scholarly journals Genetic Diversity of Soil Bacteria

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 414
Author(s):  
Carmine Crecchio
Keyword(s):  
Genetic Diversity ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Agricultural Soils ◽  
Field Trials ◽  
Laboratory Scale ◽  
Special Issue ◽  
Soil Bacterial Communities ◽  
Review Articles ◽  
Different Types

The Special Issue “Genetic Diversity of Soil Bacterial Communities” collected research and review articles addressing some relevant and unclear aspects of the composition and functioning of bacterial communities in rich or marginal agricultural soils, in field trials as well as in laboratory-scale experiments, at different latitudes and under different types of management.

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 Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo

2013 ◽  
Vol 79 (23) ◽  
pp. 7290-7297 ◽  
Author(s):  
Larisa Lee-Cruz ◽  
David P. Edwards ◽  
Binu M. Tripathi ◽  
Jonathan M. Adams
Keyword(s):  
Forest Soil ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Forest Conversion ◽  
Soil Bacterial Communities ◽  
Oil Palm Plantation ◽  
Β Diversity ◽  
Logged Forest ◽  
Soil Bacterial

ABSTRACTTropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.

scholarly journals Different types of agricultural land use drive distinct soil bacterial communities

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shin Ae Lee ◽  
Jeong Myeong Kim ◽  
Yiseul Kim ◽  
Jae-Ho Joa ◽  
Seong-Soo Kang ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Communities ◽  
Agricultural Land ◽  
Agricultural Management ◽  
Agricultural Land Use ◽  
Community Structures ◽  
Soil Bacterial Communities ◽  
Microbial Network ◽  
Land Use Types ◽  
Different Types

Abstract Biogeographic patterns in soil bacterial communities and their responses to environmental variables are well established, yet little is known about how different types of agricultural land use affect bacterial communities at large spatial scales. We report the variation in bacterial community structures in greenhouse, orchard, paddy, and upland soils collected from 853 sites across the Republic of Korea using 16S rRNA gene pyrosequencing analysis. Bacterial diversities and community structures were significantly differentiated by agricultural land-use types. Paddy soils, which are intentionally flooded for several months during rice cultivation, had the highest bacterial richness and diversity, with low community variation. Soil chemical properties were dependent on agricultural management practices and correlated with variation in bacterial communities in different types of agricultural land use, while the effects of spatial components were little. Firmicutes, Chloroflexi, and Acidobacteria were enriched in greenhouse, paddy, and orchard soils, respectively. Members of these bacterial phyla are indicator taxa that are relatively abundant in specific agricultural land-use types. A relatively large number of taxa were associated with the microbial network of paddy soils with multiple modules, while the microbial network of orchard and upland soils had fewer taxa with close mutual interactions. These results suggest that anthropogenic agricultural management can create soil disturbances that determine bacterial community structures, specific bacterial taxa, and their relationships with soil chemical parameters. These quantitative changes can be used as potential biological indicators for monitoring the impact of agricultural management on the soil environment.

scholarly journals High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12105
Author(s):  
Fangnan Xiao ◽  
Yuanyuan Li ◽  
Guifang Li ◽  
Yaling He ◽  
Xinhua Lv ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Soil Bacteria ◽  
High Throughput Sequencing ◽  
Soil Bacterial Community ◽  
Tarim River ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
And Function

Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was employed to predict the functional genes. A total of 6,195 KEGG ortholog genes were obtained. The function of soil bacteria was annotated, and six metabolic pathways in level 1, 41 metabolic pathways in level 2, and 307 metabolic pathways in level 3 were enriched, among which the functional gene related to metabolism, genetic information processing, and environmental information processing was found to have the dominant advantage. The results showed that the nebkhas and canopy of Tamarix shrubs had a certain enrichment effect on soil nutrients content, and bacterial abundance and significant effects on the structure and function of the soil bacterial community.

scholarly journals Potential effects of temperature levels on soil bacterial community structure

2021 ◽  
Vol 292 ◽  
pp. 01008
Author(s):  
Jing Fang ◽  
Shuli Wei ◽  
Gongfu Shi ◽  
Yuchen Cheng ◽  
Xiangqian Zhang ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Soil Bacteria ◽  
Soil Microorganisms ◽  
Temperature Gradients ◽  
Control Treatment ◽  
Effect Of Temperature ◽  
Main Reaction ◽  
Soil Bacterial Communities ◽  
Infrared Temperature Measurement ◽  
Soil Bacterial

Soil microorganisms play a crucial role in the response to global warming in terrestrial ecosystems. Soils with higher microbial diversity have more ecological functions, higher resistance to environmental stress and higher crop production capacity. At present, the research on the effect of temperature change on soil microorganisms mostly adopts the methods of outdoor infrared temperature measurement or exchange and transplantation of soil with different temperature zones. Here, we investigate how temperature gradients potentially affect soil bacterial communities to change. For this reason, we used indoor precise temperature control treatment and combined high-throughput sequencing with bioinformatics to systematically analyze the diversity and species composition of soil bacteria under different temperature gradients, and to clarify the variation trend and interaction relationships of different species with temperature gradients. The results showed that temperature significantly affected the Alpha diversity of soil bacterial communities (P<0.05).Soil bacteria has different sensitivity and adaptability to temperature. In the range of 0-40℃, insensitive bacteria includes Proteobacteria, Gemmatimonadetes and Chloroflexi. Sensitive bacteria includes Sphingomonas, Ellin6055 and norank_f_67-14. The main reaction types of two bacteria showed four trends: ① Proteobacteria and Sphingomonas showed an “arch” variation; ② Gemmatimonadetes and Chloroflexi showed “inverted arch”. ③ Norank_f_67-14 showed an “inverted S type” change; ④ Ellin6055 shows a” parabolic ” shape. In different classification levels such as phylum and genus, the higher the classification level is, the higher degree it is weakened by temperature on, and the lower the classification level is, the stronger effect temperature has on it. In short, when temperature changes, soil bacteria can respond positively or negatively according to their ability to adapt to temperature, and accordingly form certain regular changes.

scholarly journals Soil Bacterial Communities and Diversity in Alpine Grasslands on the Tibetan Plateau Based on 16S rRNA Gene Sequencing

2021 ◽  
Vol 9 ◽  
Author(s):  
Hongmao Jiang ◽  
Youchao Chen ◽  
Yang Hu ◽  
Ziwei Wang ◽  
Xuyang Lu
Keyword(s):  
Tibetan Plateau ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Alpine Grassland ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Alpine Grasslands ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Grassland Types

The Tibetan Plateau, widely known as the world’s “Third Pole,” has gained extensive attention due to its susceptibility to climate change. Alpine grasslands are the dominant ecosystem on the Tibetan Plateau, albeit little is known about the microbial community and diversity among different alpine grassland types. Here, soil bacterial composition and diversity in the upper soils of five alpine grassland ecosystems, alpine meadow (AM), alpine steppe (AS), alpine meadow steppe (AMS), alpine desert (AD), and alpine desert steppe (ADS), were investigated based on the 16S rRNA gene sequencing technology. Actinobacteria (46.12%) and Proteobacteria (29.67%) were the two dominant soil bacteria at the phylum level in alpine grasslands. There were significant differences in the relative abundance at the genus level among the five different grassland types, especially for the Rubrobacter, Solirubrobacter, Pseudonocardia, Gaiella, Haliangium, and Geodermatophilus. Six alpha diversity indices were calculated based on the operational taxonomic units (OTUs), including Good’s coverage index, phylogenetic diversity (PD) whole tree index, Chao1 index, observed species index, Shannon index, and Simpson index. The Good’s coverage index value was around 0.97 for all the grassland types in the study area, meaning the soil bacteria samplings sequenced sufficiently. No statistically significant difference was shown in other diversity indices’ value, indicating the similar richness and evenness of soil bacteria in these alpine grasslands. The beta diversity, represented by Bray–Curtis dissimilarity and the non-metric multidimensional scaling (NMDS), showed that OTUs were clustered within alpine grasslands, indicating a clear separation of soil bacterial communities. In addition, soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), pH, and soil water content (SWC) were closely related to the variations in soil bacterial compositions. These results indicated that soil bacterial taxonomic compositions were similar, while soil bacterial community structures were different among the five alpine grassland types. The environmental conditions, including SOM, TN, TP, pH, and SWC, might influence the soil bacterial communities on the Tibetan Plateau.

scholarly journals Molecular identification of bacteria present in the soils of the Madhupur Sal and the Sunderban mangrove forests of Bangladesh

2012 ◽  
Vol 21 (2) ◽  
pp. 117-123
Author(s):  
Mihir Lal Saha ◽  
Mohammad Nurul Islam ◽  
Chaman Binta Aziz ◽  
Mohammad Zabed Hossain
Keyword(s):  
16S Rdna ◽  
Forest Soils ◽  
Bacterial Communities ◽  
Mangrove Forest ◽  
Soil Bacteria ◽  
Mangrove Forests ◽  
Phylogenetic Tree Analysis ◽  
Soil Bacterial Communities ◽  
Sal Forest ◽  
Identification Of Bacteria

  The present study aimed at identifying the soil bacterial communities in the Madhupur Sal and the Sunderban mangrove forests, the two important forests of Bangladesh. Soil bacteria were identified through sequencing of PCR?amplified fragments of bacterial 16S rDNA. The results showed that the bacterial communities of the Madhupur Sal forest soils and that of the Sunderban mangrove forest soils differed in the morphology of the cells. Data presented here also showed that the bacterial communities of the Sunderban mangrove forest soils were more diverse than that of the Madhupur Sal forest soils as revealed by phylogenetic tree analysis of the 16S rDNA sequences.DOI: http://dx.doi.org/10.3329/dujbs.v21i2.11509Dhaka Univ. J. Biol. Sci. 21(2): 117?123, 2012 (July)

scholarly journals The Toxicity Exerted by the Antibiotic Sulfadiazine on the Growth of Soil Bacterial Communities May Increase over Time

2020 ◽  
Vol 17 (23) ◽  
pp. 8773
Author(s):  
Vanesa Santás-Miguel ◽  
Laura Rodríguez-González ◽  
Avelino Núñez-Delgado ◽  
Montserrat Díaz-Raviña ◽  
Manuel Arias-Estévez ◽  
...  
Keyword(s):  
Bacterial Growth ◽  
Bacterial Communities ◽  
Agricultural Soils ◽  
Soil Samples ◽  
Short Term ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
First Time ◽  
Toxicity Effects

The toxicity exerted by the antibiotic sulfadiazine on the growth of soil bacterial communities was studied in two agricultural soils for a period of 100 days. In the short-term (2 days of incubation), the effect of sulfadiazine on bacterial growth was low (no inhibition or inhibition <32% for a dose of 2000 mg·kg−1). However, sulfadiazine toxicity increased with time, achieving values of 40% inhibition, affecting bacterial growth in both soils after 100 days of incubation. These results, which were here observed for the first time for any antibiotic in soil samples, suggest that long-term experiments would be required for performing an adequate antibiotics risk assessment, as short-term experiments may underestimate toxicity effects.

scholarly journals Catabolic Fingerprinting and Diversity of Bacteria in Mollic Gleysol Contaminated with Petroleum Substances

2018 ◽  
Vol 8 (10) ◽  
pp. 1970 ◽  
Author(s):  
Agnieszka Wolińska ◽  
Anna Gałązka ◽  
Agnieszka Kuźniar ◽  
Weronika Goraj ◽  
Natalia Jastrzębska ◽  
...  
Keyword(s):  
Metabolic Activity ◽  
Contaminated Soil ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Microbial Populations ◽  
Metabolic Potential ◽  
Soil Bacterial Communities ◽  
Biolog Ecoplate ◽  
Rhodococcus Species

This study focused on the determination of both catabolic and genetic fingerprinting of bacteria inhabiting soil contaminated with car fuels. A surface layer (0–20 cm) of Mollic Gleysol was used for the experiment and was contaminated with car fuels—unleaded 95-octane petrol and diesel at a dose of 15 g per 10 g of soil. The experiment lasted 42 days and was performed at 20 °C. The metabolic potential of soil bacterial communities was evaluated using the Biolog EcoPlate system. The results demonstrated that petroleum substances influenced the structure of the microbial populations and their catabolic activity. The Arthrobacter, Paenibacillus, and Pseudomonas genera were found in diesel-contaminated soil, whilst Bacillus and Microbacterium were found in petrol-contaminated soil. Rhodococcus species were identified in both variants of impurities, suggesting the widest capability of car fuel degradation by this bacterial genus. The contamination with unleaded 95-octane petrol caused rapid inhibition of the metabolic activity of soil bacteria in contrast to the diesel treatment, where high metabolic activity of bacteria was observed until the end of the incubation period. Higher toxicity of petrol in comparison with diesel car fuel was evidenced.

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