scholarly journals Diversity of Soil Bacterial Community Is Influenced by Spatial Location and Time but Not Potato Cultivar

2020 ◽  
Vol 4 (3) ◽  
pp. 225-238
Author(s):  
Kamrun Nahar ◽  
Jean-Baptiste Floc’h ◽  
Claudia Goyer ◽  
Bernie J. Zebarth ◽  
Sean Whitney
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Common Scab ◽  
Potato Cultivar ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Streptomyces Spp ◽  
Β Diversity ◽  
Soil Bacterial ◽  
Spatial Locations

Potato cultivars susceptible to common scab were previously reported to harbor five to six times more abundant pathogenic Streptomyces spp. in the rhizosphere soils compared with tolerant cultivars. It is still unclear if the diversity of soil bacterial communities is related to the abundance of pathogenic Streptomyces spp. This study evaluated the effects of potato cultivar on the diversity of bacterial communities in three spatial locations (soil located close to the plant [SCP], in the rhizosphere soil [RS], and in the geocaulosphere soil [GS]) in 2013 and 2014. Common scab tolerant (Goldrush and Hindenburg) and susceptible cultivars (Green Mountain and Agria) were planted in a field infested with pathogenic Streptomyces spp. causing common scab. The β-diversity of the bacterial community was significantly different between years and on dates within each year according to a permutational multivariate analysis of variance. The β-diversity also varied significantly among spatial locations (i.e., SCP, RS, and GS), probably due to changes in soil properties, but did not change significantly among potato cultivars. The architecture of the bacterial network in RS in 2014 was more complex compared with 2013 with a 2.5-fold increase in the number of bacteria included according to a co-occurrence analysis. These results indicated that the soil bacterial community diversity changed temporally and spatially. However, bacterial community diversity and richness were not affected by potato cultivar, suggesting that there were no relationships between bacterial community diversity or richness and the abundance of pathogenic Streptomyces spp.

Effects of inoculation with organic-phosphorus-mineralizing bacteria on soybean (Glycine max) growth and indigenous bacterial community diversity

2017 ◽  
Vol 63 (5) ◽  
pp. 392-401 ◽  
Author(s):  
Wei Sun ◽  
Xun Qian ◽  
Jie Gu ◽  
Xiao-Juan Wang ◽  
Yang Li ◽  
...  
Keyword(s):  
Glycine Max ◽  
Carbon Source ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Organic Phosphorus ◽  
Community Diversity ◽  
Carbon Source Utilization ◽  
Soil Bacterial Communities ◽  
Bacterial Community Diversity ◽  
Soil Bacterial

Three different organic-phosphorus-mineralizing bacteria (OPMB) strains were inoculated to soil planted with soybean (Glycine max), and their effects on soybean growth and indigenous bacterial community diversity were investigated. Inoculation with Pseudomonas fluorescens Z4-1 and Brevibacillus agri L7-1 increased organic phosphorus degradation by 22% and 30%, respectively, compared with the control at the mature stage. Strains P. fluorescens Z4-1 and B. agri L7-1 significantly improved the soil alkaline phosphatase activity, average well color development, and the soybean root activity. Terminal restriction fragment length polymorphism analysis demonstrated that P. fluorescens Z4-1 and B. agri L7-1 could persist in the soil at relative abundances of 2.0%–6.4% throughout soybean growth. Thus, P. fluorescens Z4-1 and B. agri L7-1 could potentially be used in organic-phosphorus-mineralizing biofertilizers. OPMB inoculation altered the genetic structure of the soil bacterial communities but had no apparent influence on the carbon source utilization profiles of the soil bacterial communities. Principal components analysis showed that the changes in the carbon source utilization profiles of bacterial community depended mainly on the plant growth stages rather than inoculation with OPMB. The results help to understand the evolution of the soil bacterial community after OPMB inoculation.

scholarly journals Soil Bacterial Community Shifts Are Driven by Soil Nutrient Availability along a Teak Plantation Chronosequence in Tropical Forests in China

Biology ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1329
Author(s):  
Zhi Yu ◽  
Kunnan Liang ◽  
Guihua Huang ◽  
Xianbang Wang ◽  
Mingping Lin ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Soil Bacterial Community ◽  
Community Diversity ◽  
Soil Bacterial Communities ◽  
Bacterial Community Diversity ◽  
Teak Plantation ◽  
Soil Bacterial ◽  
Total Potassium ◽  
Significant Factors

Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and co-occurrence patterns of soil bacterial communities in rhizosphere and bulk soils along a chronosequence of teak plantations and adjacent native grassland as control. Stand ages significantly shifted the structure of soil bacterial communities but had no significant impact on bacterial community diversity. Bacterial community diversity in bulk soils was significantly higher than that in rhizosphere soils. The number of nodes and edges in the bacterial co-occurrence network first increased and then decreased with the chronosequence. The number of strongly positive correlations per network was much higher than negative correlations. Available potassium, total potassium, and available phosphorus were significant factors influencing the structure of the bacterial community in bulk soils. In contrast, urease, total potassium, pH, and total phosphorus were significant factors affecting the structure of the bacterial community in the rhizosphere soils. These results indicate that available nutrients in the soil are the main drivers regulating soil bacterial community variation along a teak plantation chronosequence.

scholarly journals Bacterial Community Is Affected by Locations and Time Rather Than Potato Varieties but Streptomyces spp. Are Related to Potato Varieties

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 659
Author(s):  
Geon Seung Lee ◽  
Mahesh Adhikari ◽  
Jae E. Yang ◽  
Hyuck Soo Kim ◽  
Kyu Suk Han ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Common Scab ◽  
Soil Samples ◽  
Metagenomic Sequencing ◽  
Potato Varieties ◽  
Bacterial Phyla ◽  
Streptomyces Spp ◽  
The Common ◽  
Spatial Locations

Improved knowledge and a better understanding of the functions of bacterial communities are vital for effective crop disease management. This study was conducted to study a bacterial community’s relationship with the common scab in four different potato varieties (Dejima, DJ; Atlantic, DS; Seohong, SH; Haryeong, HY) at two different locations (Gangneung and Chuncheon) and spatial locations (rhizosphere and furrow) at two different times (preharvest and postharvest). In addition, metagenomic sequencing was performed by extracting genomic DNA from soil samples to observe the dominant bacterial microbes and disease severity of the common scab in all the tested varieties in spatial location and time. The results suggest that the most dominant bacterial phyla in all the soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Additionally, Streptomyces spp. were found to be more abundant in the susceptible variety (DJ) than in other varieties (DS, SH, and HY). Interestingly, bacterial communities were found to be more diverse across the two different geographical locations, spatial locations, and harvesting times, rather than the variety of potato, according to PCoA analysis. There were no interlinked changes in bacterial communities among the varieties. Moreover, the 14 most dominant bacterial genus correlation networks with Streptomyces spp. suggested that there was a significant positive and negative correlation to some extent. Alpha and beta diversity results clearly indicated that the possible reason for differences in bacterial communities might have been due to the different spatial locations, in comparison with varieties, which suggests that there was no significant correlation between bacterial community richness and diversity among the varieties.

scholarly journals Increase in Bacterial Community Diversity in Subsurface Aquifers Receiving Livestock Wastewater Input

2000 ◽  
Vol 66 (3) ◽  
pp. 956-965 ◽  
Author(s):  
Jang-Cheon Cho ◽  
Sang-Jong Kim
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Community Diversity ◽  
Similarity Coefficients ◽  
Livestock Wastewater ◽  
Contaminated Aquifer ◽  
Bacterial Community Diversity ◽  
Rdna Sequences ◽  
Wastewater Samples ◽  
The Impact

ABSTRACT Despite intensive studies of microbial-community diversity, the questions of which kinds of microbial populations are associated with changes in community diversity have not yet been fully solved by molecular approaches. In this study, to investigate the impact of livestock wastewater on changes in the bacterial communities in groundwater, bacterial communities in subsurface aquifers were analyzed by characterizing their 16S rDNA sequences. The similarity coefficients of restriction fragment length polymorphism (RFLP) patterns of the cloned 16S ribosomal DNAs showed that the bacterial communities in livestock wastewater samples were more closely related to those in contaminated aquifer samples. In addition, calculations of community diversity clearly showed that bacterial communities in the livestock wastewater and the contaminated aquifer were much more diverse than those in the uncontaminated aquifer. Thus, the increase in bacterial-community diversity in the contaminated aquifer was assumed to be due to the infiltration of livestock wastewater, containing high concentrations of diverse microbial flora, into the aquifer. Phylogenetic analysis of the sequences from a subset of the RFLP patterns showed that the Cytophaga-Flexibacter-Bacteroidesand low-G+C gram-positive groups originating from livestock wastewater were responsible for the change in the bacterial community in groundwater. This was evidenced by the occurrence of rumen-related sequences not only in the livestock wastewater samples but also in the contaminated-groundwater samples. Rumen-related sequences, therefore, can be used as indicator sequences for fecal contamination of groundwater, particularly from livestock.

scholarly journals Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

2020 ◽  
Author(s):  
Zhang tao ◽  
Wang Zhongke ◽  
Lv Xinhua ◽  
Dang Hanli ◽  
Zhuang Li
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Physicochemical Factors ◽  
Rhizosphere Bacterial Community ◽  
Ferula Sinkiangensis ◽  
Rhizosphere Bacterial Communities

Ferula sinkiangensis is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, Ferula sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of Ferula sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and variation trends of Ferula sinkiangensis rhizosphere bacterial community diversity and abundance on a fine spatial scale (Slope position and soil depth) and Found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in Ferula sinkiangensi s rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in Ferula sinkiangensis . In addition, Soil physicochemical factors jointly explained 24.28% of variation in Ferula sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of Ferula sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

scholarly journals Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tao Zhang ◽  
Zhongke Wang ◽  
Xinhua Lv ◽  
Hanli Dang ◽  
Li Zhuang
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Physicochemical Factors ◽  
Rhizosphere Bacterial Community ◽  
Ferula Sinkiangensis ◽  
Rhizosphere Bacterial Communities

Abstract Ferula sinkiangensis (F. sinkiangensis) is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, F. sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of F. sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and changed trend of F. sinkiangensis rhizosphere bacterial community diversity and abundance on slope position and soil depth and found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in F. sinkiangensis rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in F. sinkiangensis. In addition, Soil physicochemical factors jointly explained 24.28% of variation in F. sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of F. sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

scholarly journals Uterine and vaginal bacterial community diversity prior to artificial insemination between pregnant and nonpregnant postpartum cows1

2019 ◽  
Vol 97 (10) ◽  
pp. 4298-4304 ◽  
Author(s):  
Taylor B Ault ◽  
Brooke A Clemmons ◽  
Sydney T Reese ◽  
Felipe G Dantas ◽  
Gessica A Franco ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Artificial Insemination ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Beef Cows ◽  
Community Diversity ◽  
Rrna Gene ◽  
Bacterial Community Diversity ◽  
Hypervariable Regions ◽  
Time Of Breeding

Abstract The present study evaluated the bovine vaginal and uterine bacterial community diversity and its relationship to fertility. Postpartum beef cows (n = 68) were synchronized beginning on day −21 and ending with timed artificial insemination (TAI) on day 0. Pregnancy was diagnosed 30 d after TAI. Uterine and vaginal flushes were collected on day −21, −9, and −2 for bacterial DNA extraction to sequence the V1 to V3 hypervariable regions of the 16S rRNA gene. Results indicated a decrease in the number of bacterial species over time in the uterus of resulting pregnant and nonpregnant beef cows (P < 0.0001). Principal coordinate analyses (PCoA) depicted clustering of samples, indicating closely related bacterial communities, by day in the uterus and vagina (P < 0.0001). At day −2, uterine samples from nonpregnant and pregnant animals clustered separately (P < 0.0001), with nonpregnant animal samples clustering tightly together. Overall, the current study suggests the shift in the reproductive bacterial communities’ diversity and phylogenetic relationship leading up to the time of breeding may contribute to successful pregnancy establishment.

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