scholarly journals Phylogenetic Comparisons of Bacterial Communities from Serpentine and Nonserpentine Soils

2006 ◽  
Vol 72 (11) ◽  
pp. 6965-6971 ◽  
Author(s):  
David K. Oline
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
Regional Scale ◽  
Serpentine Soils ◽  
Operational Taxonomic Units ◽  
Microbial Biogeography ◽  
Soil Bacterial Communities ◽  
Culture Independent ◽  
Control Community ◽  
16S Rrna Clone Libraries

ABSTRACT I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale (∼100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography.

scholarly journals Streptomyces strains modulate dynamics of soil bacterial communities and their efficacy in disease suppression caused by Phytophthora capsici

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Abbasi Sakineh ◽  
Spor Ayme ◽  
Sadeghi Akram ◽  
Safaie Naser
Keyword(s):  
Bacterial Communities ◽  
Phytophthora Capsici ◽  
Illumina Miseq ◽  
Disease Suppression ◽  
Positive Interactions ◽  
Alpha And Beta Diversity ◽  
Operational Taxonomic Units ◽  
Soil Bacterial Communities ◽  
Phosphate Solubilizing ◽  
And Control

AbstractThe responses of rhizosphere bacterial communities of Streptomyces (SS14 and IT20 stains) treated-pepper plants following inoculation by Phytophthora capsici (PC) was investigated using Illumina MiSeq sequencing. Distinct modulation of the bacteriome composition was found for PC samples with the highest relative abundance (RA) of Chitinophaga (22 ± 0.03%). The RA of several bacterial operational taxonomic units (OTUs) was affected and caused changes in alpha and beta-diversity measures. In IT20, the RA of Cyanobacteria was enriched compared to SS14 (72%) and control samples (47%). Phylotypes belonging to Devosia, Promicromonospora, Kribbella, Microbacterium, Amylocolatopsis, and Pseudomonas genera in the rhizosphere were positively responding against the pathogen. Our findings show that the phosphate solubilizing strain IT20 has higher microbial community responders than the melanin-producing strain SS14. Also, positive interactions were identified by comparing bacterial community profiles between treatments that might allow designing synthetic bio-inoculants to solve agronomic problems in an eco-friendly way.

scholarly journals Understanding the Responses of Soil Bacterial Communities to Long-Term Fertilization Regimes Using DNA and RNA Sequencing

Agronomy ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2425
Author(s):  
Juan Li ◽  
Yanchen Wen ◽  
Xiangdong Yang
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
Alkaline Soil ◽  
Soil Dna ◽  
Olsen P ◽  
Soil Bacterial Communities ◽  
Dna And Rna ◽  
Relative Abundances ◽  
Soil Bacterial

Studies of soil DNA-based and RNA-based bacterial communities under contrasting long-term fertilization regimes can provide valuable insights into how agricultural management affects soil microbial structure and functional diversity. In this study, soil bacterial communities subjected to six fertility treatments in an alkaline soil over 27 years were investigated by 454 pyrosequencing based on 16S rDNA and 16S rRNA. Long-term fertilization showed significant influences on the diversity of the soil DNA-based bacteria, as well as on their RNA-based members. The top five phyla (Proteobacteria, Acidobacteria, Chloroflexi, Actinobacteria, and Planctomycetes) were found in both the DNA- and RNA-based samples. However, the relative abundances of these phyla at both DNA and RNA levels were showed significantly different. Analysis results showed that the diversity of the 16S rRNA samples was consistently lower than that of the rDNA samples, however, 16S rRNA samples had higher relative abundance. PICRUSt analysis indicated that glycan biosynthesis and metabolism were detected mainly in the DNA samples, while metabolism and degradation of xenobiotics and the metabolism of amino acids, terpenoids and polyketides were relatively higher in the RNA samples. Bacilli were significantly more abundant in all the OM-fertilized soils. Redundancy analysis indicated that the relative abundances of both DNA- and RNA-based bacterial groups were correlated with soil total organic carbon content, nitrogen content, Olsen-P, and soil pH. Moreover, the RNA-based Bacilli were positively correlated with available phosphorus (Olsen-P).

Rare unclassified 16S rRNA operational taxonomic units from the uncharted Engaño Bay (Argentinean Patagonia)

2018 ◽  
Vol 64 (1) ◽  
pp. 91-96
Author(s):  
Andrea Y. Calvo ◽  
Julieta M. Manrique ◽  
Leandro R. Jones
Keyword(s):  
16S Rrna ◽  
Community Dynamics ◽  
Sequence Data ◽  
River Estuary ◽  
Fragmented Habitats ◽  
Operational Taxonomic Units ◽  
Microbial Community Dynamics ◽  
Argentinean Patagonia ◽  
Culture Independent ◽  
Taxonomic Assignments

Rare microbes make up most of the diversity of marine microbiomes, and recent works have highlighted their importance for microbial community dynamics and in fragmented habitats. Rare taxa have been infrequently studied in comparison with abundant groups, and rare unclassified sequences are common in culture-independent studies. Here, we describe a detailed analysis of nonclassifiable sequences from the Chubut river estuary at the Argentinean Patagonia. Standard taxonomic assignments of environmental 16S rRNA sequences resulted in about 13% unclassified operational taxonomic units (OTUs). The potential affiliations of these OTUs could be narrowed by mapping the classification software assignments on a phylogeny obtained directly from our environmental sequence data. Customized BLAST analyses were remarkably consistent with these phylogenetic assignments, especially when the unclassified OTUs were blasted against sequences from cultured and type microorganisms. In addition, our BLAST analyses revealed significant similarities between several unclassified OTUs and a plethora of unclassified sequences from around the world. Further phylogenetic comparisons with 6194 carefully selected reference sequences showed that these unclassified sequences may correspond to 5 unnamed groups, possibly encompassing ranks from subclass to family inside the Alphaproteobacteria, and to an unknown Gracilibacteria lineage. Overall, these results demonstrate the value of straight phylogenetic analysis, customized BLAST searches, and comparisons with sequences from type material, for the systematic study of rare unclassified sequences.

scholarly journals High-Resolution Profiling of Gut Bacterial Communities in an Invasive Beetle using PacBio SMRT Sequencing System

Insects ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 248 ◽  
Author(s):  
Letian Xu ◽  
Liuwei Sun ◽  
Shihan Zhang ◽  
Shanshan Wang ◽  
Min Lu
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Severe Damage ◽  
Rrna Sequencing ◽  
Culture Independent ◽  
Taxonomic Uncertainty ◽  
Invasive Beetle ◽  
Pacbio Smrt Sequencing ◽  
Rrna Sequences

Dendroctonus valens, an invasive bark beetle, has caused severe damage to Chinese forests. Previous studies have highlighted the importance of the gut microbiota and its fundamental role in host fitness. Culture-dependent and culture-independent methods have been applied in analyzing beetles’ gut microbiota. The former method cannot present a whole picture of the community, and the latter mostly generates short read lengths that cannot be assigned to species. Here, the PacBio sequencing system was utilized to capture full-length 16S rRNA sequences in D. valens gut throughout its ontogeny. A total of eight phyla, 55 families, 102 genera, and 253 species were identified. Bacterial communities in colonized beetles have the greatest richness but the lowest evenness in all life stages, which is different from those in young larvae. Pseudomonas sp., Serratia liquefaciens possess high abundance throughout its ontogeny and may serve as members of the core bacteriome. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis predicted that gut microbiota in larvae are rich in genes involved in carbohydrate, energy metabolism. Gut microbiota in both larvae and colonized beetles are rich in xenobiotics and terpenoids biodegradation, which are decreased in dispersal beetles. Considering that the results are based mainly on the analysis of 16S rRNA sequencing and PICRUSt prediction, further confirmation is needed to improve the knowledge of the gut microbiota in D. valens and help to resolve taxonomic uncertainty at the species level.

scholarly journals Comparison of Diversities and Compositions of Bacterial Populations Inhabiting Natural Forest Soils

2004 ◽  
Vol 70 (9) ◽  
pp. 5057-5065 ◽  
Author(s):  
Evelyn Hackl ◽  
Sophie Zechmeister-Boltenstern ◽  
Levente Bodrossy ◽  
Angela Sessitsch
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Community Composition ◽  
Forest Soils ◽  
Bacterial Communities ◽  
Pine Forests ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

ABSTRACT The diversity and composition of soil bacterial communities were compared among six Austrian natural forests, including oak-hornbeam, spruce-fir-beech, and Austrian pine forests, using terminal restriction fragment length polymorphism (T-RFLP, or TRF) analysis and sequence analysis of 16S rRNA genes. The forests studied differ greatly in soil chemical characteristics, microbial biomass, and nutrient turnover rates. The aim of this study was to relate these differences to the composition of the bacterial communities inhabiting the individual forest soils. Both TRF profiling and clone sequence analysis revealed that the bacterial communities in soils under Austrian pine forests, representing azonal forest types, were distinct from those in soils under zonal oak-hornbeam and spruce-fir-beech forests, which were more similar in community composition. Clones derived from an Austrian pine forest soil were mostly affiliated with high-G+C gram-positive bacteria (49%), followed by members of the α-Proteobacteria (20%) and the Holophaga/Acidobacterium group (12%). Clones in libraries from oak-hornbeam and spruce-fir-beech forest soils were mainly related to the Holophaga/Acidobacterium group (28 and 35%), followed by members of the Verrucomicrobia (24%) and the α-Proteobacteria (27%), respectively. The soil bacterial communities in forests with distinct vegetational and soil chemical properties appeared to be well differentiated based on 16S rRNA gene phylogeny. In particular, the outstanding position of the Austrian pine forests, which are determined by specific soil conditions, was reflected in the bacterial community composition.

scholarly journals Effect of pH on Isolation and Distribution of Members of Subdivision 1 of the Phylum Acidobacteria Occurring in Soil

2006 ◽  
Vol 72 (3) ◽  
pp. 1852-1857 ◽  
Author(s):  
Michelle Sait ◽  
Kathryn E. R. Davis ◽  
Peter H. Janssen
Keyword(s):  
16S Rrna ◽  
Soil Ph ◽  
Strong Correlation ◽  
Bacterial Communities ◽  
Growth Conditions ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Effect Of Ph ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

ABSTRACT The pH strongly influenced the development of colonies by members of subdivision 1 of the phylum Acidobacteria on solid laboratory media. Significantly more colonies of this group formed at pH 5.5 than at pH 7.0. At pH 5.5, 7 to 8% of colonies that formed on plates that were incubated for 4 months were formed by subdivision 1 acidobacteria. These colonies were formed by bacteria that spanned almost the entire phylogenetic breadth of the subdivision, and there was considerable congruence between the diversity of this group as determined by the cultivation-based method and by surveying 16S rRNA genes in the same soil. Members of subdivision 1 acidobacteria therefore appear to be readily culturable. An analysis of published libraries of 16S rRNAs or 16S rRNA genes showed a very strong correlation between the abundance of subdivision 1 acidobacteria in soil bacterial communities and the soil pH. Subdivision 1 acidobacteria were most abundant in libraries from soils with pHs of <6, but rare or absent in libraries from soils with pHs of >6.5. This, together with the selective cultivation of members of the group on lower-pH media, indicates that growth of many members of subdivision 1 acidobacteria is favored by slightly to moderately acidic growth conditions.

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