Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance

2002 ◽  
Vol 48 (7) ◽  
pp. 655-674 ◽  
Author(s):  
Paige E Axelrood ◽  
Monica L Chow ◽  
Christopher C Radomski ◽  
Joseph M McDermott ◽  
Julian Davies
Keyword(s):  
Organic Matter ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soils ◽  
Soil Compaction ◽  
Mineral Soil ◽  
Soil Samples ◽  
Rrna Gene ◽  
Whole Tree Harvesting ◽  
Whole Tree

Bacteria from forest soils were characterized by DNA sequence analysis of cloned 16S rRNA gene fragments (16S clones). Surface organic matter and mineral soil samples from a British Columbia Ministry of Forests Long-Term Soil Productivity (LTSP) installation were collected during winter and summer from two disturbance treatments: whole-tree harvesting with no soil compaction (plot N) and whole-tree harvesting plus complete surface organic matter removal with heavy soil compaction (plot S). Phylogenetic analyses revealed that 87% of 580 16S clones were classified as Proteobacteria, Actinobacteria, Acidobacterium, Verrucomicrobia, Bacillus/Clostridium group, Cytophaga-Flexibacter-Bacteroides group, green nonsulfur bacteria, Planctomyces, and candidate divisions TM6 and OP10. Seventy-five 16S clones could not be classified into known bacterial divisions, and five 16S clones were related to chloroplast DNA. Members of Proteobacteria represented 46% of the clone library. A higher proportion of 16S clones affiliated with γ-Proteobacteria were from plot N compared with plot S. 16S rRNA gene fragments amplified with Pseudomonas-specific primers and cloned (Ps clones) were examined from mineral-soil samples from plots N and S from three LTSP installations. A significantly greater proportion of sequenced Ps clones from plot N contained Pseudomonas 16S rRNA gene fragments compared with Ps clones from plot S.Key words: bacterial diversity, 16S rRNA gene, forest soil.

Cultivation-dependent characterization of bacterial diversity from British Columbia forest soils subjected to disturbance

2002 ◽  
Vol 48 (7) ◽  
pp. 643-654 ◽  
Author(s):  
Paige E Axelrood ◽  
Monica L Chow ◽  
Clarke S Arnold ◽  
Karen Lu ◽  
Joseph M McDermott ◽  
...  
Keyword(s):  
Organic Matter ◽  
Fatty Acid ◽  
Soil Compaction ◽  
Acid Methyl Ester ◽  
Soil Samples ◽  
Bacterial Isolates ◽  
Fame Analysis ◽  
Acid Methyl ◽  
Whole Tree Harvesting ◽  
Whole Tree

Bacteria from forest surface organic matter and mineral soil horizons were cultivated using four methods and characterized by fatty acid methyl ester (FAME) analysis. Soil samples from a British Columbia Ministry of Forests Long-Term Soil Productivity (LTSP) installation were collected during winter and summer from two disturbance treatments (whole-tree harvesting with no soil compaction (plot N) and whole-tree harvesting plus complete surface organic matter removal with heavy soil compaction (plot S)) and from an unlogged reference plot (REF). Seventy-five percent of 1795 bacterial isolates were affiliated with 42 genera representing β- and γ-Proteobacteria, Actinobacteria, the Bacillus/Clostridium group, and the Cytophaga-Flexibacter-Bacteroides group. Approximately half of the culture collection represented genetic diversity confined to four bacterial genera: Pseudomonas, Bacillus, Paenibacillus, and Arthrobacter. A significantly higher proportion of bacterial isolates belonging to Actinobacteria, and the member genus Arthrobacter, were isolated from plot S soil samples compared with soil samples from plots N and REF. Twenty-five percent of bacterial isolates were not conclusively identified to genus with FAME analysis. MIDI Tracker cluster analysis and partial 16S rRNA gene sequence analysis enabled classification of a subset of these isolates.Key words: bacterial diversity, fatty acid methyl ester analysis (FAME), forest soil.

Soil aggregate-based nucleic acid analyses of the impact of maize roots and their root hairs on the structural diversity of microbial communities

2021 ◽  
Author(s):  
Christoph Tebbe ◽  
Damini Damini ◽  
Damien Finn ◽  
Nataliya Bilyera ◽  
Minh Ganther ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Root Hair ◽  
Soil Aggregates ◽  
Root Hairs ◽  
Soil Samples ◽  
Plant Roots ◽  
Bulk Soil ◽  
Rrna Gene ◽  
The Impact

<p>The deposition of energy rich carbon sources released by plant roots during their growth fuels microbially driven ecosystem processes in soil, but there is a lack of understanding how microorganisms interact and collaborate. The objective of this research was therefore to characterize microbial networks as they assemble under the influence of plant roots. To identify the specific importance of root hairs, we compared the impact of a maize wild-type to a root-air defective mutant (rth3; (1).</p><p>The microbial community structure was analyzed by qPCR and 16S rRNA gene amplicon sequencing from soil DNA. In order to increase the probability of detecting truly interacting microbial partners as a basis for network analyses, we first evaluated a new protocol to obtain DNA from as little as 1 mg instead of the usual 250 mg soil samples, thereby approaching the aggregate level (2). While the diversity of bacterial 16S rRNA gene amplicons of 250-mg samples taken from the same soil was not distinct, DNA analyses from individual aggregates clearly differed from each other underlining that soil aggregates represent distinct microbial habitats.</p><p>Soil column experiments with maize grown in a loam soil (3) revealed distinct communities between rhizosphere and bulk soil. The community composition of individual aggregates showed more differences in bulk soil compared to rhizosphere. Less elaborated networks were seen in bulk soil and a profound effect of root hairs could be unravelled. Null model testing demonstrated that Actinobacteria were equally important for network connectivity independent of the root hair mutation, but for networks of the wildtype, Acidobacteria were essential for synergistic interactions and overall network structure. In contrast, Proteobacteria and Firmicutes connectivity became more important. The observed differences in community composition and interactions suggests carbon cycling, and perhaps other microbially-driven functions, are markedly affected by the presence of root hairs.</p><p>Utilizing maize root soil microcosms for studying soil zymography in the rhizosphere allowed to obtain soil samples from regions with distinct specific enzyme activities. In order to enhance the detection of actively metabolizing bacterial community members, we studied rRNA sequences and compared it to rRNA gene sequences from the same samples. Currently the data are under analysis.</p><p>References</p><p>(1) Wen, T-J, Schnable PS (1994) Analyses of mutants of three genes that influence root hair development in Zea mays (Gramineae) suggest that root hairs are dispensable. Am. J. Bot. 81, 833–842.</p><p>(2) Szoboszlay M, Tebbe CC (2020) Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates. Microbiol. Open, e1144. DOI: 10.1002/mbo3.1144</p><p>(3) Vetterlein D et al. (2020) Experimental platforms for the investigation of spatiotemporal patterns in the rhizosphere – laboratory and field scale. J. Plant Nutr. Soil Sci., 000, 1–16 DOI: 10.1002/jpln.202000079</p>

scholarly journals Paenibacillus ferrarius sp. nov., isolated from iron mineral soil

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 165-170 ◽  
Author(s):  
Yajing Cao ◽  
Fang Chen ◽  
Yanzhi Li ◽  
Sha Wei ◽  
Gejiao Wang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Mineral Soil ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Iron Mineral ◽  
Link Type

A Gram-reaction-positive, endospore-forming, aerobic bacterium, designated strain CY1T, was isolated from iron mineral soil of Hunan Province, China. The isolate was rod-shaped and motile by means of peritrichous flagella. The major cellular fatty acids were anteiso-C15 : 0 and iso-C16 : 0 and the major quinone was menaquinone 7. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol phosphatidylethanolamine. The genomic DNA G+C content was 50.5 mol% and the major diagnostic diamino acid in cell-wall peptidoglycan was meso-diaminopimelic acid. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain CY1T is most closely related to Paenibacillus chondroitinus DSM 5051T (97.7 % 16S rRNA gene sequence similarity), Paenibacillus pocheonensis Gsoil 1138T (97.4 %) and Paenibacillus frigoriresistens YIM 016T (97.0 %). DNA–DNA hybridization dissociation values were lower than 49 % with the most closely related species. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, strain CY1T is affiliated to the genus Paenibacillus , but could be distinguished from the species of this genus. A novel species with the name Paenibacillus ferrarius sp. nov. is proposed. The type strain is CY1T ( = KCTC 33419T = CCTCC AB 2013369T).

scholarly journals Uncovering a hidden diversity: optimized protocols for the extraction of bacteriophages from soil

2019 ◽  
Author(s):  
Pauline C. Göller ◽  
Jose M. Haro-Moreno ◽  
Francisco Rodriguez-Valera ◽  
Martin J. Loessner ◽  
Elena Gómez-Sanz
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ecological Model ◽  
Extraction Process ◽  
Extraction Methods ◽  
Soil Samples ◽  
Rrna Gene ◽  
Optimization Strategy ◽  
Data Set ◽  
Soil Matrix

AbstractBackgroundBacteriophages are the most numerous biological entities on earth and play a crucial role in shaping microbial communities. Investigating the bacteriophage community from soil samples will shed light not only on the yet largely unknown phage diversity, but also may result in novel insights into phage biology and functioning. Unfortunately, the study of soil viromes lags far behind any other ecological model system, due to the heterogeneous soil matrix that rises major technical difficulties in the extraction process. Resolving these technical challenges and establishing a standardized extraction protocol is therefore a fundamental prerequisite for replicable results and comparative virome studies.ResultsWe here report the optimization of protocols for extraction of bacteriophage DNA from soil preceding metagenomic analysis such that the protocol can equally be harnessed for phage isolation. As an optimization strategy, soil samples were spiked with a viral community consisting of phages from different families (106 PFU/g soil): Listeria phage ΦA511 (Myovirus), Staphylococcus phage Φ2638AΔLCR (Siphovirus), and Escherichia phage ΦT7 (Podovirus). The efficacy of bacteriophage (i) elution, (ii) filtration, (iii) concentration, and (iv) DNA extraction methods was tested. Successful extraction routes were selected based on spiked phage recovery and low bacterial 16S rRNA gene contaminants. Natural agricultural soil viromes were then extracted with the optimized methods and shotgun sequenced. Our approach yielded sufficient amounts of inhibitor-free viral DNA for non-amplification dependent sequencing and low 16S rRNA gene contamination levels (≤ 0.2 ‰). Compared to previously published protocols, the number of bacterial read contamination was decreased by 65 %. In addition, 468 novel circularized soil phage genomes in size up to 235 kb were obtained from over 29,000 manually identified viral contigs, promising the discovery of a large, previously inaccessible viral diversity.ConclusionWe have shown a dramatically enhanced extraction of the soil phage community by protocol optimization that has proven robustness in both a culture-depended as well as through metaviromic analysis. Our huge data set of manually curated soil viral contigs roughly doubles the amount of currently available soil virome data, and provide insights into the yet largely undescribed soil viral sequence space.

scholarly journals Correlation of the Abundance of Betaproteobacteria on Mineral Surfaces with Mineral Weathering in Forest Soils

2012 ◽  
Vol 78 (19) ◽  
pp. 7114-7119 ◽  
Author(s):  
C. Lepleux ◽  
M. P. Turpault ◽  
P. Oger ◽  
P. Frey-Klett ◽  
S. Uroz
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soils ◽  
Mineral Weathering ◽  
Rrna Gene ◽  
Mineral Surfaces ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type

ABSTRACTPyrosequencing-based analysis of 16S rRNA gene sequences revealed a significant correlation between apatite dissolution and the abundance of betaproteobacteria on apatite surfaces, suggesting a role for the bacteria belonging to this phylum in mineral weathering. Notably, the cultivation-dependent approach demonstrated that the most efficient mineral-weathering bacteria belonged to the betaproteobacterial genusBurhkolderia.

Paenibacillus selenitireducens sp. nov., a selenite-reducing bacterium isolated from a selenium mineral soil

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 805-811 ◽  
Author(s):  
Rong Yao ◽  
Rui Wang ◽  
Dan Wang ◽  
Jing Su ◽  
Shixue Zheng ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Mineral Soil ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, rod-shaped, facultatively anaerobic bacterium, designated strain ES3-24T, was isolated from a selenium mineral soil. The isolate was endospore-forming, nitrate-reducing and motile by means of peritrichous flagella. The major menaquinone was menaquinone 7 (MK-7) and the predominant fatty acids (>5 %) were anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and two unknown aminophospholipids. Strain ES3-24T contained meso-diaminopimelic acid in the cell-wall peptidoglycan and the DNA G+C content was 49.6 mol%. According to phylogenetic analysis based on the 16S rRNA gene sequence, strain ES3-24T was most closely related to Paenibacillus terrigena A35T, with 16S rRNA gene sequence identity of 98.3 %, while the other members of the genus Paenibacillus had 16S rRNA gene sequence identities of less than 95.0 %. DNA–DNA relatedness between strain ES3-24T and P. terrigena CCTCC AB206026T was 39.3 %. In addition, strain ES3-24T showed obvious differences from closely related species in major polar lipids, nitrate reduction and other physiological and biochemical characteristics. The data from our polyphasic taxonomic study reveal that strain ES3-24T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus selenitireducens sp. nov. is proposed. The type strain is ES3-24T ( = KCTC 33157T = CCTCC AB2013097T).

scholarly journals Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

2012 ◽  
Vol 78 (20) ◽  
pp. 7398-7406 ◽  
Author(s):  
Astrid Naether ◽  
Bärbel U. Foesel ◽  
Verena Naegele ◽  
Pia K. Wüst ◽  
Jan Weinert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Plant Diversity ◽  
Forest Soils ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Vascular Plant ◽  
Environmental Parameters ◽  
Rrna Gene ◽  
Content Type

ABSTRACTIn soil,Acidobacteriaconstitute on average 20% of all bacteria, are highly diverse, and are physiologically activein situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1Acidobacteria. The analysis of a large number of sites (n= 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed thatAcidobacteriadiversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations ofAcidobacteriasubpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters withAcidobacteria, individual populations within subgroups have to be considered.

scholarly journals Influence of Soil Characteristics on the Diversity of Bacteria in the Southern Brazilian Atlantic Forest

2010 ◽  
Vol 76 (14) ◽  
pp. 4744-4749 ◽  
Author(s):  
H. Faoro ◽  
A. C. Alves ◽  
E. M. Souza ◽  
L. U. Rigo ◽  
L. M. Cruz ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Atlantic Forest ◽  
16S Rrna Gene Sequencing ◽  
Diversity Indices ◽  
Physicochemical Characteristics ◽  
Soil Samples ◽  
Rrna Gene ◽  
Brazilian Atlantic Forest ◽  
Bacterial Biodiversity

ABSTRACT The Brazilian Atlantic Forest is one of the 25 biodiversity hot spots in the world. Although the diversity of its fauna and flora has been studied fairly well, little is known of its microbial communities. In this work, we analyzed the Atlantic Forest ecosystem to determine its bacterial biodiversity, using 16S rRNA gene sequencing, and correlated changes in deduced taxonomic profiles with the physicochemical characteristics of the soil. DNAs were purified from soil samples, and the 16S rRNA gene was amplified to construct libraries. Comparison of 754 independent 16S rRNA gene sequences from 10 soil samples collected along a transect in an altitude gradient showed the prevalence of Acidobacteria (63%), followed by Proteobacteria (25.2%), Gemmatimonadetes (1.6%), Actinobacteria (1.2%), Bacteroidetes (1%), Chloroflexi (0.66%), Nitrospira (0.4%), Planctomycetes (0.4%), Firmicutes (0.26%), and OP10 (0.13%). Forty-eight sequences (6.5%) represented unidentified bacteria. The Shannon diversity indices of the samples varied from 4.12 to 3.57, indicating that the soils have a high level of diversity. Statistical analysis showed that the bacterial diversity is influenced by factors such as altitude, Ca2+/Mg2+ ratio, and Al3+ and phosphorus content, which also affected the diversity within the same lineage. In the samples analyzed, pH had no significant impact on diversity.

scholarly journals Paenibacillus selenii sp. nov., isolated from selenium mineral soil

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2662-2667 ◽  
Author(s):  
Wanwan Xiang ◽  
Gejiao Wang ◽  
Yuantao Wang ◽  
Rong Yao ◽  
Fujun Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Mineral Soil ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strain W126T, a Gram-reaction-positive, spore-forming, rod-shaped, facultatively anaerobic bacterium, motile by means of peritrichous flagella, was isolated from selenium mineral soil in Hubei province of China. 16S rRNA gene sequence analysis demonstrated that this isolate belonged to the genus Paenibacillus , with 97.9 % sequence similarity to Paenibacillus anaericanus MH21T, while compared with the other species of the genus Paenibacillus , the 16S rRNA gene sequence similarities were less than 96.0 %. DNA–DNA hybridization between strain W126T and Paenibacillus anaericanus DSM 15890T was 24 %. The major isoprenoid menaquinone was menaquinone-7. Anteiso-C15 : 0 was the major fatty acid. The DNA G+C content was 42.3 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown aminophospholipids and an unknown lipid. Strain W126T contained A1γ-meso-diaminopimelic acid in the cell-wall peptidoglycan. The phenotypic, chemotaxonomic and genotypic data indicate that strain W126T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus selenii sp. nov. is proposed. The type strain is W126T ( = KCTC 33420T = CCTCC AB 2014003T).

Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning

1999 ◽  
Vol 65 (4) ◽  
pp. 1662-1669 ◽  
Author(s):  
John Dunbar ◽  
Shannon Takala ◽  
Susan M. Barns ◽  
Jody A. Davis ◽  
Cheryl R. Kuske
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Soil Samples ◽  
Community Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Clone Libraries ◽  
Bacterial Community Diversity

ABSTRACT Techniques based on amplification of 16S rRNA genes for comparing bacterial communities are now widely used in microbial ecology, but calibration of these techniques with traditional tools, such as cultivation, has been conspicuously absent. In this study, we compared levels of bacterial community diversity in two pinyon rhizosphere soil samples and two between-tree (interspace) soil samples by analyzing 179 cultivated bacterial isolates and 801 16S rRNA genes amplified from extracted soil DNA. Phylotypes were defined by performing a restriction fragment length polymorphism analysis of 16S rRNA gene sequences with the enzymes RsaI and BstUI. The average level of 16S rRNA gene sequence similarity of members of a phylotype was 86.6% based on an analysis of partial sequences. A total of 498 phylotypes were identified among the 16S ribosomal DNA (rDNA) clones, while 34 phylotypes occurred among the cultivated isolates. Analysis of sequences from a subset of the phylotypes showed that at least seven bacterial divisions were represented in the clone libraries, whereas the isolates represented only three. The phylotype richness, frequency distribution (evenness), and composition of the four culture collections and the four clone libraries were investigated by using a variety of diversity indices. Although cultivation and 16S rRNA cloning analyses gave contradictory descriptions of the relative phylotype richness for one of the four environments, the two methods identified qualitatively consistent relationships when levels of evenness were compared. The levels of phylotype similarity between communities were uniformly low (15 to 31%). Both methods consistently indicated that one environment was distinct from the other three. Our data illustrate that while 16S rDNA cloning and cultivation generally describe similar relationships between soil microbial communities, significant discrepancies can occur.

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