Hsaio and colleagues link gut microbes to autism spectrum disorders (ASD) in a mouse model. They show that ASD symptoms are triggered by compositional and structural shifts of microbes and associated ...metabolites, but symptoms are relieved by a Bacteroides fragilis probiotic. Thus probiotics may provide therapeutic strategies for neurodevelopmental disorders.
Microscopic eukaryotes are abundant, diverse and fill critical ecological roles across every ecosystem on Earth, yet there is a well-recognized gap in understanding of their global biodiversity. ...Fundamental advances in DNA sequencing and bioinformatics now allow accurate en masse biodiversity assessments of microscopic eukaryotes from environmental samples. Despite a promising outlook, the field of eukaryotic marker gene surveys faces significant challenges: how to generate data that are most useful to the community, especially in the face of evolving sequencing technologies and bioinformatics pipelines, and how to incorporate an expanding number of target genes.
Despite decades of interest, few studies have provided evidence supporting theoretical expectations for coupled relationships between aboveground and belowground diversity and ecosystem functioning ...in non-manipulated natural ecosystems. We characterized plant species richness and density, soil bacterial, fungal and eukaryotic species richness and phylogenetic diversity (using 16S, ITS, and 18S gene sequencing), and ecosystem function (levels of soil C and N, and rates of microbial enzyme activities) along a natural gradient in plant richness and density in high-elevation, C-deficient soils to examine the coupling between above- and belowground systems. Overall, we observed a strong positive relationship between aboveground (plant richness and density) and belowground (bacteria, fungi, and non-fungal eukaryotes) richness. In addition to the correlations between plants and soil communities, C and N pools, and rates of enzyme activities increased as plant and soil communities became richer and more diverse. Our results suggest that the theoretically expected positive correlation between above- and belowground communities does exist in natural systems, but may be undetectable in late successional ecosystems due to the buildup of legacy organic matter that results in extremely complex belowground communities. In contrast, microbial communities in early successional systems, such as the system described here, are more directly dependent on contemporary inputs from plants and therefore are strongly correlated with plant diversity and density.
Despite recent great interest in glacier ecosystems in the continental Antarctic, little is known about their maritime counterparts. Our study presents descriptive data on cryoconite sediments and ...cryoconite holes on Ecology Glacier (King George Island) to accomplish three main objectives: (a) to identify main eukaryotic (algae, invertebrates) and prokaryotic (cyanobacteria) components of microbial communities; (b) to provide a “baseline” of community composition, organic matter and artificial contamination; and (c) to identify key abiotic factors that might be important in community assembly. Cryoconite holes were sampled along an altitudinal gradient of Ecology Glacier in January, mid Austral Summer 2017. Cryoconite holes located in lower altitude were deeper than those located in the middle and the highest altitude. Seventeen species of algae and cyanobacteria with biomass of 0.79 to 5.37 μg/cm3 have been found in sediments. Dominant species were cyanobacterial Pseudanabaena frigida and Bacillariophyceae Microcostaus sp. Biomass of Bacillariophyceae was significantly higher than that of Chlorophyta and Cyanobacteria. We found three species of rotifers (potentially two new to science) and for the first time a glacier dwelling Acari (suspension feeder, Nanorchestes nivalis). Organic matter content ranged from 5.4% to 7.6%. Investigated artificial radionuclides included 137Cs, 238Pu, 239+240Pu and 241Am. 210Pb seems to be related to organic matter content. Overall, cryoconite holes on Ecology Glacier present unique habitats that serve as biodiversity hotspots of psychrophiles, source of organic matter, matrices for radioactivity tracking and model for observing changes in supraglacial ecosystems in the maritime Antarctic.
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•17 taxa of algae and cyanobacteria, 3 taxa of rotifers, and 1 of mite were found•Cryoconite holes on Ecology Glacier were dominated by Bacillariophyceae•In cryoconite holes, a suspention-feeding mite species was observed and identified first time•Investigated artificial radionuclides included 137Cs, 238Pu, 239+240Pu and 241Am•Cryoconite holes on Ecology Glacier present unique inland habitats for psychrophiles
Although abiotic environmental factors have been historically regarded as the dominant deterministic process in microbial community assembly, recent studies indicate that biotic interactions may be ...equally significant. However, the extent to which both processes are important in assembly of belowground communities is unknown. Along two environmental gradients: alkalinity (ranging from pH ~7 to ~11) and habitat type (lakes, shorelines, and prairies around lakes) present in the Western Nebraska Sandhills, we used 18S rRNA gene marker metabarcoding and statistical analyses, including generalized dissimilarity modelling (GDM), to evaluate the dynamics between abiotic and biotic factors that might play a role in nematode community assembly. Lakes supported the least diverse and prairies the most diverse communities with completely distinct compositions. We also observed a potential role of alkalinity in shaping these communities but only in lakes. Generally, GDMs indicated the influence of both abiotic and biotic factors. However, their relative importance in explaining community variability was dependent on the habitat. Biotic factors influenced the lake communities most, followed by shorelines and prairies, explaining ~47%, 27% and 8% of the variation, respectively. In contrast, the role of abiotic factors was relatively similar in lakes, shorelines and prairies (~15%, 18% and 14% of the variation, respectively). Most variation in the shorelines (62%) and prairies (82%) remained unexplained, suggesting the potential importance of factors associated with specific traits or a stronger role of stochastic processes. Nevertheless, our findings suggest both deterministic processes are important in nematode community assembly, but their specific contributions are context‐dependent.
Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential ...adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.
Abstract
Ice-lidded cryoconite holes on glaciers in the Taylor Valley, Antarctica, provide a unique system of natural mesocosms for studying community structure and assembly. We used high-throughput ...DNA sequencing to characterize both microbial eukaryotic communities and bacterial communities within cryoconite holes across three glaciers to study similarities in their spatial patterns. We expected that the alpha (phylogenetic diversity) and beta (pairwise community dissimilarity) diversity patterns of eukaryotes in cryoconite holes would be related to those of bacteria, and that they would be related to the biogeochemical gradient within the Taylor Valley. We found that eukaryotic alpha and beta diversity were strongly related to those of bacteria across scales ranging from 140 m to 41 km apart. Alpha diversity of both was significantly related to position in the valley and surface area of the cryoconite hole, with pH also significantly correlated with the eukaryotic diversity. Beta diversity for both bacteria and eukaryotes was significantly related to position in the valley, with bacterial beta diversity also related to nitrate. These results are consistent with transport of sediments onto glaciers occurring primarily at local scales relative to the size of the valley, thus creating feedbacks in local chemistry and diversity.
Bacterial and eukaryotic alpha and beta diversity in Antarctic cryoconite holes were strongly correlated, reflecting a gradient of organic material and chemistry in the surrounding streams and soils.
Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when ...molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.
Recent work examining nematode and tardigrade gut microbiomes has identified species-specific relationships between host and gut community composition. However, only a handful of species from either ...phylum have been examined. How microbiomes differ among species and what factors contribute to their assembly remains unexplored. Cyanobacterial mats within Antarctic Dry Valley streams host a simple and tractable natural ecosystem of identifiable microinvertebrates to address these questions. We sampled 2 types of coexisting mats (i.e., black and orange) across four spatially isolated streams, hand-picked single individuals of two nematode species (i.e., Eudorylaimus antarcticus and Plectus murrayi) and tardigrades, to examine their gut microbiomes using 16S and 18S rRNA metabarcoding. All gut microbiomes (bacterial and eukaryotic) were significantly less diverse than the mats they were isolated from. In contrast to mats, microinvertebrates' guts were depleted of Cyanobacteria and differentially enriched in taxa of Bacteroidetes, Proteobacteria, and Fungi. Among factors investigated, gut microbiome composition was most influenced by host identity while environmental factors (e.g., mats and streams) were less important. The importance of host identity in predicting gut microbiome composition suggests functional value to the host, similar to other organisms with strong host selected microbiomes.
Large scale diversity patterns are well established for terrestrial macrobiota (e.g. plants and vertebrates), but not for microscopic organisms (e.g. nematodes). Due to small size, high abundance, ...and extensive dispersal, microbiota are assumed to exhibit cosmopolitan distributions with no biogeographical patterns. This assumption has been extrapolated from local spatial scale studies of a few taxonomic groups utilizing morphological approaches. Recent molecularly-based studies, however, suggest something quite opposite. Nematodes are the most abundant metazoans on earth, but their diversity patterns are largely unknown. We conducted a survey of nematode diversity within three vertical strata (soil, litter, and canopy) of rainforests at two contrasting latitudes in the North American meridian (temperate: the Olympic National Forest, WA, U.S.A and tropical: La Selva Biological Station, Costa Rica) using standardized sampling designs and sample processing protocols. To describe nematode diversity, we applied an ecometagenetic approach using 454 pyrosequencing. We observed that: 1) nematode communities were unique without even a single common species between the two rainforests, 2) nematode communities were unique among habitats in both rainforests, 3) total species richness was 300% more in the tropical than in the temperate rainforest, 4) 80% of the species in the temperate rainforest resided in the soil, whereas only 20% in the tropics, 5) more than 90% of identified species were novel. Overall, our data provided no support for cosmopolitanism at both local (habitats) and large (rainforests) spatial scales. In addition, our data indicated that biogeographical patterns typical of macrobiota also exist for microbiota.
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