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189
Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 6, 12.PLoS One 7
, 2011
"... Background: Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affec ..."
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Background: Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition. Methodology/Principal Findings: We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (.1 % of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of
R (2010) Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution
- Nature Methods
"... We developed a fast method for denoising pyrosequencing for community 16S rRNA analysis. We observe a 2–4 fold reduction in the number of observed OTUs (operational taxonomic units) comparing denoised with non-denoised data. ~50,000 sequences can be denoised on a laptop within an hour, two orders of ..."
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Cited by 16 (0 self)
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We developed a fast method for denoising pyrosequencing for community 16S rRNA analysis. We observe a 2–4 fold reduction in the number of observed OTUs (operational taxonomic units) comparing denoised with non-denoised data. ~50,000 sequences can be denoised on a laptop within an hour, two orders of magnitude faster than published techniques. We demonstrate the effects of denoising on alpha and beta diversity of large 16S rRNA datasets. Keywords next generation DNA sequencing; ribosomal RNA; community sequence analysis; microbial ecology; denoising Pyrosequencing1 has revolutionized microbial community analysis by allowing the simultaneous assessment of hundreds of microbial communities in multiplex with sufficient depth to resolve meaningful biological patterns2. These techniques have been used to gain striking new insight into microbial processes on scales ranging from continents3 to within an individual’s body4. Although powerful new analysis tools such as GAST5, Mothur6, and QIIME7 greatly
Desert Farming Benefits from Microbial Potential in Arid Soils and Promotes Diversity and Plant Health
"... Background: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still n ..."
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Background: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. Methodology/Principal Findings: We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96 % of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after
A high-throughput DNA sequence aligner for microbial ecology studies
- PLoS ONE
, 2009
"... As the scope of microbial surveys expands with the parallel growth in sequencing capacity, a significant bottleneck in data analysis is the ability to generate a biologically meaningful multiple sequence alignment. The most commonly used aligners have varying alignment quality and speed, tend to dep ..."
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Cited by 14 (0 self)
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As the scope of microbial surveys expands with the parallel growth in sequencing capacity, a significant bottleneck in data analysis is the ability to generate a biologically meaningful multiple sequence alignment. The most commonly used aligners have varying alignment quality and speed, tend to depend on a specific reference alignment, or lack a complete description of the underlying algorithm. The purpose of this study was to create and validate an aligner with the goal of quickly generating a high quality alignment and having the flexibility to use any reference alignment. Using the simple nearest alignment space termination algorithm, the resulting aligner operates in linear time, requires a small memory footprint, and generates a high quality alignment. In addition, the alignments generated for variable regions were of as high a quality as the alignment of full-length sequences. As implemented, the method was able to align 18 full-length 16S rRNA gene sequences and 58 V2 region sequences per second to the 50,000-column SILVA reference alignment. Most importantly, the resulting alignments were of a quality equal to SILVA-generated alignments. The aligner described in this study will enable scientists to rapidly generate robust multiple sequences alignments that are implicitly based upon the predicted secondary structure of the 16S rRNA molecule. Furthermore, because the implementation is not connected to a specific database it is easy to generalize the method to reference alignments for any DNA sequence.
Mangroves: A Review. In
, 1974
"... doi: 10.3389/fphar.2011.00064 Targeting GIRK channels for the development of new therapeutic agents ..."
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doi: 10.3389/fphar.2011.00064 Targeting GIRK channels for the development of new therapeutic agents
Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes
- PLoS ONE
, 2013
"... Most of our time is spent indoors where we are exposed to a wide array of different microorganisms living on surfaces and in the air of our homes. Despite their ubiquity and abundance, we have a limited understanding of the microbial diversity found within homes and how the composition and diversity ..."
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Cited by 12 (1 self)
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Most of our time is spent indoors where we are exposed to a wide array of different microorganisms living on surfaces and in the air of our homes. Despite their ubiquity and abundance, we have a limited understanding of the microbial diversity found within homes and how the composition and diversity of microbial communities change across different locations within the home. Here we examined the diversity of bacterial communities found in nine distinct locations within each of forty homes in the Raleigh-Durham area of North Carolina, USA, using high-throughput sequencing of the bacterial 16S rRNA gene. We found that each of the sampled locations harbored bacterial communities that were distinct from one another with surfaces that are regularly cleaned typically harboring lower levels of diversity than surfaces that are cleaned infrequently. These location-specific differences in bacterial communities could be directly related to usage patterns and differences in the likely sources of bacteria dispersed onto these locations. Finally, we examined whether the variability across homes in bacterial diversity could be attributed to outdoor environmental factors, indoor habitat structure, or the occupants of the home. We found that the presence of dogs had a significant effect on bacterial community composition in multiple locations within homes as the homes occupied by dogs harbored more diverse communities and higher relative abundances of dog-associated bacterial taxa. Furthermore, we found a significant correlation between the types of bacteria deposited on surfaces outside the home and those found inside the home, highlighting that microbes from outside the
FeFe]-hydrogenase in Yellowstone National Park: evidence of dispersal limitation and phylogenetic niche conservatism
- The ISME Journal
, 2010
"... Hydrogen (H 2 ) has an important role in the anaerobic degradation of organic carbon and is the basis for many syntrophic interactions that commonly occur in microbial communities. Little is known, however, with regard to the biotic and/or abiotic factors that control the distribution and phylogene ..."
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Cited by 7 (2 self)
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Hydrogen (H 2 ) has an important role in the anaerobic degradation of organic carbon and is the basis for many syntrophic interactions that commonly occur in microbial communities. Little is known, however, with regard to the biotic and/or abiotic factors that control the distribution and phylogenetic diversity of organisms which produce H 2 in microbial communities. In this study, we examined the [FeFe]-hydrogenase gene (hydA) as a proxy for fermentative bacterial H 2 production along physical and chemical gradients in various geothermal springs in Yellowstone National Park (YNP), WY, USA. The distribution of hydA in YNP geothermal springs was constrained by pH to environments co-inhabited by oxygenic phototrophs and to environments predicted to have low inputs of abiotic H 2 . The individual HydA asssemblages from YNP springs were more closely related when compared with randomly assembled communities, which suggests ecological filtering. Model selection approaches revealed that geographic distance was the best explanatory variable to predict the phylogenetic relatedness of HydA communities. This evinces the dispersal limitation imposed by the geothermal spring environment on HydA phylogenetic diversity even at small spatial scales. pH differences between sites is the second highest ranked explanatory variable of HydA phylogenetic relatedness, which suggests that the ecology related to pH imposes strong phylogenetic niche conservatism. Collectively, these results indicate that pH has imposed strong niche conservatism on fermentative bacteria and that, within a narrow pH realm, YNP springs are dispersal limited with respect to fermentative bacterial communities.
Evolutionary relationships of wild hominids recapitulated by gut microbial communities
- PLoS Biol
, 2010
"... Multiple factors over the lifetime of an individual, including diet, geography, and physiologic state, will influence the microbial communities within the primate gut. To determine the source of variation in the composition of the microbiota within and among species, we investigated the distal gut m ..."
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Multiple factors over the lifetime of an individual, including diet, geography, and physiologic state, will influence the microbial communities within the primate gut. To determine the source of variation in the composition of the microbiota within and among species, we investigated the distal gut microbial communities harbored by great apes, as present in fecal samples recovered within their native ranges. We found that the branching order of host-species phylogenies based on the composition of these microbial communities is completely congruent with the known relationships of the hosts. Although the gut is initially and continuously seeded by bacteria that are acquired from external sources, we establish that over evolutionary timescales, the composition of the gut microbiota among great ape species is phylogenetically conserved and has diverged in a manner consistent with vertical inheritance.
The rate of permafrost carbon release under aerobic and anaerobic conditions and its potential effects on climate
"... Recent observations suggest that permafrost thaw may create two completely different soil environments: aerobic in relatively well-drained uplands and anaerobic in poorly drained wetlands. The soil oxygen availability will dictate the rate of permafrost carbon release as carbon dioxide (CO 2) and as ..."
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Cited by 6 (0 self)
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Recent observations suggest that permafrost thaw may create two completely different soil environments: aerobic in relatively well-drained uplands and anaerobic in poorly drained wetlands. The soil oxygen availability will dictate the rate of permafrost carbon release as carbon dioxide (CO 2) and as methane (CH 4), and the overall effects of these emitted greenhouse gases on climate. The objective of this study was to quantify CO2 and CH4 release over a 500-day period from permafrost soil under aerobic and anaerobic conditions in the laboratory and to compare the potential effects of these emissions on future climate by estimating their relative climate forcing. We used permafrost soils collected from Alaska and Siberia with varying organic matter characteristics and simultaneously incubated them under aerobic and anaerobic conditions to determine rates of CO 2 and CH 4 production. Over 500 days of soil incubation at 15 °C, we observed that carbon released under aerobic conditions was 3.9–10.0 times greater than anaerobic conditions. When scaled by greenhouse warming potential to account for differences between CO 2 and CH 4, relative climate forcing ranged between 1.5 and 7.1. Carbon release in organic soils was nearly 20 times greater than mineral soils on a per gram soil basis, but when compared on a per gram carbon basis, deep permafrost mineral soils showed carbon release rates similar to organic soils for some soil types. This suggests that permafrost carbon may be very labile, but that there are significant differences across soil types depending on the processes that controlled initial permafrost
The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms
- FEMS Microbiol Rev
, 2013
"... plant–microbe interactions; plant growth promotion; food safety; disease-suppressive soils; core and minimal microbiome; metagenomics. Microbial communities play a pivotal role in the functioning of plants by influ-encing their physiology and development. While many members of the rhizo-sphere micro ..."
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Cited by 6 (1 self)
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plant–microbe interactions; plant growth promotion; food safety; disease-suppressive soils; core and minimal microbiome; metagenomics. Microbial communities play a pivotal role in the functioning of plants by influ-encing their physiology and development. While many members of the rhizo-sphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protec-tive microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when intro-duced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizo-sphere microbiome and what they are doing. Here, we review the main func-tions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight sev-eral strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health.
