Substrate-induced changes in microbial community-level physiological profiles and their application to discriminate soil microbial communities

The addition of simple substrates could affect the microbial respiration in soils. This substrate-induced respiration is widely used to estimate the soil microbial biomass, but little attention has been paid to its influence on the changes of community-level physiological profiles. In this study, the process of microbial communities responding to the added substrate using sole-carbon-source utilization （BIOLOG） was investigated. BIOLOG is biased toward fast-growing bacteria; this advantage was taken to detect the prompt response of the active microbial communities to the added substrate. Four soil samples from agricultural fields adjacent to heavy metal mines were amended with L-arginine, citric acid, or D-glucose. Substrate amendments could, generally, not only increase the metabolic activity of the microbial communities, but also change the metabolic diverse patterns compared with no-substrate control. By tracking the process, it was found that the variance between substrate-induced treatment and control fluctuated greatly during the incubation course, and the influences of these three substrates were different. In addition, the application of these induced changes to discriminate soil microbial communities was tested. The distance among all samples was greatly increased, which further showed the functional variance among microbial communities in soils. This can be very useful in the discrimination of microbial communities even with high similarity.

Soil Microbial Community-Level Physiological Profiling as Related to Carbon and Nitrogen Availability Under Different Land Uses

The goal of this work was to assess soil microbial respiration, determined by the assay of community-level physiological profiling in an oxygen-sensitive microplate （O2-CLPP）, in response to endogenous C and several individual C substrates in the soils with different organic C contents （as a function of soil type and management practice）. We also used the O2-CLPP to determine the respiratory response of these soils to endogenous C and amended C substrates with N addition. A respiratory quotient （RQ） was calculated based on the ratio of the response to endogenous soil C vs. each C-only substrate, and was related to total organic carbon （TOC）. For assessing N availability for microbial activity, the effect of N supplementation on soil respiration, expressed as Nr^tio, was calculated based on the response of several substrates to N addition relative to the response without N. Soils clustered in 4 groups after a principal component analysis （PCA）, based on TOC and their respiratory responses to substrates and endogenous C. These groups reflected differences among soils in their geographic origin, land use and C content. Calculated RQ values were significantly lower in natural forest soils than in managed soils for most C-only substrates. TOC was negatively correlated with RQ （r = -0.65）, indicating that the soils with higher organic matter content increased respiratory efficiency. The N addition in the assay in the absence of C amendment （i. e., only endogenous soil C present） had no effect on microbial respiration in any soil, indicating that these soils were not intrinsically N-limited, but substrate-dependent variation in Nr^tio within soil groups was observed.

Degradation of chlorpyrifos in laboratory soil and its impact on soil microbial functional diversity

Degradation of chlorpyrifos at different concentrations in soil and its impact on soil microbial functional diversity were investigated under laboratory condition. The degradation half-live of chlorpyrifos at levels of 4, 8, and 12 mg/kg in soil were calculated to be 14.3, 16.7, and 18.0 d, respectively. The Biolog study showed that the average well color development （AWCD） in soils was significantly （P 〈 0.05） inhibited by chlorpyrifos within the first two weeks and thereafter recovered to a similar level as the control. A similar variation in the diversity indices （Simpson index lID and McIntosh index U） was observed, but no significant difference among the values of the Shannon-Wiener index H＇ was found in chlorpyrifos-treated soils. With an increasing chlorpyrifos concentration, the half-life of chlorpyrifos was significantly （P ≤ 0.05） extended and its inhibitory effect on soil microorganisms was aggravated. It is concluded that chlorpyrifos residues in soil had a temporary or short-term inhibitory effect on soil microbial functional diversity.

Effect of Different Vegetation Types on the Rhizosphere Soil Microbial Community Structure in the Loess Plateau of China

The Loess Plateau in China is one of the most eroded areas in the world. Accordingly, vegetation restoration has been implemented in this area over the past two decades to remedy the soil degradation problem. Understanding the microbial community structure is essential for the sustainability of ecosystems and for the reclamation of degraded arable land. This study aimed to determine the effect of different vegetation types on microbial processes and community structure in rhizosphere soils in the Loess Plateau. The six vegetation types were as follows：two natural grassland （Artemisia capillaries and Heteropappus altaicus）, two artificial grassland （Astragalus adsurgens and Panicum virgatum）, and two artificial shrubland （Caragana korshinskii and Hippophae rhamnoides） species. The microbial community structure and functional diversity were examined by analyzing the phospholipid fatty acids （PLFAs） and community-level physiological profiles. The results showed that rhizosphere soil sampled from the H. altaicus and A. capillaries plots had the highest values of microbial biomass C, average well color development of carbon resources, Gram-negative （G-） bacterial PLFA, bacterial PLFA, total PLFA, Shannon richness, and Shannon evenness, as well as the lowest metabolic quotient. Soil sampled from the H. rhamnoides plots had the highest metabolic quotient and Gram-positive （G＋） bacterial PLFA, and soil sampled from the A. adsurgens and A. capillaries plots had the highest fungal PLFA and fungal：bacterial PLFA ratio. Correlation analysis indicated a signiifcant positive relationship among the microbial biomass C, G- bacterial PLFA, bacterial PLFA, and total PLFA. In conclusion, plant species under arid climatic conditions signiifcantly affected the microbial community structure in rhizosphere soil. Among the studied plants, natural grassland species generated the most favorable microbial conditions.

Nitrogen availability regulates deep soil priming effect by changing microbial metabolic efficiency in a subtropical forest

In terrestrial ecosystems,deep soils(below 30 cm)are major organic carbon(C)pools.The labile carbon input could alter soil organic carbon(SOC)mineralization,resulting in priming effect(PE),which could be modified by nitrogen(N)availability,however,the underlying mechanism is unclear for deep soils,which complicates the prediction of deep soil C cycling in response to N deposition.A series of N applications with ^(13)C labeled glucose was set to investigate the effect of labile C and N on deep SOC mineralization.Microbial biomass,functional community,metabolic efficiency and enzyme activities were examined for their effects on SOC mineralization and PE.During incubation,glucose addition promoted SOC mineralization,resulting in positive PE.The magnitude of PE decreased significantly with increasing N.The N-regulated PE was not dependent on extracellular enzyme activities but was positively correlated with carbon use efficiency and negatively with metabolic quotient.Higher N levels resulted in higher microbial biomass and SOC-derived microbial biomass than lower N levels.These results suggest that the decline in the PE under high N availability was mainly controlled by higher microbial metabolic efficiency which allocated more C for growth.Structural equation modelling also revealed that microbial metabolic efficiency rather than enzyme activities was the main factor regulating the PE.The negative effect of additional N suggests that future N deposition could promote soil C sequestration.

Mutually Enhancing Community Detection and Sentiment Analysis on Twitter Networks

The burgeoning use of Web 2.0-powered social media in recent years has inspired numerous studies on the content and composition of online social networks (OSNs). Many methods of harvesting useful information from social networks’ immense amounts of user-generated data have been successfully applied to such real-world topics as politics and marketing, to name just a few. This study presents a novel twist on two popular techniques for studying OSNs: community detection and sentiment analysis. Using sentiment classification to enhance community detection and community partitions to permit more in-depth analysis of sentiment data, these two techniques are brought together to analyze four networks from the Twitter OSN. The Twitter networks used for this study are extracted from four accounts related to Microsoft Corporation, and together encompass more than 60,000 users and 2 million tweets collected over a period of 32 days. By combining community detection and sentiment analysis, modularity values were increased for the community partitions detected in three of the four networks studied. Furthermore, data collected during the community detection process enabled more granular, community-level sentiment analysis on a specific topic referenced by users in the dataset.

Metabolic diversity and seasonal variation of soil microbial communities in natural forested wetlands

This study explores the effects of vegetation and season on soil microorganisms and enzymatic activity of different wetlands in a temperate climate.Microbial carbon metabolism diversity was assessed using community-level physiological profiles(CLPP)with 31 different carbon substrates.CLPP indicated that significant interactions occur during carbon substrate metabolism of the microorganisms.Furthermore,the different types of vegetation present in the wetland ecosystem combined with the seasonal effects to influence microbial carbon metabolism and enzymatic activity.The most significant differences occurred to carbohydrates,carboxylic acids,and amino acids.The Mantel test confirmed positive correlations between soil enzymatic activities and microbial carbon metabolism.Soil microorganisms in Betula ovalifolia and Carex schmidtii wetlands used carbon substrates more efficiently in summer than those in other forested wetlands during other periods.Enzymatic activities also showed a similar trend as microbial carbon metabolism.The results demonstrate that microbial carbon metabolism patterns can be used as biological indicators in wetland ecological alterations due to vegetation type or to seasonal factors.

Straw addition increases enzyme activities and microbial carbon metabolism activities in bauxite residue

Recovery of microbial functions is one of the critical processes in the nutrient cycling of bauxite residue for improving revegetation.Straw is considered to be effective to increase microbial diversity and drive the development of the microbial community,but its effect on microbial carbon metabolism has not been illustrated.The present study evaluated the effects of phosphogypsum(PG),straw(SF)and phosphogypsum plus straw(PGSF)on physicochemical properties,enzyme activities,and microbial carbon metabolism activities in bauxite residue.After 180 days incubation,PG,SF and PGSF treatment significantly reduced the residue pH from 10.85 to 8.64,9.39 and 8.06,respectively.Compared to CK treatment,SF treatment significantly increased the content of total organic carbon(TOC)and organic carbon fractions(DOC,MBC,EOC,and POC).In addition,straw addition significantly increased glucosidase,cellulose,urease,and alkaline phosphatase by 7.2-9.1 times,5.8-7.1 times,11.1-12.5 times,and 1.1-2.2 times,respectively.The Biolog results showed that straw addition significantly increased microbial metabolic activity(AWCD)and diversity in bauxite residue.Redundancy analysis indicated total nitrogen(TN)and carbon fractions(POC,MBC and DOC)were the most important environmental factors affecting microbial metabolic activity and diversity in bauxite residue.These findings provided us with a biogeochemical perspective to reveal soil formation in bauxite residue and suggested that nutrient supplement and regulation of salinity-alkalinity benefit the establishment of microbial communities and functions in bauxite residue.

Facilitation by nurse plants contributes to vegetation recovery in human-disturbed desert ecosystems

Aims Facilitation by nurse plants is a common interaction in harsh environments and this positive plant-plant interaction may promote vegetation recovery in ecosystems affected by human activities.Determining the relevance of this process,however,requires assessing how nurse plants influence the establishment of other species,as well as the proportion of species in the regional species pool that would benefit from the presence of nurse plants in human-disturbed areas.Further,since vegetation recovery is a time-dependent process,the community-level consequences of facilitation are likely to vary among landscapes with different disturbance history.Thus,an integrative perspective of the relevance of nurse plants for vegetation recovery could be obtained by measuring their effects across different human-disturbed landscapes of the target region.This study focuses on these issues and uses a regional-scale approach to assess the community-level effects of a widespread nurse plant of American deserts,the creosotebush(Larrea tridentata).Methods This study was conducted in the southernmost portion of Chihuahuan Desert because most floodplain valleys of this region have been affected by human activities during the past centuries.For this study,we selected 10 floodplain valleys differing in their age(i.e.the time elapsed after human activities were ceased).At each landscape,we measured the cover of creosotebushes and the proportion of plant species positively associated with them,as well as the density of seeds in the soil beneath creosotebush canopies.All these data were regressed against the age of the landscapes.Further,to assess whether positive association patterns were due to facilitation or other processes,we conducted field experiments and measured the ecophysiological performance of plant species established beneath and outside creosotebush canopies.Important Findings Most plant species from the target region were positively associated to creosotebushes,and our field experiments and ecophysiological measures indicated that these distribution patterns can be attributed to facilitative interactions.In most landscapes,the density of seeds was higher beneath creosotebushes than in the surrounding habitats,suggesting that these shrubs may also act as seed traps.The community-level effects of creosotebushes increased with landscape age and creosotebush cover,indicating that magnitude of these effects depends on the disturbance history of each site.These results highlight the relevance of performing large-scale assessments for identifying the consequences of facilitation on vegetation recovery across space and time.We then propose that this kind of large-scale approach should be taken into account in the development of conservation programs aimed at the recovery and preservation of plant biodiversity in harsh environments.

Effects of Maize Residue Quality and Soil Water Content on Soil Labile Organic Carbon Fractions and Microbial Properties

Investigating the effects of residue chemical composition on soil labile organic carbon （LOC） will improve our understanding of soil carbon sequestration. The effects of maize residue chemical composition and soil water content on soil LOC fractions and microbial properties were investigated in a laboratory incubation experiment. Maize shoot and root residues were incorporated into soil at 40% and 70% field capacity. The soils were incubated at 20 ℃ for 150 d and destructive sampling was conducted after 15, 75, and 150 d. Respiration, dissolved organic carbon （DOC）, hot-water extractable organic carbon （HEOC）, and microbial biomass carbon （MBC） were recorded, along with cellulase and β-glucosidase activities and community-level physiological profiles. The results showed that the cumulative respiration was lower in root-amended soils than in shoot-amended soils, indicating that root amendment may be beneficial to C retention in soil. No significant differences in the contents of DOG, HEOC and MBC, enzyme activities, and microbial functional diversity were observed between shoot- and root-amended soils. The high soil water content treatment significantly increased the cumulative respiration, DOC and HEOC contents, and enzyme activities compared to the low soil water content treatment. However, the soil water content treatments had little influence on the MBC content and microbial functional diversity. There were significantly positive correlations between LOC fractions and soil microbial properties. These results indicated that the chemical composition of maize residues had little influence on the DOC, HEOC, and MBC contents, enzyme activities, and microbial functional diversity, while soil water content could significantly influence DOC and HEOC contents and enzyme activities.

Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities

Background:Synthetic microbial communities,with different strains brought together by balancing their nutrition and promoting their interactions,demonstrate great advantages for exploring complex performance of communities and for further biotechnology applications.The potential of such microbial communities has not been explored,due to our limited knowledge of the extremely complex microbial interactions that are involved in designing and controlling effective and stable communities.Results:Genome-scale metabolic models(GEM)have been demonstrated as an effective tool for predicting and guiding the investigation and design of microbial communities,since they can explicitly and efficiently predict the phenotype of organisms from their genotypic data and can be used to explore the molecular mechanisms of microbehabitats and microbe-microbe interactions.In this work,we reviewed two main categories of GEM-based approaches and three uses related to design of synthetic microbial communities:predicting multi-species interactions,exploring environmental impacts on microbial phenotypes,and optimizing community-level performance.Conclusions:Although at the infancy stage,GEM-based approaches exhibit an increasing scope of applications in designing synthetic microbial communities.Compared to other methods,especially the use of laboratory cultures,GEM-based approaches can greatly decrease the trial-and-error cost of various procedures for designing synthetic communities and improving their functionality,such as identifying community members,determining media composition,evaluating microbial interaction potential or selecting the best community configuration.Future efforts should be made to overcome the limitations of the approaches,ranging from quality control of GEM reconstructions to community-level modeling algorithms,so that more applications of GEMs in studying phenotypes of microbial communities can be expected.

Impact of Socioeconomic Status and Demographic Composition on Disaster Mortality: Community‑Level Analysis for the 2011 Tohoku Tsunami

On 11 March 2011, the Tohoku tsunami hit the northeastern region of Japan, causing massive damage to people and property. The tsunami was bigger than any other in Japan’s recorded history, but the damage varied by community. This research addressed the effects of socioeconomic status and demographic composition on mortality in the 2011 Tohoku tsunami using community-level data.These effects were estimated using regression analysis, taking into account a variety of potential contributing aspects at the community level, including strength of the tsunami,population characteristics, gender, age, education, household composition, evacuation methods, and occupation. It was found that the height of the tsunami and the shares of threegeneration households and employees in the manufacturing industry are all positively correlated with tsunami mortality.The impacts of these factors on mortality are particularly large for the older adults.