Heterotrophic Bacteria Play an Important Role in Endemism of Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang, 2007, a Full-Year Shooting Woody Bamboo

The previous studies show soil microbes play a key role in the material and nutrient cycles in the forest ecosystem, but little is known about how soil microbes respond to plant distribution, especially in the soil bacterial community in woody bamboo forests. Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang, 2007 is known as the only bamboo species producing shoots all year round in natural conditions. Endemic to the Dawei mountain in Yunnan of China, this species is a good case to study how soil bacteria respond to plant endemic distribution. In this work, we assayed the soil chemical properties, enzyme activity, changes in the bacterial community along the distribution range of the C. pingbianense forest. The results showed that soil nutrients at the range edge were nitrogen-rich but phosphorus-deficient, and soil pH value and soil urease activity were significantly lower than that of the central range. No significant difference was detected in soil bacterial diversity, community composition, and function between the central and marginal range of C. pingbianense forest. Notably, the relative abundance of heterotrophy bacteria, such as Variibacter and Acidothermus, in the soil of the C. pingbianense forest was significantly higher than that of the outside range, which may lead to a higher soil organic carbon mineralization rate. These results imply that abundant heterotrophy bacteria were linked to the endemism and full-year shooting in C. pingbianense. Our study is amongst the first cases demonstrating the important role of heterotrophy bacteria in the distribution formation of endemic woody bamboos in special soil habitats, and provides insight into germplasm conservation and forest management in woody bamboos.

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Regulating soil bacterial diversity, community structure and enzyme activity using residues from golden apple snails

Scientific Reports ◽

10.1038/s41598-020-73184-z ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Jiaxin Wang ◽

Xuening Lu ◽

Jiaen Zhang ◽

Guangchang Wei ◽

Yue Xiong

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Diversity ◽

Soil Nutrients ◽

Pomacea Canaliculata ◽

Soil Bacterial Diversity ◽

Amended Soils ◽

Soil Bacterial ◽

The Impact ◽

Amended Soil

Abstract It has been shown that the golden apple snail (GAS, Pomacea canaliculata), which is a serious agricultural pest in Southeast Asia, can provide a soil amendment for the reversal of soil acidification and degradation. However, the impact of GAS residue (i.e., crushed, whole GAS) on soil bacterial diversity and community structure remains largely unknown. Here, a greenhouse pot experiment was conducted and 16S rRNA gene sequencing was used to measure bacterial abundance and community structure in soils amended with GAS residue and lime. The results suggest that adding GAS residue resulted in a significant variation in soil pH and nutrients (all P < 0.05), and resulted in a slightly alkaline (pH = 7.28–7.75) and nutrient-enriched soil, with amendment of 2.5–100 g kg−1 GAS residue. Soil nutrients (i.e., NO3-N and TN) and TOC contents were increased (by 132–912%), and some soil exocellular enzyme activities were enhanced (by 2–98%) in GAS residue amended soil, with amendment of 1.0–100 g kg−1 GAS residue. Bacterial OTU richness was 19% greater at the 2.5 g kg−1 GAS residue treatment than the control, while it was 40% and 53% lower at 100 g kg−1 of GAS residue and 50 g kg−1 of lime amended soils, respectively. Firmicutes (15–35%) was the most abundant phylum while Bacterioidetes (1–6%) was the lowest abundant one in GAS residue amended soils. RDA results suggest that the contents of soil nutrients (i.e., NO3-N and TN) and soil TOC explained much more of the variations of bacterial community than pH in GAS residue amended soil. Overuse of GAS residue would induce an anaerobic soil environment and reduce bacterial OTU richness. Soil nutrients and TOC rather than pH might be the main factors that are responsible for the changes of bacterial OTU richness and bacterial community structure in GAS residue amended soil.

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Changes in the Composition of the Soil Bacterial Community in Heavy Metal-Contaminated Farmland

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18168661 ◽

2021 ◽

Vol 18 (16) ◽

pp. 8661

Author(s):

Shu-chun Tseng ◽

Chih-ming Liang ◽

Taipau Chia ◽

Shan-shin Ton

Keyword(s):

Heavy Metal ◽

Bacterial Community ◽

Structural Changes ◽

Ph Value ◽

Deep Layer ◽

Soil Bacterial Community ◽

Rrna Gene ◽

Zinc Tolerance ◽

Copper And Zinc ◽

Soil Bacterial

The structural changes of microorganisms in soil are the focus of soil indicators research. The purpose of this study was to investigate the changes in the composition of the soil bacterial community in heavy metal-contaminated soil. A total of six soil samples (two sampling times) were collected from contaminated farmland at three different depths (surface, middle, and deep layer). The pH value was measured. The concentrations of heavy metals (Cr, Ni, Cu, Zn, Cd, and Pb) and the soil bacterial community were analyzed using ICP-OES and 16S rRNA gene sequencing. The results of the two samplings showed that the pH value in the deep layer decreased from 6.88 to 6.23, and the concentrations of Cu, Zn, Cd, and Pb, with a smaller ion radius, increased by 16–28%, and Shannon, Chao1 increased by ~13%. The bacteria community composition at the three depths changed, but Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla. In the copper and zinc tolerance test, the isolated bacterium that was able to tolerate copper and zinc was Bacillus sp. We found that, the longer the heavy metal pollution was of concern, the higher the tolerance. These results can be used as references for the microbial remediation of heavy metal-contaminated farmland.

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Diversity and composition of soil bacterial community respond to A. palmeri invasion under heterogeneous habitats

10.21203/rs.3.rs-595834/v1 ◽

2021 ◽

Author(s):

Mei Zhang ◽

Jianhua Han ◽

Xueying Li ◽

Pufan Zheng ◽

Zhenlu Qiu ◽

...

Keyword(s):

Bacterial Community ◽

Alpha Diversity ◽

Soil Bacterial Community ◽

Soil Bacterial Diversity ◽

Core Microbiome ◽

Non Invasive ◽

Heterogeneous Habitats ◽

Soil Bacterial ◽

The Impact ◽

Nmds Analysis

Abstract The impact of A. palmeri invasion on soil bacterial community under different habitats is unclear. In this work, the influence of A. palmeri invasion on soil bacterial diversity and community structure were investigated using full-length 16S rRNA sequencing technology under four typical habitats of riverbank (A), roadside (B), wasteland (C) and farmland (D). A two-way ANOVA analysis showed that habitat, invasion and the interaction of them had little effect on alpha diversity, expect for habitat factor had a significant effect on Simpson indices (P<0.05). NMDS analysis demonstrated that soil bacterial community structures among different invasive habitats were clearly distinguished. In addition, the most abundant phyla in the non-invasive plots were Proteobacteria, Planctomycetes and Gemmatimonadetes. However, the third predominant phyla converted from Bacteroidetes to Gemmatimonadetes with the invasion of A. palmeri. LEfSe analysis revealed that the core microbiome, Burkholderiaceae and Betaproteobacteriales (riverbank habitat), Gemmatimonadetes and Gemmatimonadaceae (wasteland habitat), Sphingomonas_sediminicola (roadside habitat), Nitrosomonadaceae (farmland habitat), which played important roles in facilitating the establishment of A. palmeri to heterogeneous habitats.

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Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau

Microorganisms ◽

10.3390/microorganisms9010139 ◽

2021 ◽

Vol 9 (1) ◽

pp. 139

Author(s):

Quanchao Zeng ◽

Shaoshan An

Keyword(s):

Community Structure ◽

Environmental Factors ◽

Bacterial Community ◽

Bacterial Diversity ◽

Bacterial Communities ◽

Land Uses ◽

The Loess Plateau ◽

Soil Bacterial Diversity ◽

Soil Bacterial ◽

Rare Bacteria

High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3-V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.

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Effects of Imazapyr on Spartina alterniflora and Soil Bacterial Communities in a Mangrove Wetland

Water ◽

10.3390/w13223277 ◽

2021 ◽

Vol 13 (22) ◽

pp. 3277

Author(s):

Xue Mo ◽

Panpan Dong ◽

Lumeng Xie ◽

Yujiao Xiu ◽

Yanqi Wang ◽

...

Keyword(s):

Bacterial Diversity ◽

Spartina Alterniflora ◽

Bacterial Communities ◽

Available Phosphorus ◽

Soil Bacterial Diversity ◽

Factors Affecting ◽

Soil Bacterial Communities ◽

Mangrove Wetland ◽

Significant Difference ◽

Soil Bacterial

The invasion of Spartina alterniflora (S. alterniflora) has caused serious damage to coastal wetland ecosystems in China, especially the mangrove wetlands in South China. This study aimed to validate the effect of imazapyr on S. alterniflora and soil. The controlled experiment was conducted in May 2021 at the Zhangjiangkou Mangrove Wetland Reserve. In the experiment, 25% (W) imazapyr was used, and six treatments were set up: 3035, 6070, and 9105 mL/acre 25% imazapyr and 1299, 2604, and 5202 mL/acre of AGE 809 + 6070 mL/acre 25% imazapyr. The results showed no side effects on mangrove plants in the spraying area. The highest control efficiency (95.9%) was given by 2604 mL/acre of AGE 809 + 6070 mL/acre 25% imazapyr. The residues of imazapyr in different soils were reduced to 0.10–0.59 mg/kg. The sequencing results showed no significant difference in the overall bacterial communities under different treatments (p > 0.05). The soil bacterial diversity in the samples with adjuvant was higher than that in the samples without adjuvant, while the abundance values were the opposite. There were 10 main communities (>0.3%) at phylum level in all soil samples, among which Proteobacteria, Bacteroidetes, Acidobacteria, Chloflexi, and Actinobacteria were the dominant communities, and the latter four’s abundance changed significantly (p < 0.05). There were significant abundance differences between the groups of oligotrophic and eutrophic bacteria. The redundancy analysis and Monte Carlo tests showed that the total organic carbon (TOC), total phosphorus (TP), available phosphorus (AP), ammonia nitrogen, and total nitrogen were the main factors affecting soil bacterial diversity. At the same time, TOC, AP, and TP were the most critical factors affecting the overall characteristics of soil bacterial communities in different treatments, while soil residues had no significant effect on bacteria. This might be due to the addition and degradation of imazapyr and the coverage of S. alterniflora. The best recommendation is 2604 mL/acre of AGE 809 + 6070 mL/acre 25% imazapyr to be applied in China’s mangrove wetland reserves and coastal wetlands.

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Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter

10.7287/peerj.preprints.3161v1 ◽

2017 ◽

Author(s):

Quanchao Zeng ◽

Yang Liu ◽

Shaoshan An

Keyword(s):

Bacterial Community ◽

Litter Decomposition ◽

Relative Abundance ◽

Bacterial Communities ◽

Terrestrial Ecosystems ◽

Soil Bacterial Diversity ◽

Litter Addition ◽

Normal Quantity ◽

Soil Bacterial ◽

Litter Quantity

The forest ecosystem is the main component of terrestrial ecosystems. The global climate and the functions and processes of soil microbes in the ecosystem are all influenced by litter decomposition. The effects of litter decomposition on the abundance of soil microorganisms remain unknown. Here, we analyzed soil bacterial communities during the litter decomposition process in an incubation experiment under treatment with different litter quantities based on annual litterfall data (normal quantity, 200 g/(m2/yr); double quantity, 400 g/(m2/yr) and control, no litter). The results showed that litter quantity had significant effects on soil carbon fractions, nitrogen fractions, and bacterial community compositions, but significant differences were not found in the soil bacterial diversity. The normal litter quantity enhanced the relative abundance of Actinobacteria and Firmicutes and reduced the relative abundance of Bacteroidetes, Plantctomycets and Nitrospiare. The Beta-, Gamma-, and Deltaproteobacteria were significantly less abundant in the normal quantity litter addition treatment, and were subsequently more abundant in the double quantity litter addition treatment. The bacterial communities transitioned from Proteobacteria-dominant (Beta-, Gamma-, and Delta) to Actinobacteria-dominant during the decomposition of the normal quantity of litter. A cluster analysis showed that the double litter treatment and the control had similar bacterial community compositions. These results suggested that the double quantity litter limited the shift of the soil bacterial community. Our results indicate that litter decomposition alters bacterial dynamics under the accumulation of litter during the vegetation restoration process, which provides important significant guidelines for the management of forest ecosystems.

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Drivers on The Halophytes' Rhizosphere Bacteria Community and Functions in North China Salinized Areas

10.21203/rs.3.rs-215157/v1 ◽

2021 ◽

Author(s):

Fating Yin ◽

Fenghua Zhang ◽

Zhibo Cheng ◽

Haoran Wang

Keyword(s):

Bacterial Community ◽

North China ◽

High Throughput Sequencing ◽

Environmental Changes ◽

Rhizosphere Soil ◽

Ph Value ◽

Northern China ◽

Soil Bacterial Community ◽

Leymus Chinensis ◽

Soil Bacterial

Abstract Soil salinity is a serious environmental issue in arid China. Soil bacteria play a fundamental role in soil systems and respond rapidly to environmental changes. However, the responses of soil bacterial community to the different halophytes remains poorly understood. We investigated rhizosphere soil bacterial community changes under different halophytes in north China using high-throughput sequencing. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, and Chloroflexi across three halophytic vegetation. These bacteria have important assistance for halophytes adapt to saline soil. PICRUSt forecasts demonstrated that energy metabolism, amino acid metabolism and carbohydrate metabolism are main bacterial functions in halophyte vegetation soil, and the abundance of metabolism these bacterial functions in SG was significantly higher than that in LC and PT. The pH value of different halophyte rhizosphere soils has a more significant effect on bacterial diversity than EC and soil trophic status, and soil water content (SWC) was important effect factors leading to differences in bacterial functions. These results give us a deeper understanding of the diversity and functional differences of rhizosphere soil bacterial communities in the typical halophytic vegetation of northern China.

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Soil Bacterial Diversity and Its Relationship with Soil CO2 and Mineral Composition: A Case Study of the Laiwu Experimental Site

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph17165699 ◽

2020 ◽

Vol 17 (16) ◽

pp. 5699

Author(s):

Hongying Zhang ◽

Zongjun Gao ◽

Mengjie Shi ◽

Shaoyan Fang

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Mineral Composition ◽

High Throughput Sequencing ◽

Soil Depth ◽

Bacterial Flora ◽

Soil Co2 ◽

Soil Bacterial Diversity ◽

Experimental Site ◽

Soil Bacterial

To better understand the characteristics of soil bacterial diversity in different environments, the Laiwu Qilongwan experimental site was selected as it is of great significance for the study of geochemical cycles. The soil CO2, mineral composition and bacterial community were analyzed by an EGM-4 portable environmental gas detector, an X-ray diffractometer and 16S rDNA high-throughput sequencing, and soil bacterial diversity and the relationship between soil bacterial diversity and environmental factors were studied. The results showed that with increasing soil depth, the CO2 content increased, the feldspar and amphibole contents increased, the quartz content decreased, the richness of the soil bacterial community increased, the relative richness of Nitrospirae increased, and Chloroflexi decreased. The dominant bacteria were Proteobacteria, Actinobacteria and Acidobacteria. There were slight differences in soil CO2, mineral composition and dominant bacterial flora at the same depth. Actinobacteria, Proteobacteria and Firmicutes were the dominant phyla of L02. The CO2 was lowest in bare land, and the quartz and K-feldspar contents were the highest. Soil CO2 mainly affected the deep bacterial diversity, while shallow soil bacteria were mainly affected by mineral components (quartz and K-feldspar). At the same depth, amphibole and clay minerals had obvious effects on the bacterial community, while CO2 had obvious effects on subdominant bacteria.

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Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter

10.7287/peerj.preprints.3161 ◽

2017 ◽

Author(s):

Quanchao Zeng ◽

Yang Liu ◽

Shaoshan An

Keyword(s):

Bacterial Community ◽

Litter Decomposition ◽

Relative Abundance ◽

Bacterial Communities ◽

Terrestrial Ecosystems ◽

Soil Bacterial Diversity ◽

Litter Addition ◽

Normal Quantity ◽

Soil Bacterial ◽

Litter Quantity

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Time-Dependent Effect of Graphene on the Microbial Activity of the Soil Under Single and Repeated Exposures

10.21203/rs.3.rs-1049681/v1 ◽

2021 ◽

Author(s):

Wenjuan Liu ◽

Yufeng Guo ◽

Guoli Chai ◽

Wenbo Deng

Keyword(s):

Bacterial Community ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Soil Bacterial Community ◽

Soil Bacterial Diversity ◽

Single Exposure ◽

Soil Bacterial ◽

The Difference ◽

And Function ◽

The Impact

Abstract Graphene (GR) has huge industrial and biomedical potential, and its adverse effect on soil microorganisms has been evaluated in some ecotoxicological studies. These studies focus on a single exposure to GR, but repeated exposures are more likely to occur in soil. In this study, we compared the impact of single and repeated exposures (one, two and three exposures that resulted in the same final concentration) of GR on structure, abundance and function of soil bacterial community based on soil enzyme activity and high-throughput sequencing. The activities of urease and fluorescein diacetate esterase and alpha diversity demonstrate that repeated exposure to GR increase the diversity of soil bacterial diversity after 4 days of incubation following the last application of GR to soil. And the PCoA and sample level clustering tree showed single exposure to GR after 4 days alter the soil bacterial community to some extent, but the difference has been narrowed with the extension of time. During the entire incubation process, no matter what kind of exposure scenarios to GR, the majority of bacterial phylotypes remained unchanged except for Proteobacteria and Actinobacteria according to the relative abundance of phylotypes.

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