scholarly journals Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media

2019 ◽  
Vol 86 (1) ◽  
Author(s):  
Hannah Kleyer ◽  
Robin Tecon ◽  
Dani Or
Keyword(s):  
Bacterial Community ◽  
Aqueous Phase ◽  
Community Assembly ◽  
Bacterial Communities ◽  
Critical Role ◽  
Abundant Species ◽  
Special Focus ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

ABSTRACT The complexity of natural soils presents a challenge to the systematic identification and disentanglement of governing processes that shape natural bacterial communities. Studies have highlighted the critical role of the soil aqueous phase in shaping interactions among soil bacterial communities. To quantify and improve the attributability of soil aqueous-phase effects, we introduced a synthetic and traceable bacterial community to simple porous microcosms and subjected the community to constant or dynamic hydration conditions. The results were expressed in terms of absolute abundance and show species-specific responses to hydration and nutrient conditions. Hydration dynamics exerted a significant influence on the fraction of less-abundant species, especially after extended incubation periods. Phylogenetic relationships did not explain the group of most abundant species. The ability to quantify species-level dynamics in a bacterial community offers an important step toward deciphering the links between community composition and functions in dynamic terrestrial environments. IMPORTANCE The composition and activity of soil bacteria are central to various ecosystem services and soil biogeochemical cycles. A key factor for soil bacterial activity is soil hydration, which is in a constant state of change due to rainfall, drainage, plant water uptake, and evaporation. These dynamic changes in soil hydration state affect the structure and function of soil bacterial communities in complex ways often unobservable in natural soil. We designed an experimental system that retains the salient features of hydrated soil yet enables systematic evaluation of changes in a representative bacterial community in response to cycles of wetting and drying. The study shows that hydration cycles affect community abundance, yet most changes in composition occur with the less-abundant species (while the successful ones remain dominant). This research offers a new path for an improved understanding of bacterial community assembly in natural environments, including bacterial growth, maintenance, and death, with a special focus on the role of hydrological factors.

scholarly journals Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

2009 ◽  
Vol 75 (15) ◽  
pp. 5111-5120 ◽  
Author(s):  
Christian L. Lauber ◽  
Micah Hamady ◽  
Rob Knight ◽  
Noah Fierer
Keyword(s):  
Bacterial Community ◽  
Soil Ph ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Spatial Scales ◽  
Bacterial Community Composition ◽  
Phylogenetic Structure ◽  
Soil Bacterial Communities ◽  
Soil Bacterial Community Structure ◽  
Soil Bacterial

ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

scholarly journals The Influence of Land Use Patterns on Soil Bacterial Community Structure in the Karst Graben Basin of Yunnan Province, China

Forests ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 51 ◽  
Author(s):  
Jiangmei Qiu ◽  
Jianhua Cao ◽  
Gaoyong Lan ◽  
Yueming Liang ◽  
Hua Wang ◽  
...  
Keyword(s):  
Land Use ◽  
Surface Layer ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Yunnan Province ◽  
Soil Bacterial Community ◽  
Land Use Patterns ◽  
Use Patterns ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Land use patterns can change the structure of soil bacterial communities. However, there are few studies on the effects of land use patterns coupled with soil depth on soil bacterial communities in the karst graben basin of Yunnan province, China. Consequently, to reveal the structure of the soil bacterial community at different soil depths across land use changes in the graben basins of the Yunnan plateau, the relationship between soil bacterial communities and soil physicochemical properties was investigated for a given area containing woodland, shrubland, and grassland in Yunnan province by using next-generation sequencing technologies coupled with soil physicochemical analysis. Our results indicated that the total phosphorus (TP), available potassium (AK), exchangeable magnesium (E-Mg), and electrical conductivity (EC) in the grassland were significantly higher than those in the woodland and shrubland, yet the total nitrogen (TN) and soil organic carbon (SOC) in the woodland were higher than those in the shrubland and grassland. Proteobacteria, Verrucomicrobia, and Acidobacteria were the dominant bacteria, and their relative abundances were different in the three land use types. SOC, TN, and AK were the most important factors affecting soil bacterial communities. Land use exerts strong effects on the soil bacterial community structure in the soil’s surface layer, and the effects of land use attenuation decrease with soil depth. The nutrient content of the soil surface layer was higher than that of the deep layer, which was more suitable for the survival and reproduction of bacteria in the surface layer.

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

2017 ◽  
Vol 63 (5) ◽  
pp. 392-401 ◽  
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.

scholarly journals The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6147 ◽  
Author(s):  
Shu-Hong Wu ◽  
Bing-Hong Huang ◽  
Jian Gao ◽  
Siqi Wang ◽  
Pei-Chun Liao
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Chemical Properties ◽  
Soil Chemical Properties ◽  
Soil Microbiome ◽  
Apparent Lack ◽  
Soil P ◽  
Soil Bacterial Communities ◽  
Abundant Otus ◽  
Soil Bacterial

Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.

scholarly journals Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

2020 ◽  
Author(s):  
Juanjuan Fu ◽  
Yilan Luo ◽  
Pengyue Sun ◽  
Jinzhu Gao ◽  
Donghao Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Bacterial Communities ◽  
Shade Tolerance ◽  
Soil Microorganisms ◽  
Rhizosphere Soil ◽  
Photosynthetic Capacity ◽  
Soil Bacterial Communities ◽  
Plant Soil ◽  
Soil Bacterial

Abstract Background: The shade represents one of the major environmental limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. The composition of the soil bacterial community was assayed using high-throughput sequencing. Results: OJ maintained higher photosynthetic capacity and root growth than LP under shade stress, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. The shade and live soil decreased LP growth, but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Shade stress had little impact on the diversity of the OJ and the LP bacterial communities, but instead impacted their composition. The OJ soil bacterial communities were mostly composed of Proteobacteria and Acidobacteria. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Soil microorganisms mediate plant responses to shade stress via plant-soil feedback and shade-induced change in the rhizosphere soil bacterial community structure for OJ and LP plants. These findings emphasize the importance of understanding plant-soil interactions and their role in the mechanisms underlying shade tolerance in shade-tolerant turfgrasses.

scholarly journals Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies

Agronomy ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 14 ◽  
Author(s):  
Yadong Yang ◽  
Peixin Wang ◽  
Zhaohai Zeng
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Hierarchical Cluster ◽  
Organic Manure ◽  
Community Structures ◽  
Long Term Effects ◽  
Inorganic Fertilizers ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Fertilization plays important roles in improving soil fertility and in increasing crop yield. Soil microbial communities are sensitive indicators of soil quality and health, which could be affected by fertilization strategy. However, our knowledge on how organic–inorganic fertilizers application affects soil bacterial communities remains largely poorly understood. In this study, we investigated the long-term effects of different organic–inorganic fertilization strategies: without fertilizer (CK), fertilizers NPK (CF), fertilizers NPK, plus 30% organic manure (CFM1), and fertilizers NPK plus 60% organic manure (CFM2) on soil bacterial communities in paddy fields. Results showed that the bacterial 16S ribosomal DNA (rDNA) gene abundances in treatments CF, CFM1, and CFM2 were 1.44, 1.54, and 1.28 times higher than that in CK and the ACE index in treatment CFM1 was 9.0% greater than that in treatment CFM2, respectively. Fertilization strategy significantly changed the relative abundance of Nitrospirae, Gemmatimonadetes, and unclassified bacteria at the phylum level and bacteria belonging to order Nitrospira, candidate bacterium SBR2076, unclassified bacteria, Syntrophobacterales, and Solibacterales at the order level, respectively. High organic–inorganic fertilizer application rates inhibited the growth of Nitrospirae by 20–35%, and stimulated the growth of Gemmatimonadetes by 14–77%, relative to the rest of the treatments, respectively. Hierarchical cluster and principal coordinate analysis (PCoA) showed that the fertilization strategy affected the bacterial community structures, and the organic–inorganic fertilized treatments possessed similar bacterial community structures. Furthermore, soil pH, total nitrogen (TN), and soil organic carbon (SOC) were the main driving factors altering the bacterial communities. Our results suggested that combined organic–inorganic fertilizers application increased soil nutrient contents and bacterial abundances, and this could be an optimized fertilization strategy in regulating soil bacterial communities for rice production.

scholarly journals Effects of Vegetation Restoration on Soil Bacterial Communities, Enzyme Activities, and Nutrients of Reconstructed Soil in a Mining Area on the Loess Plateau, China

2019 ◽  
Vol 11 (8) ◽  
pp. 2295 ◽  
Author(s):  
Pengfei Li ◽  
Xingchang Zhang ◽  
Mingde Hao ◽  
Yongxing Cui ◽  
Shilei Zhu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Mining Area ◽  
Biochemical Properties ◽  
Vegetation Restoration ◽  
The Loess Plateau ◽  
Soil Biochemical Properties ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Reconstructed Soil

Soil microbes are the main driving forces and influencing factors of biochemical reactions in the environment. Study of ecological recovery after mining activities has prompted wider recognition of the importance of microbial diversity to ecosystem recovery; however, the response of soil bacterial communities to vegetation restoration types and soil biochemical properties remains poorly understood. The purpose of this research was to explore the soil bacterial communities and soil biochemical properties at four sampling sites (brushland (BL), forestland (FL), grassland (GL) and unreclaimed land (UL)) on the Loess Plateau, China, to evaluate the effect of vegetation restoration on the reconstructed soil in mining areas. In August 2017, samples were collected at the Heidaigou coal mine dumps. Illumina MiSeq sequencing was used to identify the structure of the soil bacterial community and evaluate its relationships with soil biochemical properties. The results showed that soil biochemical properties (soil organic matter, available phosphorus, urease, sucrase, microbial biomass carbon and microbial biomass nitrogen) were significantly increased in BL, FL and GL relative to UL, indicating that the soil quality was significantly improved by vegetation restoration. In addition, the results showed that the vegetation restoration on the reconstructed soil in the mining area could significantly improve the operational taxonomic units (OTUs), abundance (ACE and Chao1) and diversity (Shannon and Simpson) indices of bacterial community and the dominant phyla were Proteobacteria, Actinobacteria and Acidobacteria. With vegetation restoration, the relative abundance of Proteobacteria and Acidobacteria showed an increasing trend, while that of Actinobacteria showed a decreasing trend, and the dominant phyla were only significantly correlated with a few biochemical properties. Moreover, there were no changes in soil bacterial community structures across the four sampling sites and the response of the bacterial community to biochemical properties was not obvious. This implies that, although the region has experienced about 20 years of vegetation restoration, the microbial community still maintains good stability and lagging response to soil biochemical properties. Since the BL soil had better biochemical properties and higher bacterial richness and diversity, it was recommended as the optimum vegetation restoration type for soil reclamation in this area.

scholarly journals Land-use changes influence soil bacterial communities in a meadow grassland in Northeast China

Solid Earth ◽  
2017 ◽  
Vol 8 (5) ◽  
pp. 1119-1129 ◽  
Author(s):  
Chengyou Cao ◽  
Ying Zhang ◽  
Wei Qian ◽  
Caiping Liang ◽  
Congmin Wang ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Land Use Changes ◽  
Chemical Properties ◽  
Soil Bacterial Communities ◽  
Land Use Types ◽  
Soil Bacterial ◽  
Physical And Chemical ◽  
And Chemical Properties

Abstract. The conversion of natural grassland into agricultural fields is an intensive anthropogenic perturbation commonly occurring in semiarid regions, and this perturbation strongly affects soil microbiota. In this study, the influences of land-use conversion on the soil properties and bacterial communities in the Horqin Grasslands in Northeast China were assessed. This study aimed to investigate (1) how the abundances of soil bacteria changed across land-use types, (2) how the structure of the soil bacterial community was altered in each land-use type, and (3) how these variations were correlated with soil physical and chemical properties. Variations in the diversities and compositions of bacterial communities and the relative abundances of dominant taxa were detected in four distinct land-use systems, namely, natural meadow grassland, paddy field, upland field, and poplar plantation, through the high-throughput Illumina MiSeq sequencing technique. The results indicated that land-use changes primarily affected the soil physical and chemical properties and bacterial community structure. Soil properties, namely, organic matter, pH, total N, total P, available N and P, and microbial biomass C, N, and P, influenced the bacterial community structure. The dominant phyla and genera were almost the same among the land-use types, but their relative abundances were significantly different. The effects of land-use changes on the structure of soil bacterial communities were more quantitative than qualitative.

scholarly journals Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

SOIL ◽  
2016 ◽  
Vol 2 (3) ◽  
pp. 459-474 ◽  
Author(s):  
Michael P. Ricketts ◽  
Rachel S. Poretsky ◽  
Jeffrey M. Welker ◽  
Miquel A. Gonzalez-Meler
Keyword(s):  
Climate Change ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Chemical Properties ◽  
Winter Precipitation ◽  
Snow Accumulation ◽  
Soil Microbial ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Abstract. Soil microbial communities play a central role in the cycling of carbon (C) in Arctic tundra ecosystems, which contain a large portion of the global C pool. Climate change predictions for Arctic regions include increased temperature and precipitation (i.e. more snow), resulting in increased winter soil insulation, increased soil temperature and moisture, and shifting plant community composition. We utilized an 18-year snow fence study site designed to examine the effects of increased winter precipitation on Arctic tundra soil bacterial communities within the context of expected ecosystem response to climate change. Soil was collected from three pre-established treatment zones representing varying degrees of snow accumulation, where deep snow  ∼ 100 % and intermediate snow  ∼ 50 % increased snowpack relative to the control, and low snow ∼ 25 % decreased snowpack relative to the control. Soil physical properties (temperature, moisture, active layer thaw depth) were measured, and samples were analysed for C concentration, nitrogen (N) concentration, and pH. Soil microbial community DNA was extracted and the 16S rRNA gene was sequenced to reveal phylogenetic community differences between samples and determine how soil bacterial communities might respond (structurally and functionally) to changes in winter precipitation and soil chemistry. We analysed relative abundance changes of the six most abundant phyla (ranging from 82 to 96 % of total detected phyla per sample) and found four (Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi) responded to deepened snow. All six phyla correlated with at least one of the soil chemical properties (% C, % N, C : N, pH); however, a single predictor was not identified, suggesting that each bacterial phylum responds differently to soil characteristics. Overall, bacterial community structure (beta diversity) was found to be associated with snow accumulation treatment and all soil chemical properties. Bacterial functional potential was inferred using ancestral state reconstruction to approximate functional gene abundance, revealing a decreased abundance of genes required for soil organic matter (SOM) decomposition in the organic layers of the deep snow accumulation zones. These results suggest that predicted climate change scenarios may result in altered soil bacterial community structure and function, and indicate a reduction in decomposition potential, alleviated temperature limitations on extracellular enzymatic efficiency, or both. The fate of stored C in Arctic soils ultimately depends on the balance between these mechanisms.

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