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102 results for “bacterial diversity”
Soil bacterial diversity inventories along small-scale stress gradients in the Arctic, Antarctic, and Chihuahuan Deserts (2022-2023)
Bacteria form the foundation of soil ecosystems in desert ecosystems, driving soil function, diversity, and ecology. Soil physicochemistry is largely dictated by larger topographical variations and can directly drive bacterial community composition and the relationships within. Bacteria may form complex networks of interactions with other bacteria and other soil taxa that have implications for emergent properties such as diversity and stability, but the way these interactions are impacted by environmental stressors remains poorly understood. Here, we sampled soil bacterial communities of three desert ecosystems at different latitudes: the McMurdo Dry Valleys, Antarctica; the northern Chihuahuan Desert, Jornada Experimental Range (JER), New Mexico, USA; and the Arctic tundra at the Canadian High Arctic Research Research Station (CHARS), Victoria Island, Nunavut, Canada. In each system, a holistic stress-gradient was sampled based on local topographical variation, vegetation cover, and water availability. Sampling along the stress-gradient was conducted at four distinct stress levels, namely lower elevation with vegetation cover, lower elevation without vegetation cover, higher elevation with vegetation cover, and higher elevation without vegetation cover. To allow robust biodiversity inference and co-occurrence network construction, 30 replicates were collected at each stress level, and this was done at two independent stress gradients for the Chihuahuan Desert and Arctic sites. The Antarctic samples consisted of two independent stress gradients, one ranging from low, middle to high elevation without vegetation cover, and one consisting of two levels with and without vegetation cover. For each site, soil pH and gravimetric water content was also measured. Each replicate was then sequenced on an Illumina MiSeq for 2x250 paired-end sequencing of the 16S rRNA marker. Sequences were archived in NCBI under BioProject PRJNA1098956, with accession numbers included herein.
Community diversity determines the evolution of synthetic bacterial communities under artificial selection
<p>These data and script are related to the article entitled "Community diversity determines the evolution of synthetic bacterial communities under artificial selection". This study reports the results of an experiment that involved bacterial communities differing for their richness level (1, 2, 4, 8, 16 species) and subjected to artificial selection or not. The property under selection was the optical density (OD). All the data needed to reproduce the figures and tables presented in the manuscript are provided.</p>
One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus
<p>Bacterial endosymbionts of the groups <em>Wolbachia</em>, <em>Cardinium </em>and <em>Rickettsiaceae </em>are well-known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analyzed a unique system in which the dwarf spider <em>Oedothorax gibbosus</em> is co-infected with up to five different endosymbionts affiliated with <em>Wolbachia</em>, ‘<em>Candidatus </em>Tisiphia’ (formerly Torix group <em>Rickettsia</em>), <em>Cardinium, </em>and <em>Rhabdochlamydia</em>. Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among <em>O. gibbosus</em> populations and are frequently found co-infecting spider individuals. To study this intricate host-endosymbiont system on a genome resolved level, we used long-read sequencing to reconstruct closed genomes of the <em>Wolbachia</em>, ‘<em>Ca. </em>Tisiphia’ and <em>Cardinium </em>endosymbionts. We provide insights in the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the <em>Cardinium</em>, ‘<em>Ca. </em>Tisiphia’ and <em>Wolbachia </em>endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on earth, and show the usefulness of transposable elements as an evolutionary “contact-tracing” tool.</p>
Figure 6 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 6. Analysis of principal coordinates of sampling sectors according to the distribution of bacterial families reported at 40% contribution according to SIMPER analysis.
Figure 2 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 2. Good quality DNA samples from bacterial populations divided by sampling time factor in soils with pre-sowing levels (A), Lepidium meyenii hypocotyl development (B) and post-harvest (C).
Figure 7 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 7. Dendogram of bacterial families at 40% contribution according to SIMPER analysis in fields disturbed by Lepidium meyenii culture under the effect of the two factors under study (use pressure and sampling period).
Figure 8 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 8. Analysis of the behavior of the clusters of bacterial families significantly differentiated (p<0.05) according to the SIMPROF analysis at a 40% contribution of the total of families registered in soils under the factors use pressure and sampling period.
Figure 3 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 3. Band migration in bacterial populations according to the V3 - V4 region of the 16S bacterial rRNA genes, for the 12 samples divided by the sampling time factor in soils with pre-sowing levels (A),Lepidium meyenii hypocotyl development (B) and post-harvest (C).
Figure 5 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 5. Non-metric MSD and cluster analysis of sampling sectors divided by use pressure and sampling period factors.
FIG. 3 in The Bacterial Diversity Lurking in Protist Cell Cultures
FIG. 3. Relative abundance of each bacterial scaffold in Illumina sequencing libraries, represented as proportion of length normalized read pairs for the portion of each sequencing library mapping to the bacterial scaffolds. The two Alcanivorax sp. DSM 26293 scaffolds are marked with asterisks (*).
Data for: Skin bacterial microbiome diversity predicts lower activity levels in female, but not male, guppies, Poecilia reticulata
<p>While the link between the gut microbiome and host behaviour is well established, how the microbiomes of other organs correlate with behaviour remains unclear. Additionally, behaviour–microbiome correlations are likely sex-specific because of sex differences in behaviour and physiology, but this is rarely tested. Here, we tested whether the skin microbiome of the Trinidadian guppy, Poecilia reticulata , predicts fish activity level and shoaling tendency in a sex-specific manner. High-throughput sequencing revealed that the bacterial community richness on the skin (Faith's phylogenetic diversity) was correlated with both behaviours differently between males and females. Females with richer skin-associated bacterial communities spent less time actively swimming. Activity level was significantly correlated with community membership (unweighted UniFrac), with the relative abundances of 16 bacterial taxa significantly negatively correlated with activity level. We found no association between skin microbiome and behaviours among male fish. This sex-specific relationship between the skin microbiome and host behaviour may indicate sex-specific physiological interactions with the skin microbiome. More broadly, sex specificity in host–microbiome interactions could give insight into the forces shaping the microbiome and its role in the evolutionary ecology of the host.</p>
Supplement: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
<p>Background<br> Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments.</p> <p>Results<br> We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles.</p> <p>Conclusions<br> Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry.</p>
Data for: Skin bacterial microbiome diversity predicts lower activity levels in female, but not male, guppies, Poecilia reticulata
Open the record for dataset details and reuse information.
Microbiome diversity and zoonotic bacterial pathogen prevalence in Peromyscus mice from agricultural landscapes and synanthropic habitat
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Exploring archaeal and bacterial diversity and co-occurrence in Lake Geneva
<p>Fastq files, OTU tables, tags list.</p>
Data from: Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host
The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin of amphibians, and has caused severe declines and extinctions of amphibians globally. In this study, we investigate the interaction between Bd and the bacterial skin microbiome of the endangered Sierra Nevada yellow-legged frog, Rana sierrae, using both culture-dependent and culture-independent methods. Samples were collected from two populations of R. sierrae that likely underwent Bd epizootics in the past, but that continue to persist with Bd in an enzootic disease state, and we address the hypothesis that such "persistent" populations are aided by mutualistic skin microbes. Our 16S rRNA metabarcoding data reveal that the skin microbiome of highly infected juvenile frogs is characterized by significantly reduced species richness and evenness, and by strikingly lower variation between individuals, compared to juveniles and adults with lower infection levels. Over 90% of DNA sequences from the skin microbiome of highly infected frogs were derived from bacteria in a single order, Burkholderiales, compared to just 54% in frogs with lower infection levels. In a culture-dependent Bd-inhibition assay, the bacterial metabolites we evaluated all inhibited the growth of Bd. Together, these results illustrate the disruptive effects of Bd infection on host skin microbial community structure and dynamics, and suggest possible avenues for the development of anti-Bd probiotic treatments.
Data from: Diversity and stability of egg-bacterial assemblages: the role of paternal care in the glassfrog Hyalinobatrachium colymbiphyllum
Embryos of oviparous organisms must cope with harsh environments and are especially susceptible to disease, considering that many immune mechanisms do not develop until later in life. Parents may transmit symbiotic microflora to eggs, which can contribute to embryo immune defense. Despite the importance of symbiotic microbes for immune function and survival of adult amphibians, vertical transfer of symbionts in amphibians has received less attention than in other taxa. Here, we test the role of male-only parental care in establishing and maintaining the diversity of egg-bacterial assemblages in a Neotropical glassfrog (Centrolenidae). Previous research suggests that father Hyalinobatrachium colymbiphyllum may transfer bacterial symbionts to their eggs. We combined a male-removal experiment in situ with 16S rRNA gene amplicon sequencing to determine whether egg attendance by father H. colymbiphyllum influences the bacterial community and survival of eggs. We found that eggs harbor a diverse and stable bacterial assemblage. Despite different host environments, we found that adult skin and eggs supported very similar bacterial assemblages—even after removing fathers. While we found overlap in the bacteria present on eggs and their fathers, our experiment reveals that extended male care does not contribute to the maintenance of egg-bacterial communities, so there may be other potential routes of transfer. This study contributes to our understanding of the diversity and maintenance of egg microbiomes, and motivates further research on how initial bacteria are acquired and the ontogenetic development of host–symbiont communities.
Data from: Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia
Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and ß diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in Southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.
Diversity of bacterial communities on four frequently used surfaces in a large Brazilian teaching hospital
<p>Frequently used hand-touch surfaces in hospital settings have been implicated as a vehicle of microbial transmission. In this study, we aimed to investigate the overall bacterial population on four frequently used surfaces using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Surface samples were collected from four sites, namely elevator buttons (EB), bank machine keyboard buttons (BMKB), restroom surfaces, and the employee biometric time clock system (EBTCS), in a large public and teaching hospital in Sao Paulo. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Actinobacteria and Proteobacteria, with a total of 926 bacterial families and 2832 bacterial genera. Moreover, our analysis revealed the presence of some potential pathogenic bacterial genera, including <em>Salmonella enterica</em>, <em>Klebsiella pneumoniae</em>, and <em>Staphylococcus aureus</em>. The presence of these pathogens in frequently used surfaces enhances the risk of exposure to any susceptible individuals. Some of the factors that may contribute to the richness of bacterial diversity on these surfaces are poor personal hygiene and ineffective routine schedules of cleaning, sanitizing, and disinfecting. Strict standards of infection control in hospitals and increased public education about hand hygiene are recommended to decrease the risk of transmission in hospitals among patients.</p>
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes
<p>Bacterial specialized metabolites are a proven source of antibiotics and cancer therapeutics, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~ 170,000 bacterial genomes and ~ 47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We found that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation of secondary metabolite biosynthetic diversity drops significantly on a genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on Relative Evolutionary Distance revealed that <em>Streptomyces</em> bacteria encode the largest biosynthetic diversity by far, with <em>Amycolatopsis</em>, <em>Kutzneria</em> and <em>Micromonospora</em> also encoding substantial chemical diversity. Finally we find that several less-well-studied taxa such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), <em>Pleurocapsa</em> and Nostocaceae (Cyanobacteria) have potential to produce highly diverse secondary metabolites that warrant further investigation.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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