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 Characterisation of Bt maize IE09S034 in decomposition and response of soil bacterial communities

2021 ◽  
Author(s):  
Xiaoli Zhou ◽  
Jingang Liang ◽  
Ying Luan ◽  
Xinyuan Song ◽  
Zhengguang Zhang
Keyword(s):  
Metabolic Activity ◽  
Bacterial Communities ◽  
Bt Maize ◽  
Gm Crop ◽  
Soil Bacterial Communities ◽  
Significant Difference ◽  
Maize Residues ◽  
Soil Bacterial ◽  
June July ◽  
The Impact

Returning straw to the soil is an effective way to improve the soil quality. As genetically modified (GM) crops experience expanded growing scales, returning straw to the soil could also be necessary. However, the impact of GM crop straws on soil safety remains unclear. The environment (including soil types, humidity and temperature) can result in a significant difference in the diversity of soil bacterial communities. Here, we compared the impacts of the straw from Bt maize IE09S034 (IE) and near-isogenic non-Bt maize Zong31 (CK) on soil bacterial community and microbial metabolic activity in three different environments. Sampling was carried out following 6–10 months of decomposition (May, June, July, and August) in three localities in Chinese cities (Changchun, Jinan, and Beijing). Our results showed that Bt maize residues posed no direct impact on soil bacterial communities in contrast to the environment and decomposed time. The microbial functional diversity and metabolic activity showed no significant difference between IE and CK. The results could be a reference for further assessing the effect of Bt maize residues on the soil that promotes the commercialisation of Bt maize IE09S034.

The presence of tetracycline in cow manure changes the impact of repeated manure application on soil bacterial communities

2016 ◽  
Vol 52 (8) ◽  
pp. 1121-1134 ◽  
Author(s):  
Luigi Chessa ◽  
Sven Jechalke ◽  
Guo-Chun Ding ◽  
Alba Pusino ◽  
Nicoletta Pasqualina Mangia ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Cow Manure ◽  
Manure Application ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
The Impact

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 Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Sammy Frenk ◽  
Yitzhak Hadar ◽  
Dror Minz
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Resource Availability ◽  
Bacterial Communities ◽  
Anthropogenic Activities ◽  
Bacterial Community Composition ◽  
Treated Wastewater ◽  
Soil Bacterial Communities ◽  
High Resource ◽  
Soil Bacterial

ABSTRACTAnthropogenic activities alter the structure and function of a bacterial community. Furthermore, bacterial communities structured by the conditions the anthropogenic activities present may consequently reduce their stability in response to an unpredicted acute disturbance. The present mesocosm-scale study exposed soil bacterial communities to different irrigation water types, including freshwater, fertilized freshwater, treated wastewater, and artificial wastewater, and evaluated their response to a disturbance caused by heat. These effectors may be considered deterministic and stochastic forces common in agricultural operations of arid and semiarid regions. Bacterial communities under conditions of high mineral and organic carbon availability (artificial wastewater) differed from the native bacterial community and showed a proteobacterial dominance. These bacterial communities had a lower resistance to the heat treatment disturbance than soils under conditions of low resource availability (high-quality treated wastewater or freshwater). The latter soil bacterial communities showed a higher abundance of operational taxonomic units (OTUs) classified asBacilli. These results were elucidated by soil under conditions of high resource availability, which lost higher degrees of functional potential and had a greater bacterial community composition change. However, the functional resilience, after the disturbance ended, was higher under a condition of high resource availability despite the bacterial community composition shift and the decrease in species richness. The functional resilience was directly connected to the high growth rates of certainBacteroidetesand proteobacterial groups. A high stability was found in samples that supported the coexistence of both resistant OTUs and fast-growing OTUs.IMPORTANCEThis report presents the results of a study employing a hypothesis-based experimental approach to reveal the forces involved in determining the stability of a soil bacterial community to disturbance. The resultant postdisturbance bacterial community composition dynamics and functionality were analyzed. The paper demonstrates the relatedness of community structure and stability under cultivation conditions prevalent in an arid area under irrigation with water of different qualities. The use of common agricultural practices to demonstrate these features has not been described before. The combination of a fundamental theoretical issue in ecology with common and concerning disturbances caused by agricultural practice makes this study unique. Furthermore, the results of the present study have applicable importance regarding soil conservation, as it enables a better characterization and monitoring of stressed soil bacterial communities and possible intervention to reduce the stress. It will also be of valued interest in coming years, as fresh water scarcity and the use of alternative water sources are expected to rise globally.

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 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 Biogeographical patterns in soil bacterial communities across the Arctic region

2019 ◽  
Author(s):  
Lucie A Malard ◽  
Muhammad Zohaib Anwar ◽  
Carsten S Jacobsen ◽  
David A Pearce
Keyword(s):  
Bacterial Communities ◽  
Variation Partitioning ◽  
Arctic Region ◽  
The Arctic ◽  
Alkaline Soils ◽  
Core Microbiome ◽  
Soil Bacterial Communities ◽  
Arctic Soil ◽  
Soil Bacterial ◽  
The Impact

AbstractThe considerable microbial diversity of soils, their variety and key role in biogeochemical cycling has led to growing interest in their global distribution and the impact that environmental change might have at the regional level. In the broadest study of Arctic soil bacterial communities to date, we used high-throughput DNA sequencing to investigate the bacterial diversity from 200 independent Arctic soil samples from 43 sites. We quantified the impact of spatial and environmental factors on bacterial community structure using variation partitioning analysis, illustrating a non-random distribution across the region. pH was confirmed as the key environmental driver structuring Arctic soil bacterial communities, while total organic carbon, moisture and conductivity were shown to have little effect. Specialist taxa were more abundant in acidic and alkaline soils while generalist taxa were more abundant in acidoneutral soils. Of 48,147 bacterial taxa, a core microbiome composed of only 13 taxa that were ubiquitously distributed and present within 95% of samples was identified, illustrating the high potential for endemism in the region. Overall, our results demonstrate the importance of spatial and edaphic factors on the structure of Arctic soil bacterial communities.

scholarly journals The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities

SOIL ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 611-637
Author(s):  
Capucine Baubin ◽  
Arielle M. Farrell ◽  
Adam Št'ovíček ◽  
Lusine Ghazaryan ◽  
Itamar Giladi ◽  
...  
Keyword(s):  
Community Composition ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Ecosystem Engineers ◽  
Patch Type ◽  
Arid Soil ◽  
Soil Bacterial Communities ◽  
Ant Nests ◽  
Soil Bacterial ◽  
And Function

Abstract. Ecosystem engineers (EEs) are present in every environment and are known to strongly influence ecological processes and thus shape the distribution of species and resources. In this study, we assessed the direct and indirect effect of two EEs (perennial shrubs and ant nests), individually and combined, on the composition and function of arid soil bacterial communities. To that end, topsoil samples were collected in the Negev desert highlands during the dry season from four patch types: (1) barren soil; (2) under shrubs; (3) near ant nests; or (4) near ant nests situated under shrubs. The bacterial community composition and potential functionality were evaluated in the soil samples (14 replicates per patch type) using 16S rRNA gene amplicon sequencing together with physico-chemical measures of the soil. We have found that the EEs affected the community composition differently. Barren patches supported a soil microbiome, dominated by Rubrobacter and Proteobacteria, while in EE patches Deinococcus-Thermus dominated. The presence of the EEs similarly enhanced the abundance of phototrophic, nitrogen cycle, and stress-related genes. In addition, the soil characteristics were altered only when both EEs were combined. Our results suggest that arid landscapes foster unique communities selected by patches created by each EE(s), solo or in combination. Although the communities' composition differs, they support similar potential functions that may have a role in surviving the harsh arid conditions. The combined effect of the EEs on soil microbial communities is a good example of the hard-to-predict non-additive features of arid ecosystems that merit further research.

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.

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