Forests

Fungi play important roles in forest ecosystems and understanding fungal diversity is crucial to address essential questions about species conservation and ecosystems management. Changes in fungal diversity can have severe impacts on ecosystem functionality. Unfortunately, little is known about fungal diversity in northern temperate and boreal forests, and we have yet to understand how abiotic variables shape fungal richness and composition. Our objectives were to make an overview of the fungal richness and the community composition in the region and identify their major abiotic drivers. We sampled 262 stands across the northern temperate and boreal Quebec forest located in the region of Abitibi-Témiscamingue, Mauricie, and Haute-Mauricie. At each site, we characterized fungal composition using Illumina sequencing, as well as several potential abiotic drivers (e.g., humus thickness, soil pH, vegetation cover, etc.). We tested effects of abiotic drivers on species richness using generalized linear models, while difference in fungal composition between stands was analyzed with permutational multivariate analysis of variance and beta-diversity partitioning analyses. Fungi from the order Agaricales, Helotiales, and Russulales were the most frequent and sites from the north of Abitibi-Témiscamingue showed the highest OTUs (Operational Taxonomic Unit) richness. Stand age and moss cover were the best predictors of fungal richness. On the other hand, the strongest drivers of fungal community structure were soil pH, average cumulative precipitation, and stand age, although much of community variance was left unexplained in our models. Overall, our regional metacommunity was characterized by high turnover rate, even when rare OTUs were removed. This may indicate strong environmental filtering by several unmeasured abiotic filters, or stronger than expected dispersal limitations in soil fungal communities. Our results show how difficult it can be to predict fungal community assembly even with high replication and efforts to include several biologically relevant explanatory variables.

Primary progressive multiple sclerosis in a Russian cohort: relationship with gut bacterial diversity

BackgroundGut microbiota has been increasingly acknowledged to shape significantly human health, contributing to various autoimmune diseases, both intestinal and non-intestinal, including multiple sclerosis (MS). Gut microbiota studies in patients with relapsing remitting MS strongly suggested its possible role in immunoregulation; however, the profile and potential of gut microbiota involvement in patients with primary progressive MS (PPMS) patients has received much less attention due to the rarity of this disease form. We compared the composition and structure of faecal bacterial assemblage using Illumina MiSeq sequencing of V3-V4 hypervariable region of 16S rRNA genes amplicons in patients with primary progressive MS and in the healthy controls.ResultsOver all samples 12 bacterial phyla were identified, containing 21 classes, 25 orders, 54 families, 174 genera and 1256 operational taxonomic units (OTUs). The Firmicutes phylum was found to be ultimately dominating both in OTUs richness (68% of the total bacterial OTU number) and in abundance (71% of the total number of sequence reads), followed by Bacteroidetes (12 and 16%, resp.) and Actinobacteria (7 and 6%, resp.). Summarily in all samples the number of dominant OTUs, i.e. OTUs with ≥1% relative abundance, was 13, representing much less taxonomic richness (three phyla, three classes, four orders, six families and twelve genera) as compared to the total list of identified OTUs and accounting for 30% of the sequence reads number in the healthy cohort and for 23% in the PPMS cohort. Human faecal bacterial diversity profiles were found to differ between PPMS and healthy cohorts at different taxonomic levels in minor or rare taxa. Marked PPMS-associated increase was found in the relative abundance of two dominant OTUs (Gemmiger sp. and an unclassified Ruminococcaceae). The MS-related differences were also found at the level of minor and rare OTUs (101 OTUs). These changes in OTUs’ abundance translated into increased bacterial assemblage diversity in patients.ConclusionThe findings are important for constructing a more detailed global picture of the primary progressive MS-associated gut microbiota, contributing to better understanding of the disease pathogenesis.

Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments

Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.

Dominance of limited arbuscular mycorrhizal fungal generalists of Sorghum bicolor in a semi-arid region in Sudan

ABSTRACT Despite the economic importance of sorghum in Sudan, its productivity is low. Arbuscular mycorrhizal fungi (AMF) enhance sorghum growth, survival, and nutrient uptake, and their manipulation may have potential in mitigating biotic and abiotic stresses during droughts. However, information on the AMF community in Sudan and the host-AMF specificity at the sorghum genotype level are unknown. We investigated the AMF community structure of 19 sorghum genotypes by next-generation sequencing in a semi-arid region. A total of 102 AMF operational taxonomic units (OTUs) were detected comprising four families: Glomeraceae (85.3%), Claroideoglomeraceae (10.8%), Paraglomeraceae (2.9%), and Diversisporaceae (1%). Among them, appearance ratio of three OTUs (2.9%) belonging to Rhizoglomus was more than 75%, whereas 75 OTUs had lower appearance ratio than 25%, indicating that the AMF community comprised a small number of generalist and a large number of rare OTUs. Non-metric multidimensional scaling and permutational multivariate analysis of variance showed no AMF specificity of the sorghum genotypes. The community assembly was strongly influenced by neutral processes, but 11 OTUs had higher relative frequency than expected by neutral model. The result includes the possibility that adaptability of AMF to soil environment and positive selection by host plant also affect the AMF community assembly. Our work showed that only a few Rhizoglomus species dominated without host plant genotype specificity in a semi-arid Sudanese cropland. Further research on functional analysis of the dominant AMF species may reveal the importance of the dominant AMF species for sorghum cultivation in Sudan.