Effect of straw biochar amendment on tobacco growth, soil properties, and rhizosphere bacterial communities

AbstractBiochar is an effective soil conditioner. However, we have limited understanding of biochar effects on the tobacco growth and bacterial communities in rhizosphere. The aim of this study was to investigate the effects of different straw biochar amendment (0, 2, 10, and 50 g/kg dry soil) on tobacco growth, soil properties, and bacterial communities in rhizosphere by pot trials. Most of tobacco agronomic traits increased when the application rate varied from 0 to 10 g/kg, but were inhibited by 50 g/kg of biochar application. Soil pH, SOC, available nutrients and soil urease, invertase, and acid phosphatase activities were all increased with the biochar application, whereas catalase activity decreased or remained unchanged. The OTUs and bacterial community diversity indices differed with the biochar application doses in rhizosphere and non-rhizosphere soils. And significant differences in bacterial communities were found between the rhizosphere and non-rhizosphere soils despite the biochar addition. Firmicutes, Proteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla in all soil samples, but they had different abundances in different treatment influenced by the rhizosphere and biochar effect. The high dose of biochar (50 g/kg) decreased the similarity of soil bacterial community structure in rhizosphere compared with those in non-rhizosphere soil. These results provide a better understanding of the microecological benefits of straw biochar in tobacco ecosystem.

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Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems

Microorganisms ◽

10.3390/microorganisms8111708 ◽

2020 ◽

Vol 8 (11) ◽

pp. 1708

Author(s):

Savvas Genitsaris ◽

Natassa Stefanidou ◽

Kleopatra Leontidou ◽

Theodora Matsi ◽

Katerina Karamanoli ◽

...

Keyword(s):

Bacterial Community ◽

Soil Properties ◽

Bacterial Communities ◽

Mediterranean Ecosystems ◽

Community Diversity ◽

Sampling Location ◽

Rrna Gene ◽

Sodic Soils ◽

Drought Tolerant ◽

Tolerant Plants

The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant’s compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.

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Effects of tobacco-cultivated soil extracts on tobacco growth and bacterial community diversity in rhizosphere soils

CHINESE JOURNAL OF ECO-AGRICULTURE ◽

10.3724/sp.j.1011.2012.01614 ◽

2013 ◽

Vol 20 (12) ◽

pp. 1614-1620 ◽

Cited By ~ 1

Author(s):

Dong-Mei CHEN ◽

Wen-Xiang WU ◽

Hai-Bin WANG ◽

Jin-Wen HUANG ◽

Lan-Lan CHEN ◽

...

Keyword(s):

Bacterial Community ◽

Community Diversity ◽

Soil Extracts ◽

Rhizosphere Soils ◽

Bacterial Community Diversity ◽

Cultivated Soil ◽

Tobacco Growth

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Variation of Microbial Communities in Aquatic Sediments under Long-Term Exposure to Decabromodiphenyl Ether and UVA Irradiation

Sustainability ◽

10.3390/su11143773 ◽

2019 ◽

Vol 11 (14) ◽

pp. 3773 ◽

Cited By ~ 2

Author(s):

Yi-Tang Chang ◽

Hsi-Ling Chou ◽

Hui Li ◽

Stephen Boyd

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Species ◽

Community Diversity ◽

High Dose ◽

Decabromodiphenyl Ether ◽

Uva Irradiation ◽

Different Types ◽

Bde 209

Abiotic components create different types of environmental stress on bacterial communities in aquatic ecosystems. In this study, the long-term exposure to various abiotic factors, namely a high-dose of the toxic chemical decabromodiphenyl ether (BDE-209), continuous UVA irradiation, and different types of sediment, were evaluated in order to assess their influence on the bacterial community. The dominant bacterial community in a single stress situation, i.e., exposure to BDE-209 include members of Comamonadaceae, members of Xanthomonadaceae, a Pseudomonas sp. and a Hydrogenophaga sp. Such bacteria are capable of biodegrading polybrominated diphenyl ethers (PBDEs). When multiple environmental stresses were present, Acidobacteria bacterium and a Terrimonas sp. were predominant, which equipped the population with multiple physiological characteristics that made it capable of both PBDE biodegradation and resistance to UVA irradiation. Methloversatilis sp. and Flavisolibacter sp. were identified as representative genera in this population that were radioresistant. In addition to the above, sediment heterogeneity is also able to alter bacterial community diversity. In total, seventeen species of bacteria were identified in the microcosms containing more clay particles and higher levels of soil organic matter (SOM). This means that these communities are more diverse than in microcosms that contained more sand particles and a lower SOM, which were found to have only twelve identifiable bacterial species. This is the first report to evaluate how changes in bacterial communities in aquatic sediment are affected by the presence of multiple variable environmental factors at the same time.

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Effects of fertilisation on microbial communities in short-term coal mine reclamation

Soil Research ◽

10.1071/sr19262 ◽

2020 ◽

Vol 58 (8) ◽

pp. 779

Author(s):

Jian Zhang ◽

Yinghe Xie ◽

Ying Wei ◽

Huisheng Meng ◽

Yanzhuan Cao ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Soil Properties ◽

Coal Mining ◽

Coal Mine ◽

Bacterial Communities ◽

Community Diversity ◽

Short Term ◽

Beneficial Effects

The recovery of the belowground microbial community structure and diversity that occurs in long-term coal mining reclamation is critical to reclamation success. However, long-term coal mining reclamation can take ~10–30 years. Therefore, finding an effective method for promoting coal mine soil restoration in the short-term is necessary to minimise reclamation time. This study investigated the response of soil bacterial communities to fertilisation along a chronosequence of short-term reclamation. Fertilised and unfertilised soils with three short-term reclamation stages were examined to characterise soil properties, as well as bacterial structure and diversity. Fertilisation promoted available nitrogen, phosphate, potassium, and soil organic matter, as well as benefits in bacterial community diversity across the three stages, with the most beneficial effects at 7 years. 16S rRNA sequencing data showed that the predominant phyla across all soils were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Gemmatimonadetes. Abundance of each phylum was altered by reclamation time and fertilisation. Clustering and functional analysis indicated that the bacterial community structure in soils with a longer reclamation time was more similar to that in natural soils, suggesting that longer reclamation resulted in increased soil activity and bacterial community diversity, which is likely also true for fertilisation. Our results demonstrate that reclamation duration is the main driving force to recover soil properties and bacterial communities, and fertilisation could enhance the beneficial effects with longer reclamation duration. Therefore, short-term reclamation, combined with fertiliser, is a potential strategy to improve soil conditions in coal mine areas and shorten the recovery time of reclaimed soils.

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Rhizobacterial communities of five co-occurring desert halophytes

PeerJ ◽

10.7717/peerj.5508 ◽

2018 ◽

Vol 6 ◽

pp. e5508 ◽

Cited By ~ 3

Author(s):

Yan Li ◽

Yan Kong ◽

Dexiong Teng ◽

Xueni Zhang ◽

Xuemin He ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Plant Species ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Community Diversity ◽

Species Identity ◽

Halostachys Caspica ◽

Lycium Ruthenicum ◽

Limonium Gmelinii

BackgroundRecently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.MethodsFive halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3–V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.ResultsSignificant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity ofHalostachys caspica,Halocnemum strobilaceumandKalidium foliatumassociated bacterial communities was lower than that ofLimonium gmeliniiandLycium ruthenicumcommunities. Furthermore, the composition of the bacterial communities ofHalostachys caspicaandHalocnemum strobilaceumwas very different from those ofLimonium gmeliniiandLycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.DiscussionHalophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

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

Phytobiomes Journal ◽

10.1094/pbiomes-01-20-0002-r ◽

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.

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

Canadian Journal of Microbiology ◽

10.1139/cjm-2016-0758 ◽

2017 ◽

Vol 63 (5) ◽

pp. 392-401 ◽

Cited By ~ 3

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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.66.3.956-965.2000 ◽

2000 ◽

Vol 66 (3) ◽

pp. 956-965 ◽

Cited By ~ 81

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.

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Effect of Bacillus mesonae H20-5 Treatment on Rhizospheric Bacterial Community of Tomato Plants under Salinity Stress

The Plant Pathology Journal ◽

10.5423/ppj.ft.10.2021.0156 ◽

2021 ◽

Vol 37 (6) ◽

pp. 662-672

Author(s):

Shin Ae Lee ◽

Hyeon Su Kim ◽

Mee Kyung Sang ◽

Jaekyeong Song ◽

Hang-Yeon Weon

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Soil Salinity ◽

Bacterial Communities ◽

Bacterial Species ◽

Rrna Gene ◽

Plant Growth Promoting Bacteria ◽

Tomato Plants ◽

Rhizosphere Soils ◽

Salinity Levels

Plant growth-promoting bacteria improve plant growth under abiotic stress conditions. However, their effects on microbial succession in the rhizosphere are poorly understood. In this study, the inoculants of Bacillus mesonae strain H20-5 were administered to tomato plants grown in soils with different salinity levels (EC of 2, 4, and 6 dS/m). The bacterial communities in the bulk and rhizosphere soils were examined 14 days after H20-5 treatment using Illumina MiSeq sequencing of the bacterial 16S rRNA gene. Although the abundance of H20-5 rapidly decreased in the bulk and rhizosphere soils, a shift in the bacterial community was observed following H20-5 treatment. The variation in bacterial communities due to H20-5 treatment was higher in the rhizosphere than in the bulk soils. Additionally, the bacterial species richness and diversity were greater in the H20-5 treated rhizosphere than in the control. The composition and structure of the bacterial communities varied with soil salinity levels, and those in the H20-5 treated rhizosphere soil were clustered. The members of Actinobacteria genera, including Kineosporia, Virgisporangium, Actinoplanes, Gaiella, Blastococcus, and Solirubrobacter, were enriched in the H20-5 treated rhizosphere soils. The microbial co-occurrence network of the bacterial community in the H20-5 treated rhizosphere soils had more modules and keystone taxa compared to the control. These findings revealed that the strain H20-5 induced systemic tolerance in tomato plants and influenced the diversity, composition, structure, and network of bacterial communities. The bacterial community in the H20-5 treated rhizosphere soils also appeared to be relatively stable to soil salinity changes.

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Variation in the nitrous oxide reductase gene (nosZ)-denitrifying bacterial community in different primary succession stages in the Hailuogou Glacier retreat area, China

10.7287/peerj.preprints.27481 ◽

2019 ◽

Author(s):

Yan Bai ◽

Xiying Huang ◽

Xiangrui Zhou ◽

Quanju Xiang ◽

Ke Zhao ◽

...

Keyword(s):

Nitrous Oxide ◽

Bacterial Community ◽

Soil Properties ◽

Bacterial Communities ◽

Redundancy Analysis ◽

Primary Succession ◽

Available Phosphorus ◽

Nitrous Oxide Reductase ◽

Reductase Gene ◽

Successional Stages

Background: The Hailuogou Glacier in the Gongga Mountain region (SW China), on the southeastern edge of the Tibetan Plateau, is well known for its low-elevation modern glaciers. Since the end of the Little Ice Age (LIA), the Hailuogou Glacier has retreated continuously due to global warming, primary vegetation succession and soil chronosequence have developed in this retreat area. The retreated area of Hailuogou Glacier has not been strongly disturbed by human activities, thus it is an ideal models for exploring the biological colonization of nitrogen in the primary successional stages of ecosystem. The nosZ gene encodes the catalytic center of nitrous oxide reductase and is an ideal molecular marker in studying the variation in the denitrifying bacterial community. Methods: Soil properties as well as abundance and composition of the denitrifying bacterial community were determined via chemical analysis, quantitative polymerase chain reaction (qPCR), and terminal restriction fragment length polymorphism (T-RFLP), respectively. The relationships between the nosZ denitrifying bacterial community and soil properties were determined using redundancy analysis (RDA). Soil properties, potential denitrify activity (PDA), and the nitrous oxide reductase gene (nosZ)-denitrifying bacterial communities significantly differed among successional stages. Results: Soil properties, potential denitrify activity (PDA), and the nitrous oxide reductase gene (nosZ)-denitrifying bacterial communities significantly differed among successional stages. Soil pH in the topsoil decreased from 8.42 to 7.19 in the course of primary succession, while soil organic carbon (SOC) and total nitrogen (TN) gradually increased with primary succession. Available phosphorus (AP) and available potassium (AK), as well as potential denitrify activity (PDA), increased gradually and peaked at the 40-year-old site. The abundance of the nosZ denitrifying bacterial community followed a similar trend. The variation in the denitrifying community composition was complex; Mesorhizobium dominated the soil in the early successional stages (0-20 years) and in the mature phase (60 years), with a relative abundance greater than 55%. Brachybacterium was increased in the 40-year-old site, with a relative abundance of 62.74%, while Azospirillum dominated the early successional stages (0-20 years). Redundancy analysis (RDA) showed that the nosZ denitrifying bacterial community correlated with soil available phosphorus and available potassium levels (P < 0.01).

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