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.

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 Changes in the Soil Bacterial Community in a Chronosequence of Temperate Walnut-Based Intercropping Systems

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 299 ◽  
Author(s):  
Pengxiang Gao ◽  
Xiaofeng Zheng ◽  
Lai Wang ◽  
Bin Liu ◽  
Shuoxin Zhang
Keyword(s):  
Bacterial Community ◽  
Soil Ph ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Agroforestry System ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Phyla ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Agroforestry (tree-based intercropping) is regarded as a promising practice in sustainable agricultural management. However, the impacts of converting cropland to an agroforestry system on microbial communities remain poorly understood. In this study, we assessed the soil bacterial communities in conventional wheat monoculture systems and a chronosequence (5–14 years) walnut-wheat agroforestry system through the high-throughput sequencing of 16S rRNA genes to investigate the effect of agroforestry age on soil bacterial communities and the correlation between soil properties and bacterial communities in the agroecosystem. Our results demonstrate that establishing and developing walnut tree-based agroforestry increased soil bacterial diversity and changed bacterial community structure. Firmicutes, Proteobacteria, Actinobacteria and Acidobacteria were the dominant soil bacterial phyla and Bacillus was the dominant genus. Crop monoculture systems were characterized by the Bacillus (Firmicutes)-dominated microbial community. The relative abundance of Bacillus decreased with agroforestry age; however, subgroups of Proteobacteria and Actinobacteria increased. Of the selected soil physicochemical properties, soil pH and bulk density were significantly correlated with bacterial alpha diversity, and soil pH and organic carbon were the principal drivers in shaping the soil microbial structure as revealed by redundancy analysis (RDA).

scholarly journals Tree rows in temperate agroforestry croplands alter the composition of soil bacterial communities

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246919
Author(s):  
Lukas Beule ◽  
Petr Karlovsky
Keyword(s):  
Bacterial Communities ◽  
Alley Cropping ◽  
Arable Land ◽  
Soil Microbial Communities ◽  
Agroforestry Systems ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Bacterial Communities ◽  
Temperate Agroforestry ◽  
Soil Bacterial

Background Tree-based intercropping (agroforestry) has been advocated to reduce adverse environmental impacts of conventional arable cropping. Modern agroforestry systems in the temperate zone are alley-cropping systems that combine rows of fast-growing trees with rows of arable crops. Soil microbial communities in these systems have been investigated intensively; however, molecular studies with high taxonomical resolution are scarce. Methods Here, we assessed the effect of temperate agroforestry on the abundance, diversity and composition of soil bacterial communities at three paired poplar-based alley cropping and conventional monoculture cropland systems using real-time PCR and Illumina sequencing of bacterial 16S rRNA genes. Two of the three systems grew summer barley (Hordeum vulgare); one system grew maize (Zea mays) in the sampling year. To capture the spatial heterogeneity induced by the tree rows, soil samples in the agroforestry systems were collected along transects spanning from the centre of the tree rows to the centre of the agroforestry crop rows. Results Tree rows of temperate agroforestry systems increased the abundance of soil bacteria while their alpha diversity remained largely unaffected. The composition of the bacterial communities in tree rows differed from those in arable land (crop rows of the agroforestry systems and conventional monoculture croplands). Several bacterial groups in soil showed strong association with either tree rows or arable land, revealing that the introduction of trees into arable land through agroforestry is accompanied by the introduction of a tree row-associated microbiome. Conclusion The presence of tree row-associated bacteria in agroforestry increases the overall microbial diversity of the system. We speculate that the increase in biodiversity is accompanied by functional diversification. Differences in plant-derived nutrients (root exudates and tree litter) and management practices (fertilization and tillage) likely account for the differences between bacterial communities of tree rows and arable land in agroforestry systems.

scholarly journals Impact of Bukit Dua Belas rainforest transformation to oil palm plantation on phylogenetic of soil bacterial communities in Sarolangun, Jambi, Sumatra, Indonesia

2019 ◽  
Vol 20 (3) ◽  
pp. 811-818
Author(s):  
MARINI WIJAYANTI ◽  
ARIS TRI WAHYUDI ◽  
MUNTI YUHANA ◽  
MARTIN ENGELHAUPT ◽  
ANJA MERYANDINI
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
Soil Ph ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Bacterial Phyla ◽  
Soil Bacterial Communities ◽  
Oil Palm Plantation ◽  
Community Shift ◽  
Soil Bacterial

Abstract. Wijayanti M, Wahyudi AT, Yuhana M, Engelhaupt M, Meryandini A. 2019. Impact of Bukit Dua Belas rainforest transformation to oil palm plantation on phylogenetic of soil bacterial communities in Sarolangun, Jambi, Sumatra, Indonesia. Biodiversitas 20: 811-818. Land use change from forest to oil palm plantation at Sumatra could decrease biodiversity, including bacterial diversity. The case of Bukit Dua Belas transformation from forest to oil palm plantation was gotten for measuring shift community of soil bacterial in both areas. The diversity of bacterial communities from rainforest and oil palm plantation topsoil in Sumatra was studied using pyrosequencing of 16S rRNA gene and common biodiversity indices. Phylogenetic approach was used to reveal the community shift of bacterial phyla and genera in both areas. Ecological approach was carried out by measuring soil pH, TC (total carbon), TN (total nitrogen), AP (available phosphorous), bacterial diversity with Shannon and Simpson indices, and bacterial richness with Chao1-ACE index and OTUs. Bacterial diversity and richness on lowland forest topsoil and oil palm plantation soil were not different, as soil pH, TC, and TN as substrate factors were not different significantly. The majority of sequences related to Acidobacteria (56.33%), Proteobacteria (27.43%), Actinobacteria (7.11%), and Cyanobacteria (5.55%) were from forest; whereas those related to Acidobacteria (50.11%), Proteobacteria (31.63%), Actinobacteria (7.58%), Chloroflexi (2.60%), and Gemmatimonadetes (2.71%) invented from oil palm plantation. Acidobacteria was the most dominant phyla in both habitats, because soil pH in both areas was acidic (3.77 - 4.80 pHH2O). The genera of alpha-proteobacteria dominated in genera phylotype of bacterial 16S rRNA phylogenetic revealed in both forest and oil palm plantation topsoil. The most genera in phylogenetic tree are Burkholderia from Beta-proteobacteria. The bacterial community shift occurred in forest transformation, even though the oil palm plantation showed more bacterial phyla and genera than the lowland rainforest.

scholarly journals Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

2009 ◽  
Vol 75 (15) ◽  
pp. 5111-5120 ◽  
Author(s):  
Christian L. Lauber ◽  
Micah Hamady ◽  
Rob Knight ◽  
Noah Fierer
Keyword(s):  
Bacterial Community ◽  
Soil Ph ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Spatial Scales ◽  
Bacterial Community Composition ◽  
Phylogenetic Structure ◽  
Soil Bacterial Communities ◽  
Soil Bacterial Community Structure ◽  
Soil Bacterial

ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

scholarly journals Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management

2016 ◽  
Vol 103 ◽  
pp. 337-348 ◽  
Author(s):  
Kayla N. Burns ◽  
Nicholas A. Bokulich ◽  
Dario Cantu ◽  
Rachel F. Greenhut ◽  
Daniel A. Kluepfel ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Bacterial Diversity ◽  
Vineyard Soil ◽  
Soil Bacterial ◽  
Vineyard Management

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).

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