Method for obtaining microbial samples from concrete and its effects on microbial community structure

Summary Resource control over abundance, structure and functional diversity of soil microbial communities is a key determinant of soil processes and related ecosystem functioning. Copiotrophic organisms tend to be found in environments which are rich in nutrients, particularly carbon, in contrast to oligotrophs, which survive in much lower carbon concentrations. We hypothesized that microbial biomass, activity and community structure in nutrient‐poor soils of an Amazonian rain forest are limited by multiple elements in interaction. We tested this hypothesis with a fertilization experiment by adding C (as cellulose), N (as urea) and P (as phosphate) in all possible combinations to a total of 40 plots of an undisturbed tropical forest in French Guiana. After 2 years of fertilization, we measured a 47% higher biomass, a 21% increase in substrate‐induced respiration rate and a 5‐fold higher rate of decomposition of cellulose paper discs of soil microbial communities that grew in P‐fertilized plots compared to plots without P fertilization. These responses were amplified with a simultaneous C fertilization suggesting P and C colimitation of soil micro‐organisms at our study site. Moreover, P fertilization modified microbial community structure (PLFAs) to a more copiotrophic bacterial community indicated by a significant decrease in the Gram‐positive : Gram‐negative ratio. The Fungi : Bacteria ratio increased in N fertilized plots, suggesting that fungi are relatively more limited by N than bacteria. Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. In contrast, community level physiological profiles under P fertilization combined with either C or N fertilization or both differed strongly from all other treatments, indicating functionally different microbial communities. While P appears to be the most critical from the three major elements we manipulated, the strongest effects were observed in combination with either supplementary C or N addition in support of multiple element control on soil microbial functioning and community structure. We conclude that the soil microbial community in the studied tropical rain forest and the processes it drives is finely tuned by the relative availability in C, N and P. Any shifts in the relative abundance of these key elements may affect spatial and temporal heterogeneity in microbial community structure, their associated functions and the dynamics of C and nutrients in tropical ecosystems.

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments.

Microbial communities composed of bacteria, archaea and fungi play a pivotal role in driving the biogeochemical cycles in the marine ecosystem. Despite the vastness of the South Indian Ocean, only a few studies reported the simultaneous analysis of bacterial, archaeal and fungal diversity therein, particularly archaeal and fungal communities in deep-sea environments received less attention previously. In this study, microbial diversity, community composition and dynamics in microbial community structure in eight deep-sea sediment samples collected from different sites at varying depths of the South Indian Ocean were explored using Next-Generation Sequencing. In total, 21 bacterial phyla representing 541 OTUs were identified from the eight samples, where phylum Proteobacteria was found as the most abundant bacterial phylum in five out of eight samples. Firmicutes and Chloroflexi were the dominant phyla in the rest of the three samples. In the case of archaea, uncultured species belonging to the phyla Thaumarchaeota and Euryarchaeota were the abundant taxa in all the samples. Similarly, Ascomycota and Basidiomycota were the most abundant fungal phyla present therein. In all the eight samples studied here, about 10-58% and 19-26% OTUs in archaeal and fungal communities were mapped to unclassified taxa respectively, suggesting the lack of representation in databases. Co-occurrence network analysis further revealed that bacterial communities tend to be more dynamic than archaeal and fungal communities. This study provides interesting insights into the microbial diversity, community composition and dynamics in microbial community structure in the deep-sea sediments of the South Indian Ocean.

Predicting the distribution patterns of soil microbial communities requires consideration of more environmental drivers. The effects of soil micronutrients on composition of microbial communities are largely unknown despite micronutrients closely relating to soil fertility and plant communities. Here we used data from 228 agricultural fields to identify the importance of micronutrients (iron, zinc, copper and manganese) in shaping structure of soil microbial communities (bacteria, fungi and protist) along latitudinal gradient over 3400 km, across diverse edaphic conditions and climatic gradients. We found that micronutrients explained more variations in the structure of microbial communities than macronutrients in maize soils. Moreover, micronutrients, particularly iron and copper, explained a unique percentage of the variation in structure of microbial communities in maize soils even after controlling for climate, soil physicochemical properties and macronutrients, but these effects were stronger for fungi and protist than for bacteria. The ability of micronutrients to predict the structure of soil microbial communities declined greatly in paddy soils. Machine learning approach showed that the addition of micronutrients substantially increased the predictive power by 9–17% in predicting the structure of soil microbial communities with up to 69–78% accuracy. These results highlighted the considerable contributions of soil micronutrients to microbial community structure, and advocated that soil micronutrients should be considered when predicting the structure of microbial communities in a changing world.

Pinus bungeana is a native but endangered plant species in China, with high ornamental value and adaptability to drought and cold. The relationship between the soil community structure and endophytic microbes in the tissues of P. bungeana under different health statuses is poorly understood. In this study, the endophytic bacterial and fungal communities of P. bungeana under different health statuses were compared and analyzed in the Xiong'an New Area. Using high-throughput deep sequencing [16S and internal transcribed spacer (ITS) rRNA] techniques, the effect of the health status of P. bungeana on the microbial communities in bulk soil, rhizospheric soil, roots, stems, and leaves was determined in this study. We observed that the diversity of the bacterial and fungal communities of the aboveground parts (stems and leaves) of healthy P. bungeana plants was much higher than that of the unhealthy plants. However, the diversity of bacterial and fungal communities in the belowground parts (bulk soil, rhizospheric soil, and roots) showed almost no difference in microbial community richness, indicating that the possible cause of illness was transmitted in a “top-down” manner. Furthermore, there were significant differences in the microbial diversity and community structure in different ecological niches of P. bungeana (P < 0.01). Proteobacteria and Actinobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the predominant fungal phyla. Redundancy analysis (RDA) revealed that soil organic matter (SOM), total phosphorous (TP), total potassium (TK), total nitrogen (TN), water content (WC), power of hydrogen (pH), total carbon (TC), and the ratio of carbon to nitrogen (C/N) were significantly correlated with the composition of the microbial communities. Altogether, these results provide a scientific basis for further studies on the mechanism underlying the “aboveground–underground” microbial interactions in plantation forests, which can aid in promoting the healthy and sustainable development of the Millennium Xiulin forest in the Xiong'an New Area.

Traceability between microbial community and environmental microbial Community in Maotai-flavor Daqu.

PurposeWe determined the microbial community diversity and structure in soil samples under different amounts of biochar added. Meanwhile, we also researched the relationships between soil microbial and soil physicochemical properties.MethodIn this study, a field experiment was set up, with a total of three experimental treatments: no biochar application, 10 t/m3 biochar application, and 20 t/m3 application. High-throughput sequencing technologies were used for soil samples of different treatment groups to understand soil microbial diversity and community structure.ResultsWe found that the soil physicochemical properties after biochar addition were better than those without biochar addition, and the alpha diversity was higher in biochar addition level of 20 t/m3 than other processing groups. Proteobacteria, Cyanobacteria, and Actinobacteria were the dominant phyla of this study. The dominant genera were Skermanella, Nostoc, Frankia, and Unclassified-p-protecbacteria. At the gate level, Actinobacteria had significant differences among the three groups with different addition amounts. The microbial community structure was mainly influenced by soil porosity, soil moisture content, nitrogen fertilizer, and potassium fertilizer other than soil phosphate fertilizer and organic matter.ConclusionsThe results suggested that changes under different amounts of biochar added generate changes in soil physicochemical properties and control the soil composition of microbial communities. This provides a new basis for soil improvement.

Changes in microbial community structure due to chronic trace element concentrations in different sizes of soil aggregates.

Abstract. Climate change can strongly alter soil microbial functioning via plant–microbe interactions, often with important consequences for ecosystem carbon and nutrient cycling. Given the high degree of intraspecific trait variability in plants, it has been hypothesized that genetic shifts within plant species yield a large potential to control the response of plant–microbe interactions to climate change. Here we examined if sea-level rise and plant genotype interact to affect soil microbial communities in an experimental coastal wetland system, using two known genotypes of the dominant salt-marsh grass Elymus athericus characterized by differences in their sensitivity to flooding stress – i.e., a tolerant genotype from low-marsh environments and an intolerant genotype from high-marsh environments. Plants were exposed to a large range of flooding frequencies in a factorial mesocosm experiment, and soil microbial activity parameters (exo-enzyme activity and litter breakdown) and microbial community structure were assessed. Plant genotype mediated the effect of flooding on soil microbial community structure and determined the presence of flooding effects on exo-enzyme activities and belowground litter breakdown. Larger variability in microbial community structure, enzyme activities, and litter breakdown in soils planted with the intolerant plant genotype supported our general hypothesis that effects of climate change on soil microbial activity and community structure can depend on plant intraspecific genetic variation. In conclusion, our data suggest that adaptive genetic variation in plants could suppress or facilitate the effects of sea-level rise on soil microbial communities. If this finding applies more generally to coastal wetlands, it yields important implications for our understanding of ecosystem–climate feedbacks in the coastal zone.

An assessment of the soil microbial status after 17 years of tillage and mineral P fertilization management

Fertilizer applications have important effects on soil microbial abundance and community structure. In this study, total soil microbial DNA and RNA were directly extracted from paddy soils of N0 (control treatment, no nitrogen fertilizer), NPK (balanced fertilization), NPK+LS (balanced fertilization with additional 3.0 t·hm-2 rice straw incorporation) and NPK+HS (balanced fertilization with additional 6.0 t·hm-2 rice straw incorporation) treatments in a long-term fertilization experiment of double rice cropping system in Changsha County, Hunan Province. Soil bacteria community structures were evaluated by analyzing the 16S rRNA gene fragments at DNA and cDNA levels with Terminal Restriction Fragment Length Polymorphism (T-RFLP) and quantitative PCR techniques. Balancing fertilization with chemical fertilizers and rice straw incorporation significantly changed the composition of bulk (DNA-based) and potentially active (mRNA-based) soil bacterial community as shown in T-RFLP profiles, and also reduced the bulk soil microbial diversity, but not the potentially active ones, as compared with the control treatment. The DNA-based abundance of 16S rRNA gene was on average 377 times as many as the m-RNA based population size. Compared to N0,balanced fertilization with rice straw incorporation (NPK+LS and NPK+HS) increased the bulk and active copy numbers of 16S rRNA gene, but not for balanced fertilization (NPK). The abundance and microbial community structure were not significantly different between the NPK+LS and NPK+HS treatments. Redundancy analysis (RDA) showed that soil ammonium was the key environmental factor determining the bulk and active soil microbial community structure among the treatments. In conclusion, the effect of fertilization on soil microbial abundance and community structure could be indicated at both DNA and cDNA levels; the cDNA information could better reflect the adaptability of bacterial community to the environmental stress.

Bacillus velezensis DQA21 is a functional strain used in the fermentation process of strong-aroma baijiu; however, its specific role in the process is still unclear. In this study, specific roles of B. velezensis DQA21 in the fermentation process were explored. Bioaugmentation of B. velezensis DQA21 increased the diversity and abundance of the bacterial community during the first 32 days of fermentation and significantly inhibited the diversity and richness of the fungal community during days 12 to 32. According to cluster analysis, changes in the microbial community structure were observed during fermentation, and the fermentation process could be divided into two stages: stage I, days 0-12; and stage II, days 12-45. Additionally, the microbial community structures during the two fermentation stages were significantly different. Co-occurrence analysis showed that bioaugmentation with Bacillus increased the correlation between microorganisms in jiupei and had a significant impact on the overall network structure of the microbial community. In addition, Bacillus significantly increased the production of flavor substances in jiupei, causing the total esters, total alcohols, and total acids contents to increase by 19.1%, 81.1%, and 25.9% respectively. The results suggested that bioaugmentation with B. velezensis DQA21 had a strong impact on the microbial community structure in strong-aroma baijiu, enhancing the volatile flavor components. Additionally, the work also provides a better understanding on the effect of augmentation on the microbial community in jiupei, which could help better regulation of solid-state fermentation in strong-aroma baijiu. © 2024 Society of Chemical Industry.

Knowledge of dynamic interactions between natural organic matter (NOM) and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C) fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM) to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soft X-ray absorption spectroscopy (sXAS). We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC) decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in subsurface groundwater.

Incorporation of 13C-labelled rice rhizodeposition into soil microbial communities under different fertilizer applications

Soil salinization is one main environmental factor restricting plant growth and agricultural productivity. However, phytoremediation is one of the important means to improve saline-alkali soil by planting halophytes or salt-tolerant plants. In order to study whether there are differences among soil microorganisms in different phytoremediation, the effects of four plants, including alfalfa (MX), oil sunflower (YK), maize (YM) and ryegrass (HMC) on soil physicochemical properties, enzyme activity and microbial community diversity and composition were investigated in this study and the relationships between microbial community structure and soil physicochemical properties, enzyme activity were analyzed. The results showed that all plants treatments significantly decreased pH, TS (total saltinity) and BD (bulk density), while increased OM (organic matter), TN (total nitrogen), AN (available nitrogen), TP (total phosphorus), AP (available phosphorus), TK (total potassium) and TPOR (total porosity), and the number of nitrite bacteria reduced by planting at the same time. Except for YM, other treatments significantly increased the number of nitrifying and denitrifying bacteria compared with CK, while only YK increased that of fungi. Additionally, all plants increased the activity of nitrite reductase and decreased that of urease. More interestingly, plants treatments shifted microbial community compositions, and only YM significantly decreased the bacterial diversity and increased the fungal diversity. Redundancy analysis suggested that TK, pH, BD, TS, AN, OM and nitrite reductase, lignin peroxidase were the key environmental factors that shaped the bacterial community structure, while that of fungi was mainly driven by OM, nitrite reductase, urease and lignin peroxidase. The results indicated that MX and YM are the best choice for remediation of saline-alkali soil. These data can provide certain theoretical basis for the further restoration of saline-alkali land. HIGHLIGHTS The effects of different phytoremediation on microbial diversity and community structure were different. Phytoremediation can significantly decreased pH, TS and BD, while increased OM, TN, AN, TP, AP, TK and TPOR in saline-alkali soil. All plants increased the activity of nitrite reductase and decreased the activity of urease.