Molecular Analysis of Bacterial Community Structure and Diversity in Unimproved and Improved Upland Grass Pastures

ABSTRACT Bacterial community structure and diversity in rhizospheres in two types of grassland, distinguished by both plant species and fertilization regimen, were assessed by performing a 16S ribosomal DNA (rDNA) sequence analysis of DNAs extracted from triplicate soil plots. PCR products were cloned, and 45 to 48 clones from each of the six libraries were partially sequenced. Phylogenetic analysis of the resultant 275 clone sequences indicated that there was considerable variation in abundance in replicate unfertilized, unimproved soil samples and fertilized, improved soil samples but that there were no significant differences in the abundance of any phylogenetic group. Several clone sequences were identical in the 16S rDNA region analyzed, and the clones comprised eight pairs of duplicate clones and two sets of triplicate clones. Many clones were found to be most closely related to environmental clones obtained in other studies, although three clones were found to be identical to culturable species in databases. The clones were clustered into operational taxonomic units at a level of sequence similarity of >97% in order to quantify diversity. In all, 34 clusters containing two or more sequences were identified, and the largest group contained nine clones. A number of diversity, dominance, and evenness indices were calculated, and they all indicated that diversity was high, reflecting the low coverage of rDNA libraries achieved. Differences in diversity between sample types were not observed. Collector’s curves, however, indicated that there were differences in the underlying community structures; in particular, there was reduced diversity of organisms of the α subdivision of the class Proteobacteria (α-proteobacteria) in improved soils.

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Analysis of Bacterial Community Structure in Sulfurous-Oil-Containing Soils and Detection of Species Carrying Dibenzothiophene Desulfurization (dsz) Genes

Applied and Environmental Microbiology ◽

10.1128/aem.67.3.1052-1062.2001 ◽

2001 ◽

Vol 67 (3) ◽

pp. 1052-1062 ◽

Cited By ~ 100

Author(s):

Gabriela Frois Duarte ◽

Alexandre Soares Rosado ◽

Lucy Seldin ◽

Welington de Araujo ◽

Jan Dirk van Elsas

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Community Structure ◽

Soil Analysis ◽

Soil Samples ◽

Sulfur Source ◽

Soil Dna ◽

Enrichment Cultures ◽

Over Time ◽

Selection Of

ABSTRACT The selective effects of sulfur-containing hydrocarbons, with respect to changes in bacterial community structure and selection of desulfurizing organisms and genes, were studied in soil. Samples taken from a polluted field soil (A) along a concentration gradient of sulfurous oil and from soil microcosms treated with dibenzothiophene (DBT)-containing petroleum (FSL soil) were analyzed. Analyses included plate counts of total bacteria and of DBT utilizers, molecular community profiling via soil DNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and detection of genes that encode enzymes involved in the desulfurization of hydrocarbons, i.e., dszA, dszB, and dszC.Data obtained from the A soil showed no discriminating effects of oil levels on the culturable bacterial numbers on either medium used. Generally, counts of DBT degraders were 10- to 100-fold lower than the total culturable counts. However, PCR-DGGE showed that the numbers of bands detected in the molecular community profiles decreased with increasing oil content of the soil. Analysis of the sequences of three prominent bands of the profiles generated with the highly polluted soil samples suggested that the underlying organisms were related to Actinomyces sp.,Arthrobacter sp., and a bacterium of uncertain affiliation.dszA, dszB, and dszC genes were present in all A soil samples, whereas a range of unpolluted soils gave negative results in this analysis. Results from the study of FSL soil revealed minor effects of the petroleum-DBT treatment on culturable bacterial numbers and clear effects on the DBT-utilizing communities. The molecular community profiles were largely stable over time in the untreated soil, whereas they showed a progressive change over time following treatment with DBT-containing petroleum. Direct PCR assessment revealed the presence of dszB-related signals in the untreated FSL soil and the apparent selection of dszA- and dszC-related sequences by the petroleum-DBT treatment. PCR-DGGE applied to sequential enrichment cultures in DBT-containing sulfur-free basal salts medium prepared from the A and treated FSL soils revealed the selection of up to 10 distinct bands. Sequencing a subset of these bands provided evidence for the presence of organisms related to Pseudomonas putida, a Pseudomonassp., Stenotrophomonas maltophilia, and Rhodococcus erythropolis. Several of 52 colonies obtained from the A and FSL soils on agar plates with DBT as the sole sulfur source produced bands that matched the migration of bands selected in the enrichment cultures. Evidence for the presence of dszB in 12 strains was obtained, whereas dszA and dszC genes were found in only 7 and 6 strains, respectively. Most of the strains carrying dszA or dszC were classified asR. erythropolis related, and all revealed the capacity to desulfurize DBT. A comparison of 37 dszA sequences, obtained via PCR from the A and FSL soils, from enrichments of these soils, and from isolates, revealed the great similarity of all sequences to the canonical (R. erythropolis strain IGTS8)dszA sequence and a large degree of internal conservation. The 37 sequences recovered were grouped in three clusters. One group, consisting of 30 sequences, was minimally 98% related to the IGTS8 sequence, a second group of 2 sequences was slightly different, and a third group of 5 sequences was 95% similar. The first two groups contained sequences obtained from both soil types and enrichment cultures (including isolates), but the last consisted of sequences obtained directly from the polluted A soil.

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Effects of different proportions of soft rock additions on organic carbon pool and bacterial community structure of sandy soil

Scientific Reports ◽

10.1038/s41598-021-84177-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Wan-ying Li ◽

Zhen Guo ◽

Juan Li ◽

Ji-chang Han

Keyword(s):

Community Structure ◽

Organic Carbon ◽

Bacterial Community ◽

Sandy Soil ◽

Bacterial Community Structure ◽

Microbial Biomass Carbon ◽

Structural Characteristics ◽

Soft Rock ◽

Evenness Indices ◽

Dominant Bacteria

AbstractThe sandy soil leaks water and fertilizer, and the ecological degradation is serious. The structural characteristics of soft rock and sandy soil are complementary, and the improvement of sandy soil by adding soft rock is of great significance to improve soil fertility, restore biodiversity, and maintain sustainable development of the Mu Us sandy land region. In this study, total organic carbon (TOC), particulate organic carbon (POC), dissolved organic carbon (DOC), easily oxidized organic carbon (ROC), microbial biomass carbon (SMBC), bacterial community structure and crop yield were examined using soft rock:sand volume ratios of 0:1 (CK), 1:5 (C1), 1:2 (C2) and 1:1 (C3). Our results indicated that, compared with the CK treatment, TOC (9.66–22.34%), POC (85.65–120.41%) and ROC (114.12–192.31%) noticeably increased in C1, C2 and C3 treatments; SMBC in treatment C3 increased by 42.77%. The three dominant bacteria in the soil (Proteobacteria, Actinobacteria and Chloroflexi), as well as Proteobacteria abundance, greatly declined in the treatments with the addition of soft rock. Pseudarthrobacter was the dominant Genus in all treatments, having an abundance between 11.83 and 19.33%. Bacterial diversity, richness and evenness indices all recorded an increase under the treatments. POC, TOC and SMBC recorded the most significant effects on the bacterial community structure. The largest increases in wheat and corn yields were recorded in the C2 treatment (16.05% and 16.30%), followed by the C1 treatment (8.28% and 8.20%, respectively). Our findings indicate that a soft rock:sand ratio between 1:5 and 1:2 recorded the most improvement in the sandy soil environment.

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Changes in Bacterial Community Structure in the Colon of Pigs Fed Different Experimental Diets and after Infection with Brachyspira hyodysenteriae

Applied and Environmental Microbiology ◽

10.1128/aem.66.8.3290-3296.2000 ◽

2000 ◽

Vol 66 (8) ◽

pp. 3290-3296 ◽

Cited By ~ 145

Author(s):

Thomas D. Leser ◽

Rikke Hvid Lindecrona ◽

Tim K. Jensen ◽

Bent B. Jensen ◽

Kristian Møller

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Fragment Length Polymorphism ◽

Rflp Analysis ◽

Control Group ◽

Brachyspira Hyodysenteriae ◽

16S Ribosomal Dna ◽

Cooked Rice

ABSTRACT Bacterial communities in the large intestines of pigs were compared using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S ribosomal DNA. The pigs were fed different experimental diets based on either modified standard feed or cooked rice supplemented with dietary fibers. After feeding of the animals with the experimental diets for 2 weeks, differences in the bacterial community structure in the spiral colon were detected in the form of different profiles of terminal restriction fragments (T-RFs). Some of the T-RFs were universally distributed, i.e., they were found in all samples, while others varied in distribution and were related to specific diets. The reproducibility of the T-RFLP profiles between individual animals within the diet groups was high. In the control group, the profiles remained unchanged throughout the experiment and were similar between two independent but identical experiments. When the animals were experimentally infected with Brachyspira hyodysenteriae, causing swine dysentery, many of the T-RFs fluctuated, suggesting a destabilization of the microbial community.

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Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time

PeerJ ◽

10.7717/peerj.3075 ◽

2017 ◽

Vol 5 ◽

pp. e3075 ◽

Cited By ~ 15

Author(s):

Sheila Torres ◽

Jonathan B. Clayton ◽

Jessica L. Danzeisen ◽

Tonya Ward ◽

Hu Huang ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Skin Microbiome ◽

Bacterial Populations ◽

Operational Taxonomic Units ◽

Hair Type ◽

Different Seasons ◽

Over Time

It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter). Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs’ microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs) identified across all dogs sampled. Taxonomic classification revealedPropionibacterium acnesandHaemophilussp. as key members of the dog skin bacterial community, along withCorynebacteriumsp. andStaphylococcus epidermidis. This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation.

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Early Changes in Soil Metabolic Diversity and Bacterial Community Structure in Sugarcane under Two Harvest Management Systems

Revista Brasileira de Ciência do Solo ◽

10.1590/01000683rbcs20140426 ◽

2015 ◽

Vol 39 (3) ◽

pp. 701-713 ◽

Cited By ~ 2

Author(s):

Lucas Carvalho Basilio Azevedo ◽

Marcio Morais ◽

Marcio Rodrigues Lambais

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Management System ◽

Bacterial Community Structure ◽

Substrate Utilization ◽

Soil Samples ◽

Management Systems ◽

Harvest Management ◽

Metabolic Diversity

Preharvest burning is widely used in Brazil for sugarcane cropping. However, due to environmental restrictions, harvest without burning is becoming the predominant option. Consequently, changes in the microbial community are expected from crop residue accumulation on the soil surface, as well as alterations in soil metabolic diversity as of the first harvest. Because biological properties respond quickly and can be used to monitor environmental changes, we evaluated soil metabolic diversity and bacterial community structure after the first harvest under sugarcane management without burning compared to management with preharvest burning. Soil samples were collected under three sugarcane varieties (SP813250, SP801842 and RB72454) and two harvest management systems (without and with preharvest burning). Microbial biomass C (MBC), carbon (C) substrate utilization profiles, bacterial community structure (based on profiles of 16S rRNA gene amplicons), and soil chemical properties were determined. MBC was not different among the treatments. C-substrate utilization and metabolic diversity were lower in soil without burning, except for the evenness index of C-substrate utilization. Soil samples under the variety SP801842 showed the greatest changes in substrate utilization and metabolic diversity, but showed no differences in bacterial community structure, regardless of the harvest management system. In conclusion, combined analysis of soil chemical and microbiological data can detect early changes in microbial metabolic capacity and diversity, with lower values in management without burning. However, after the first harvest, there were no changes in the soil bacterial community structure detected by PCR-DGGE under the sugarcane variety SP801842. Therefore, the metabolic profile is a more sensitive indicator of early changes in the soil microbial community caused by the harvest management system.

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