scholarly journals Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6042 ◽  
Author(s):  
He Zhao ◽  
Xuanzhen Li ◽  
Zhiming Zhang ◽  
Yong Zhao ◽  
Peng Chen ◽  
...  
Keyword(s):  
Habitat Type ◽  
18S Rrna Gene ◽  
Species Structure ◽  
Rrna Gene ◽  
Habitat Types ◽  
Dominant Soil ◽  
Eukaryotic Microbes ◽  
Microbial Groups ◽  
Semi Arid ◽  
Soil Habitat

The effects of environmental and species structure on soil eukaryotic microbes inhabiting semi-arid mountains remain unclear. Furthermore, whether community assembly differs in a variety of soil habitat types, for example, artificial forest, artificial bush, farmland, and natural grassland, is not well understood. Here, we explored species diversity and composition of soil eukaryotic microbes south of the Taihang Mountains (mid-western region of China) using Illumina sequencing of the 18S rRNA gene (V4) region on the MiSeq platform. The results suggest that the forest soil habitat type improved the diversity and abundance of soil eukaryotic microbes that will benefit the restoration of degraded soil. The SAR (Stramenopiles, Alveolates, Rhizaria) supergroup and Metazoa were the dominant soil eukaryotic microbial groups at the phylum level. About 26% of all operational taxonomic units were common among the different soil habitat types. The O-elements, water content, soil organic matter, and elevation significantly influenced the abundance of soil eukaryote communities (P < 0.05). Our findings provide some reference for the effectiveness of local ecological restoration and the establishment of a soil eukaryotic microbe resource databases in a semi-arid area.

scholarly journals Revealing the Composition of the Eukaryotic Microbiome of Oyster Spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS)

2021 ◽  
Author(s):  
Kevin Xu Zhong ◽  
Anna Cho ◽  
Christophe M. Deeg ◽  
Amy M. Chan ◽  
Curtis A. Suttle
Keyword(s):  
18S Rrna ◽  
Amplicon Sequencing ◽  
18S Rrna Gene ◽  
Model Organisms ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Oyster Spat ◽  
Guide Rna ◽  
16S Rna ◽  
Eukaryotic Microbes

Abstract BackgroundThe microbiome affects the health of plants and animals, including humans, and has many biological, ecological and evolutionary consequences. Microbiome studies typically rely on sequencing ribosomal 16S RNA gene fragments, which serve as taxonomic markers for prokaryotic communities; however, for eukaryotic microbes this approach is compromised, because 18S rRNA gene sequences from microbial eukaryotes are swamped by contaminating host rRNA gene sequences. ResultsTo overcome this problem, we developed CRISPR-Cas Selective Amplicon Sequencing (CCSAS), a high-resolution and efficient approach for characterizing eukaryotic microbiomes. CCSAS uses taxon-specific single-guide RNA (sgRNA) to direct Cas9 to cut 18S rRNA gene sequences of the host, while leaving protistan and fungal sequences intact. We validated the specificity of the sgRNA on ten model organisms and an artificially constructed (mock) community of nine protistan and fungal pathogens. The results showed that >96.5% of host rRNA gene amplicons were cleaved, while 18S rRNA gene sequences from protists and fungi were unaffected. When used to assess the eukaryotic microbiome of oyster spat from a hatchery, CCSAS revealed a diverse community of eukaryotic microbes, typically with much less contamination from oyster 18S rRNA gene sequences than other methods using non-metazoan or blocking primers. However, each method revealed taxonomic groups that were not detected using the other methods, showing that a single approach is unlikely to uncover the entire eukaryotic microbiome in complex communities. To facilitate the application of CCSAS, we designed taxon-specific sgRNA for ~16,000 metazoan and plant taxa, making CCSAS widely available for characterizing eukaryotic microbiomes that have largely been neglected. ConclusionCCSAS provides a high-through-put and cost-effective approach for resolving the eukaryotic microbiome of metazoa and plants with minimal contamination from host 18S rRNA gene sequences. Keywords: Eukaryotic microbiome, 18S rRNA gene, Microeukaryote, CRISPR-Cas, Taxon-specific single-guide RNA, gRNA-target-site, CasOligo, CCSAS

scholarly journals Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Máté Vass ◽  
Anna J. Székely ◽  
Eva S. Lindström ◽  
Silke Langenheder
Keyword(s):  
Community Assembly ◽  
Environmental Conditions ◽  
Null Model ◽  
Temporal Variations ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Historical Contingency ◽  
Selection Processes ◽  
Metacommunity Structure ◽  
Microbial Groups

AbstractTemporal variations in microbial metacommunity structure and assembly processes in response to shifts in environmental conditions are poorly understood. Hence, we conducted a temporal field study by sampling rock pools in four-day intervals during a 5-week period that included strong changes in environmental conditions due to intensive rain. We characterized bacterial and microeukaryote communities by 16S and 18S rRNA gene sequencing, respectively. Using a suite of null model approaches (elements of metacommunity structure, Raup-Crick beta-diversity and quantitative process estimates) to assess dynamics in community assembly, we found that strong changes in environmental conditions induced small but significant temporal changes in assembly processes and triggered different responses in bacterial and microeukaryotic metacommunities, promoting distinct selection processes. Incidence-based approaches showed that the assemblies of both communities were mainly governed by stochastic processes. In contrast, abundance-based methods indicated the dominance of historical contingency and unmeasured factors in the case of bacteria and microeukaryotes, respectively. We distinguished these processes from dispersal-related processes using additional tests. Regardless of the applied null model, our study highlights that community assembly processes are not static, and the relative importance of different assembly processes can vary under different conditions and between different microbial groups.

scholarly journals Re-evaluating the salty divide: phylogenetic specificity of transitions between marine and freshwater systems

2018 ◽  
Author(s):  
Sara F. Paver ◽  
Daniel J. Muratore ◽  
Ryan J. Newton ◽  
Maureen L. Coleman
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Environmental Changes ◽  
Habitat Type ◽  
Freshwater Ecosystems ◽  
Rrna Gene ◽  
Minimum Entropy ◽  
Habitat Types

AbstractMarine and freshwater microbial communities are phylogenetically distinct and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing datasets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages; at the same time, however, many shared taxa were observed in both environments. Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between marine and freshwater sample pairs. Gammaproteobacteria and Alphaproteobacteria contained the highest number of Minimum Entropy Decomposition nodes shared by marine and freshwater samples. Shared nodes included lineages of the abundant alphaproteobacterial group SAR11 that have not previously been reported in 16S rRNA gene surveys of freshwater lakes. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Lineages with a high degree of shared taxa or habitat-specific diversification represent targets for genome-scale investigations into microbial adaptations and evolutionary innovations. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may have novel adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change.ImportanceThe distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated datasets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed phyla and proteobacterial classes inferred to include more or less recent transitions across habitat types as well as specific lineages that are shared by marine and freshwater environments at the level of 16S rRNA sequence types. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.

scholarly journals Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems

mSystems ◽  
2018 ◽  
Vol 3 (6) ◽  
Author(s):  
Sara F. Paver ◽  
Daniel Muratore ◽  
Ryan J. Newton ◽  
Maureen L. Coleman
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Environmental Changes ◽  
Habitat Type ◽  
Freshwater Ecosystems ◽  
Rrna Gene ◽  
Data Sets ◽  
Sequencing Data ◽  
Habitat Types

ABSTRACTMarine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages. At the same time, and contrary to expectations, many shared taxa were observed in both habitats. Based on several metrics, we found thatGammaproteobacteria,Alphaproteobacteria,Bacteroidetes, andBetaproteobacteriacontained the highest number of closely related marine and freshwater sequences, suggesting comparatively recent habitat transitions in these groups. Using the abundant alphaproteobacterial group SAR11 as an example, we found evidence that new lineages, beyond the recognized LD12 clade, are detected in freshwater at low but reproducible abundances; this evidence extends beyond the 16S rRNA locus to core genes throughout the genome. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may possess adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change.IMPORTANCEThe distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated data sets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed lineages that likely experienced a recent transition across habitat types. These taxa are promising targets for studying physiological constraints on salinity tolerance. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.

scholarly journals Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions

2019 ◽  
Author(s):  
Máté Vass ◽  
Anna J. Székely ◽  
Eva S. Lindström ◽  
Silke Langenheder
Keyword(s):  
Community Assembly ◽  
Environmental Conditions ◽  
Null Model ◽  
Temporal Variations ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Historical Contingency ◽  
Selection Processes ◽  
Rrna Gene Sequencing ◽  
Microbial Groups

AbstractTemporal variations in microbial metacommunity structure and assembly processes in response to shifts in environmental conditions are poorly understood. Hence, we conducted a temporal field study by sampling rock pools in four-day intervals during a 5-week period that included strong changes in environmental conditions due to intensive rain. We characterized bacterial and microeukaryote communities by 16S and 18S rRNA gene sequencing, respectively. Using a suite of null-model approaches to assess dynamics in community assembly, we found that strong changes in environmental conditions induced small but significant temporal changes in assembly processes and triggered different responses in bacterial and microeukaryotic metacommunities, promoting distinct selection processes. Incidence-based approaches showed that the assemblies of both communities were mainly governed by stochastic processes. In contrast, abundance-based methods indicated the dominance of historical contingency and unmeasured factors in case of bacteria and microeukaryotes, respectively, which we distinguished from dispersal-related processes using additional tests. Taken together, our study highlights that community assembly processes are not static, and the relative importance of different assembly processes can vary under different conditions and between different microbial groups.

scholarly journals Revealing the composition of the eukaryotic microbiome of oyster spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS)

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Kevin Xu Zhong ◽  
Anna Cho ◽  
Christoph M. Deeg ◽  
Amy M. Chan ◽  
Curtis A. Suttle
Keyword(s):  
Fungal Pathogens ◽  
18S Rrna ◽  
Amplicon Sequencing ◽  
18S Rrna Gene ◽  
Model Organisms ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Oyster Spat ◽  
16S Rna ◽  
Eukaryotic Microbes

Abstract Background The microbiome affects the health of plants and animals, including humans, and has many biological, ecological, and evolutionary consequences. Microbiome studies typically rely on sequencing ribosomal 16S RNA gene fragments, which serve as taxonomic markers for prokaryotic communities; however, for eukaryotic microbes this approach is compromised, because 18S rRNA gene sequences from microbial eukaryotes are swamped by contaminating host rRNA gene sequences. Results To overcome this problem, we developed CRISPR-Cas Selective Amplicon Sequencing (CCSAS), a high-resolution and efficient approach for characterizing eukaryotic microbiomes. CCSAS uses taxon-specific single-guide RNA (sgRNA) to direct Cas9 to cut 18S rRNA gene sequences of the host, while leaving protistan and fungal sequences intact. We validated the specificity of the sgRNA on ten model organisms and an artificially constructed (mock) community of nine protistan and fungal pathogens. The results showed that > 96.5% of host rRNA gene amplicons were cleaved, while 18S rRNA gene sequences from protists and fungi were unaffected. When used to assess the eukaryotic microbiome of oyster spat from a hatchery, CCSAS revealed a diverse community of eukaryotic microbes, typically with much less contamination from oyster 18S rRNA gene sequences than other methods using non-metazoan or blocking primers. However, each method revealed taxonomic groups that were not detected using the other methods, showing that a single approach is unlikely to uncover the entire eukaryotic microbiome in complex communities. To facilitate the application of CCSAS, we designed taxon-specific sgRNA for ~16,000 metazoan and plant taxa, making CCSAS widely available for characterizing eukaryotic microbiomes that have largely been neglected. Conclusion CCSAS provides a high-through-put and cost-effective approach for resolving the eukaryotic microbiome of metazoa and plants with minimal contamination from host 18S rRNA gene sequences.

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