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.

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 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 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 Identification of nontuberculous mycobacteria isolated from hospital water by sequence analysis of the hsp65 and 16S rRNA genes

2017 ◽  
Vol 15 (5) ◽  
pp. 766-774 ◽  
Author(s):  
Mehdi Roshdi Maleki ◽  
Hossein Samadi Kafil ◽  
Naser Harzandi ◽  
Seyyed Reza Moaddab
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Distribution Systems ◽  
Water Distribution ◽  
Nontuberculous Mycobacteria ◽  
Cetylpyridinium Chloride ◽  
Water Distribution Systems ◽  
Single Species ◽  
16S Rrna Genes ◽  
Rrna Genes

Nontuberculous mycobacteria (NTM) have emerged as an important cause of opportunistic nosocomial infections. NTM has frequently been isolated from hospital water distribution systems. The aim of this study was to survey the risk of NTM infections and determine the prevalence of NTM species in the hospital water distribution systems in Tabriz, Iran. One hundred and twenty samples of water from different sources of Tabriz hospitals were collected. The samples were filtered through 0.45-µm pore size membranes and decontaminated with 0.01% cetylpyridinium chloride. The sediment was inoculated onto Lowenstein–Jensen medium and incubated for 8 weeks. For identification to the species level, partial sequence analysis of the hsp65 and 16S rRNA genes were used. NTM were detected in 76 (63.3%) of 120 samples. Potentially pathogenic mycobacteria and saprophytic mycobacteria were isolated. Mycobacterium gordonae was the only single species that was present in all types of water. The prevalence of NTM in Tabriz hospitals' water compared with many investigations on hospital waters was high. This indicates that the immunocompromised patients and transplant recipients are at risk of contamination which necessitates considering decontamination of water sources to prevent such potential hazards.

scholarly journals Urbanization and Carpobrotus edulis invasion alter the diversity and composition of soil bacterial communities in coastal areas

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Ana Novoa ◽  
Jan-Hendrik Keet ◽  
Yaiza Lechuga-Lago ◽  
Petr Pyšek ◽  
Johannes J Le Roux
Keyword(s):  
Community Composition ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Coastal Dunes ◽  
Coastal Dune ◽  
Western Coast ◽  
Carpobrotus Edulis ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
The Impact

ABSTRACT Coastal dunes are ecosystems of high conservation value that are strongly impacted by human disturbances and biological invasions in many parts of the world. Here, we assessed how urbanization and Carpobrotus edulis invasion affect soil bacterial communities on the north-western coast of Spain, by comparing the diversity, structure and composition of soil bacterial communities in invaded and uninvaded soils from urban and natural coastal dune areas. Our results suggest that coastal dune bacterial communities contain large numbers of rare taxa, mainly belonging to the phyla Actinobacteria and Proteobacteria. We found that the presence of the invasive C. edulis increased the diversity of soil bacteria and changed community composition, while urbanization only influenced bacterial community composition. Furthermore, the effects of invasion on community composition were conditional on urbanization. These results were contrary to predictions, as both C. edulis invasion and urbanization have been shown to affect soil abiotic conditions of the studied coastal dunes in a similar manner, and therefore were expected to have similar effects on soil bacterial communities. Our results suggest that other factors (e.g. pollution) might be influencing the impact of urbanization on soil bacterial communities, preventing an increase in the diversity of soil bacteria in urban areas.

scholarly journals Multilocus sequence analysis of Ensifer and related taxa

2007 ◽  
Vol 57 (3) ◽  
pp. 489-503 ◽  
Author(s):  
Miet Martens ◽  
Manuel Delaere ◽  
Renata Coopman ◽  
Paul De Vos ◽  
Monique Gillis ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Housekeeping Genes ◽  
16S Rrna Genes ◽  
New Combination ◽  
Rrna Genes ◽  
Multilocus Sequence Analysis ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Separate Species

Multilocus sequence analysis (MLSA) was performed on representatives of Ensifer (including species previously assigned to the genus Sinorhizobium) and related taxa. Neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) phylogenies of dnaK, gltA, glnA, recA, thrC and 16S rRNA genes were compared. The data confirm that the potential for discrimination of Ensifer species is greater using MLSA of housekeeping genes than 16S rRNA genes. In incongruence-length difference tests, the 16S rRNA gene was found to be significantly incongruent with the other genes, indicating that this gene should not be used as a single indicator of relatedness in this group. Significant congruence was detected for dnaK, glnA and thrC. Analyses of concatenated sequences of dnaK, glnA and thrC genes yielded very similar NJ, MP and ML trees, with high bootstrap support. In addition, analysis of a concatenation of all six genes essentially produced the same result, levelling out potentially conflicting phylogenetic signals. This new evidence supports the proposal to unite Ensifer and Sinorhizobium in a single genus. Support for an alternative solution preserving the two genera is less strong. In view of the opinions expressed by the Judicial Commission, the name of the genus should be Ensifer, as proposed by Young [Young, J. M. (2003). Int J Syst Evol Microbiol 53, 2107–2110]. Data obtained previously and these new data indicate that Ensifer adhaerens and ‘Sinorhizobium morelense’ are not heterotypic synonyms, but represent separate species. However, transfer to the genus Ensifer is not possible at present because the species name is the subject of a pending Request for an Opinion, which would affect whether a novel species in the genus Ensifer or a new combination based on a basonym would be created.

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