Effect Mechanism of Land Consolidation on Soil Bacterial Community: A Case Study in Eastern China

Farmland consolidation is an effective tool to improve farmland infrastructures, soil quality, and sustain a healthy farmland ecosystem and rural population, generating contributions to food security and regional sustainable development. Previous studies showed that farmland consolidation regulates soil physical and chemical properties. Soil microorganisms also play an important role in soil health and crop performance; however, few studies reported how farmland consolidation influence soil microecology. Here, we used DNA sequencing technology to compare bacterial community structure in farmlands with and without consolidation. DNA sequencing technology is the most advanced technology used to obtain biological information in the world, and it has been widely used in the research of soil micro-ecological environment. In September 2018, we collected soil samples in Jiashan County, Zhejiang Province, China, and used DNA sequence technology to compare the bacterial community structure in farmlands with and without consolidation. Our results found that (1) farmland consolidation had significant impacts on soil microbial characteristics, which were mainly manifested as changes in microbial biomass, microbial diversity and community structure. Farmland consolidation can increase the relative abundance of the three dominant bacteria phyla and the three fungal dominant phyla, but it also negatively affects the relative abundance of the six dominant bacteria phyla and the three fungal dominant phyla. (2) Farmland consolidation had an indirect impact on soil bacterial community structure by adjusting the soil physical and chemical properties. (3) The impact of heavy metals on bacterial community structure varied significantly under different levels of heavy metal pollution in farmland consolidation areas. There were 6, 3, 3, and 5 bacterial genera that had significant correlations with heavy metal content in cultivated land with low pollution, light pollution, medium pollution, and heavy pollution, respectively. The number of heavy metal-tolerant bacteria in the soil generally increased first and then decreased under heavy metal polluted conditions. Our study untangled the relationship between varied farmland consolidation strategies and bacteria through soil physcicochemical properties and metal pollution conditions. Our results can guide farmland consolidation strategies and sustain soil health and ecological balance in agriculture.

Variation in Bacterial Community Structure in Rhizosphere and Bulk Soils of Different Halophytes in the Yellow River Delta

Soil microorganisms play the important role in driving biogeochemical cycles. However, it is still unclear on soil microbial community characteristics and microbial driving mechanism in rhizosphere and bulk soils of different halophyte species. In this study, we analyzed bacterial communities in the rhizosphere and bulk soils of three typical halophytes in the Yellow River Delta, i.e., Phragmites communis, Suaeda salsa, and Aeluropus sinensis, by high-throughput sequencing. The contents of total carbon, total nitrogen, and available phosphorus in rhizosphere soils of the three halophytes were significantly higher than those in bulk soils, which suggested a nutrient enrichment effect of the rhizosphere. Rhizosphere soil bacterial α-diversity of P. communis was higher than that in bulk soil, whereas bacterial α-diversity in rhizosphere soil of S. salsa and A. sinensis was lower than those in bulk soil. The dominant bacterial phyla were Proteobacteria, Actinobacteria, Chloroflexi, and Bacteroidetes, which accounted for 31, 20.5, 16.3, and 10.3%, respectively. LDA effect size (LEfSe) analysis showed that the bacterial species with significant differences in expression abundance was obviously different in the rhizosphere and bulk soil of three halophytes. The principal component analysis (PCoA) showed that bacterial community composition was greatly different between rhizosphere and bulk soils of P. communis and S. salsa, while no difference in A. sinensis. Changed bacterial community composition was mainly ascribed to salinity in rhizosphere and bulk soils. Additionally, salinity was positively correlated with Bacteroidetes and negatively correlated with Actinobacteria and Acidobacteria. Our study clarified the variation in bacterial community structure between rhizosphere and bulk soils with soil physicochemical properties, which proved a biological reference to indicate the characteristics of saline and alkaline land.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

Lacustrine Sediments Bacterial Community Structure Vertical Succession of the Linxia Basin, NE Tibetan Plateau: Significance for Paleoenvironment Reconstruction

The study on sediments in the marginal basins of the Tibetan Plateau is of great significance for global climate change. The geological information of the Linxia Basin has been intensely investigated; however, the profiles of the microbial communities in this basin remain largely unknown. Here, based on the 16S rRNA high-throughput sequencing method, the bacterial community structure vertical succession is studied with different thicknesses of sedimentary samples. The bacterial community with a total of 1,729,658 paired reads distributed within 1,042 phylogenetic amplicon sequence variants (ASVs) from twenty sediments, and three surrounding soil samples were sequenced. First, high-throughput sequencing results highlight the surrounding soil sample bacterial community structures were significantly different from those recovered from the sediment samples. In addition, as observed in the PCoA and PERMANOVA, there is a dramatic change shift event of the community structure at M311. Our data suggest that shifts in relative abundances of the abundant taxa (˃1%) and the significant variations in the diversity of bacterial community implied community structure responses to changes in different sedimentary layers. Predicted community function changes demonstrate that the sediment bacterial community aerobic chemoheterotrophy has been significantly increased, and we believe that the possible influence of the lithofacies changes from the anaerobic system to the aerobic environment, possibly accompanied by the significant uplift of the plateau that has previously been associated with enhanced aridity in Central Asia at ∼8 Ma. Taken together, these results illustrate the potential for the microbial community as a biological indicator in sediment ecosystems to reconstruct paleoenvironments.

Effects of enrichmemt planting with native tree species on bacterial community structure and potential impact on Eucalyptus plantations in southern China

Multi-generational planting of Eucalyptus species degrades soil quality but the introduction of legumes can improve soil fertility and microbial diversity. However, the effects of introducing non-legume native tree species on soil nutrients and bacterial community structure remain poorly understood. This study investigated the impacts of the conversion of third generation monoculture Eucalyptus plantations to mixed systems including Eucalyptus urograndis with Cinnamomum camphora (EC) and E. urograndis with Castanopsis hystrix (EH), on soil chemical and biochemical properties and bacterial community structure, diversity and functions. First generation E. urophylla plantations were the control. Results show that planting the third generation Eucalyptus led to a significant decrease in pH, organic matter, nutrient content, enzyme activities (invertin, acid phosphataes, and urease), and bacterial α-diversity compare to the controls. However, the mixed planting showed significant improvement in soil chemical and biochemical attributes and bacterial α-diversity, although the E. urograndis and C. hystrix planting had no improvement. Chloroflexi (oligotrophic bacteria) were significantly enriched in third generation Eucalyptus and Eucalyptus + C. hystrix, while proteobacteria increased significantly in the E. urograndis with C. camphora plantings. The relative abundance of multiple metabolic pathways increased significantly in the third generation Eucalyptus plantations whereas membrane transport-related genes were enriched in soils of the mixed systems. The changes in bacterial community structures in the two mixed systems were driven by diversity, organic matter and acid phosphatase, while bacterial functions were affected by invertase, $${\mathrm{NO}}_{3}^{-}$$ NO 3 - -N, diversity and urease. These results suggest that the transformation of successive monoculture Eucalyptus plantations into mixed plantations reduces the depletion of soil nutrients and enhances the ecological function of soil microorganisms.

Ciprofloxacin Causes the Greatest Bacterial Community Variation in Swine Manure Composting

In this study, the influence of ciprofloxacin, chlorotetracycline, lincomycin, and sulfamethoxazole on the composition of the bacterial community structure was studied during aerobic composting with swine manure. Firmicutes (26.67%) and Chloroflexi (23.33%) were the most widely distributed phyla. Under all antibiotic treatments, the relative abundances of Bacillaceae, Streptosporangiaceae, Limnochordaceae, and Peptostreptococcaceae increased during the composting process. Moreover, norank_SBR1031, Planococcaceae, Thermomonosporaceae, Peptostreptococcaceae, Erysipelotrichaceae, Limnochordaceae, and Clostridiaceae_1 were the families showing the most significant differences across all treatments (p < 0.05). Principal co-ordinates analysis indicated that the family composition in the ciprofloxacin treatment significantly differed from the other treatments. The presence of ciprofloxacin increased both the abundance and diversity of the bacterial community (the Chao index changed from 588.44 to 680.17, and the Shannon index changed from 3.41 to 4.06) in the end of composting. Crocinitomicaceae dominated (relative abundance of 79.10%) among the unique families in the ciprofloxacin treatment. Network analysis indicated that ciprofloxacin altered the synergistic or competitive relationships between different families (norank_SBR1031 and Microscillaceae), leading to different bacterial community composition compared with other treatments. Further, a structural equation model showed that the C:N ratio was significantly negatively correlated with the bacterial community (λ = −0.869, p < 0.01), whereas pH showed a direct, significant positive relationship with the bacterial community (λ = 0.701, p < 0.01), especially in ciprofloxacin treatment. Overall, ciprofloxacin significantly influenced the physical and chemical properties of composting, altered the bacterial community structure. These findings have important implications for a better understanding of the effects of antibiotic types on bacterial community structure and the involved mechanisms during swine manure composting.

Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone

Estuarine intertidal wetlands pertain to habitats with high productivity on Earth. Bacteria in estuarine intertidal soils regulate carbon (C), nitrogen (N) and sulfur (S) cycles. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, we explored the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions in surface soils from China’s estuarine intertidal flats through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China’s estuarine intertidal soils from various latitudes and helps us understand the effects exerted by environmental factors or climate-related variations on the ecological health and microbial diversity of estuarine intertidal flats.