Functional Diversity of Bacterioplankton in Three North Florida Freshwater Lakes over an Annual Cycle

The phylogenetic diversity of freshwater bacterioplankton is widely known; however, there is minimal information on the functional diversity of the bacterial communities in these systems. Understanding the functional diversity of freshwater bacterial communities is important because heterotrophic bacteria can be impacted by anthropogenic perturbation, which in turn can alter biogeochemical cycling. The objective of this study was to use Biolog EcoPlates to acquire spatial and temporal community-level physiological profiles (CLPPs) for three freshwater lakes of different trophic levels and to assess the phylogenetic affiliation of the bacteria responsible for utilizing the various carbon guilds within them by denaturing gradient gel electrophoresis (DGGE). CLPP results showed that bacterial communities utilized the carbon guilds similarly between sites within the three lakes. However, when the metabolic profile of each lake was compared, Lake Bradford and Moore Lake were more similar to one another than to Lake Munson, the eutrophic lake. Additionally, although the bacteria that utilized the five carbon guilds included representatives from the classes α-, β-, γ-Proteobacteria, Flavobacteria and Sphingobacteria, Lake Munson had the largest number of Flavobacteria and γ-Proteobacteria in comparison to Moore Lake and Lake Bradford. Overall, Biolog analysis was useful in identifying differences in the functional diversity of bacterial communities between lakes of different trophic statuses and can be used as a tool to assess ecosystem health.     

Nutrient effects on the genetic and functional diversity of aquatic bacterial communities

Studies on the effects of biodiversity on ecosystem functioning have generally revealed a positive asymptotic relationship between biodiversity and single functions, suggesting species redundancy with respect to these functions. However, most research was performed on specific processes and did not consider ecosystem 'multifunctionality'. There is also little information on the relationship between genetic and functional diversity. To analyze this relationship, we performed a microcosm experiment on a complex lake assemblage of decomposers, in the presence of the green alga Scenedesmus obliquus, which acted as carbon source for decomposers. By manipulating nutrient enrichment and the N : P input ratio, we observed that the structures of particle-associated and free bacterial assemblages were highly predictable in response to stoichiometric constraints. For a given treatment, the taxonomic compositions of free and particle-associated bacterial communities appeared close to each other only when phosphorus was not depleted. A coinertia analysis revealed a clear coupling between the genetic diversity of the microbial community, assessed using PCR-denatured gradient gel electrophoresis, and its potential functional diversity, studied with Biolog Ecoplates. This suggests that an ecologically relevant fraction of bacterial communities is characterized by lower level of redundancy than frequently thought, highlighting the necessity of exploring further the role of biodiversity in multifunctionality within ecosystems.     

Soil and cultivar type shape the bacterial community in the potato rhizosphere

The rhizospheres of five different potato cultivars (including a genetically modified cultivar) obtained from a loamy sand soil and two from a sandy peat soil, next to corresponding bulk soils, were studied with respect to their community structures and potential function. For the former analyses, we performed bacterial 16S ribosomal RNA gene-based PCR denaturing gradient gel electrophoresis (PCR-DGGE) on the basis of soil DNA; for the latter, we extracted microbial communities and subjected these to analyses in phenotype arrays (PM1, PM2, and PM4, Biolog), with a focus on the use of different carbon, sulfur and phosphorus sources. In addition, we performed bacterial PCR-DGGE on selected wells to assess the structures of these substrate-responsive communities. Effects of soil type, the rhizosphere, and cultivar on the microbial community structures were clearly observed. Soil type was the most determinative parameter shaping the functional communities, whereas the rhizosphere and cultivar type also exerted an influence. However, no genetically modified plant effect was observed. The effects were imminent based on general community analysis and also single-compound analysis. Utilization of some of the carbon and sulfur sources was specific per cultivar, and different microbial communities were found as defined by cultivar. Thus, both soil and cultivar type shaped the potato root-associated bacterial communities that were responsive to some of the substrates in phenotype arrays.     

Effect of Soybean Monoculture on the Bacterial Communities Associated with Cysts of Heterodera glycines

The soybean cyst nematode (SCN), Heterodera glycines, can cause significant reductions in soybean yield and quality in many parts of the world. Natural biological control may play an important role in regulating SCN population. In this study the bacterial communities associated with SCN cysts obtained from fields under different lengths of soybean monoculture were explored. Soil samples were collected in 2010 and 2011 from six fields that had been used for soybean monoculture for 2 to 41 yr. SCN population densities were determined and bacterial communities from SCN cysts were investigated by Biolog and PCR-DGGE methods. SCN population densities initially increased in the first 5 yr of soybean monoculture but then declined steeply as years of soybean monoculture increased. Catabolic diversity of bacterial communities associated with cysts tended to decline as number of years of monoculture increased. Some specific PCR-DGGE bands, mainly representing Streptomyces and Rhizobium, were obtained from the cysts collected from the long-term monoculture fields. Principal component analysis of Biolog and PCR-DGGE data revealed that bacterial communities associated with cysts could be divided into two groups: those from cysts obtained from shorter (< 8 yr) vs. longer (> 8 yr) monoculture. This research demonstrates that the composition of the bacterial communities obtained from SCN cysts changes with length of soybean monoculture; the suppressive impact of these bacterial communities to SCN is yet to be determined.     

Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints

Considering the major involvement of gut microflora in the digestive function of various macro-organisms, bacterial communities inhabiting fish guts may be the main actors of organic matter degradation by fish. Nevertheless, the extent and the sources of variability in the degradation potential of gut bacterial communities are largely overlooked. Using Biolog Ecoplate? and denaturing gradient gel electrophoresis (DGGE), we explored functional (i.e. the ability to degrade organic matter) and genetic (i.e. identification of DGGE banding patterns) diversity of fish gut bacterial communities, respectively. Gut bacterial communities were extracted from fish species characterized by different diets sampled along a salinity gradient in the Patos-Mirim lagoons complex (Brazil). We found that functional diversity was surprisingly unrelated to genetic diversity of gut bacterial communities. Functional diversity was not affected by the sampling site but by fish species and diet, whereas genetic diversity was significantly influenced by all three factors. Overall, the functional diversity was consistently high across fish individuals and species, suggesting a wide functional niche breadth and a high potential of organic matter degradation. We conclude that fish gut bacterial communities may strongly contribute to nutrient cycling regardless of their genetic diversity and environment.     

Effects of fertilization on bacterial community structure and function in a black soil of Dehui region estimated by Biolog and PCR-DGGE methods

Soil microbial community structure and function are commonly used as indicators for soil quality and fertility. In this paper, the bacterial community structure and function in a black soil of Dehui region influenced by fertilization were investigated by Biolog and PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) methods. Biolog examination showed that substrate richness and catabolic diversities of bacterial communities were the highest in the treatment of farm yard manure, and the lowest in the chemical fertilizer treatment. DGGE fingerprint showed that the majority of bands were similar among all treatments, suggesting that microbial communities with those bands were stable, and not influenced by fertilization. In general, chemical fertilizer decreased the diversity of soil bacterial communities. The PCA (principal component analysis) plots of Biolog and DGGE revealed that the structure and function of bacterial communities were similar in the non-fertilized control and the treatment of farm yard manure alone, which inferred that the application of farm yard manure increased the quantity of soil microbes but had less effect on the changes of community structure. The catabolic function was similar, but the composition structure differed between the treatments of chemical fertilizer alone and combined application of farm yard manure with chemical fertilizer. These results suggest that the use of chemical fertilizer mainly decreased the catabolic activity of the fast growth bacteria or eutrophic bacteria.     

Clustering of ant communities and indicator species analysis using self-organizing maps

To understand the complex relationships that exist between ant assemblages and their habitats, we performed a self-organizing map (SOM) analysis to clarify the interactions among ant diversity, spatial distribution, and land use types in Fukuoka City, Japan. A total of 52 species from 12 study sites with nine land use types were collected from 1998 to 2012. A SOM was used to classify the collected data into three clusters based on the similarities between the ant communities. Consequently, each cluster reflected both the species composition and habitat characteristics in the study area. A detrended correspondence analysis (DCA) corroborated these findings, but removal of unique and duplicate species from the dataset in order to avoid sampling errors had a marked effect on the results; specifically, the clusters produced by DCA before and after the exclusion of specific data points were very different, while the clusters produced by the SOM were consistent. In addition, while the indicator value associated with SOMs clearly illustrated the importance of individual species in each cluster, the DCA scatterplot generated for species was not clear. The results suggested that SOM analysis was better suited for understanding the relationships between ant communities and species and habitat characteristics.     

Microbial structural diversity estimated by dilution-extinction of phenotypic traits and T-RFLP analysis along a land-use intensification gradient

The present work tested whether the relationship between functional traits and inoculum density reflected structural diversity in bacterial communities from a land-use intensification gradient applying a mathematical model. Terminal restriction fragment length polymorphism (T-RFLP) analysis was also performed to provide an independent assessment of species richness. Successive 10-fold dilutions of a soil suspension were inoculated onto Biolog GN(R) microplates. Soil bacterial density was determined by total cell and plate counts. The relationship between phenotypic traits and inoculum density fit the model, allowing the estimation of maximal phenotypic potential (Rmax) and inoculum density (KI) at which Rmax will be half-reduced. Though Rmax decreased with time elapsed since clearing of native vegetation, KI remained high in two of the disturbed sites. The genetic pool of bacterial community did not experience a significant reduction, but the active fraction responding in the Biolog assay was adversely affected, suggesting a reduction in the functional potential.     

Functional diversity and community structure of microorganisms in uncontaminated and creosote-contaminated soils as determined by sole-carbon-source-utilization

Functional diversities of microorganisms from uncontaminated and creosote-contaminated soils were assessed using sole-carbon source-utilization patterns. The microorganisms were extracted from soil samples and inoculated into Gram-negative Biolog plates incubated at 23°C. Measurement of Shannon diversity, richness, and evenness indices, principal component analysis (PCA), and colour development rank (CDR) plots were based upon substrate utilization. Calculations incorporated data from both the 95 regular Gram-negative Biolog microplate wells and a selection of 23 carbon substrates that are included on Biolog Ecoplates. There did not appear to be significant differences in Shannon diversity and richness indices, PCA, or CDR plots between aminated and creosote-contaminated soils. Significant differences in Shannon diversity and evenness indices that were apparent with the use of the 23 ecologically relevant microplate wells were mostly absent based on calculations that incorporated the regular 95 Gram-negative Biolog microplate wells. Resolution of microbial communities by PCA, however, appeared to be reduced by the use of the 23 Biolog microplate wells compared to the regular 95 carbon sources.     

生物肥与甲壳素和恶霉灵配施对香蕉枯萎病的防治效果

通过盆栽试验研究了生物肥与甲壳素和恶霉灵配施防治香蕉枯萎病效果,试验结果表明,生物肥与恶霉灵配施(H+F)处理香蕉枯萎病病情指数最高,生物肥与甲壳素配施(C+F)处理病情指数最低。单独生物肥处理防病效果为32.8%,生物肥与甲壳素配施处理为42.5%,而生物肥与恶霉灵配施加重了香蕉枯萎病病情。Biolog Eco微平板研究发现,AWCD(平均每孔颜色变化率)和Shannon等4个多样性指数变化趋势与防病效果相反:防病效果好的处理,土壤细菌功能多样性指数反而低,经检测发现病原真菌(Fusarium oxysporum f. sp. cubense)可利用Biolog Eco微平板上碳源底物并发生颜色变化,干扰测定结果。T-RFLP分析土壤细菌DNA多样性,对照(灭菌生物肥)土壤中TRFs末端限制性片段最少,生物肥与甲壳素配施处理最多。与网上数据库比较,生物肥与甲壳素配施增加了土壤中芽胞杆菌种类,与恶霉灵配施降低了芽胞杆菌种类。分析发现,T-RFLP和Biolog的主成份分析载荷图具有较高一致性。因此,生物肥与生物农药甲壳素配施,从生态角度控制土传病害,优势互补,提高了土壤细菌多样性,改善了土壤细菌群落结构,有利于提高防病效果。     

Comparison of Parental and Transgenic Alfalfa Rhizosphere Bacterial Communities Using Biolog GN Metabolic Fingerprinting and Enterobacterial Repetitive Intergenic Consensus Sequence-PCR (ERIC-PCR)

Abstract Rhizosphere bacterial communities of parental and two transgenic alfalfa (Medicago sativa L.) of isogenic background were compared based on metabolic fingerprinting using Biolog GN microplates and DNA fingerprinting of bacterial communities present in Biolog GN substrate wells by enterobacterial repetitive intergenic consensus sequence-PCR (ERIC-PCR). The two transgenic alfalfa expressed either bacterial (Bacillus licheniformis) genes for alpha-amylase or fungal (Phanerochaete chrysosporium) genes for Mn-dependent lignin peroxidase (Austin S, Bingham ET, Matthews DE, Shahan MN, Will J, Burgess RR, Euphytica 85:381–393). Cluster analysis and principal components analysis (PCA) of the Biolog GN metabolic fingerprints indicated consistent differences in substrate utilization between the parental and lignin peroxidase transgenic alfalfa rhizosphere bacterial communities. Cluster analysis of ERIC-PCR fingerprints of the bacterial communities in Biolog GN substrate wells revealed consistent differences in the types of bacteria (substrate-specific populations) enriched from the rhizospheres of each alfalfa genotype. Comparison of ERIC-PCR fingerprints of bacterial strains obtained from substrate wells to substrate community ERIC-PCR fingerprints suggested that a limited number of populations were responsible for substrate oxidation in these wells. Results of this study suggest that transgenic plant genotype may affect rhizosphere microorganisms and that the methodology used in this study may prove a useful approach for the comparison of bacterial communities. Received: 1 June 1998; Accepted: 20 October 1998     

Evidence of functional and structural changes in the microbial community beneath a succulent invasive plant in coastal dunes

海岸沙地肉质入侵植物对微生物群落功能与结构变化的影响 海岸沙地提供了诸多宝贵的生态系统服务，例如耕地保护、水分供应和生物多样性保护，因此海岸沙地代表了重要的栖息地保护区。因为海岸沙地环境恶劣、水资源匮乏、养分贫瘠，所以土壤微生物群落对维持植物多样性至关重要。就海岸沙地的生态系统保护而言，外来入侵植物是主要威胁。本文探讨了沿海地区入侵植物食用日中花(Carpobrotus edulis)对细菌群落功能及结构的各种影响。沙地中土壤有机质含量低，微生物活性有限，所以沙地是一种颇具挑战性的底物。因此，在评估食用日中花对生态系统的影响之前需要对细菌提取进行优化，并开展功能评估。本文首先从群落水平生理特征(CLPP)的角度，比较了采用不同土壤储量、样品量、提取液等12种提取方法对沙地群落功能活性的影响，然后又探讨了食用日中花入侵的沙地菌落功能(利用Biolog Ecoplates)与结构变化(利用PCR-DGGE)。血细胞计数发现盐溶液持续增殖了细菌细胞(P ≤ 0.001)。主成分分析(PCA)结果显示，在有限时间框架(0–24 h)内，碳底物消耗没有显著变化。通过对比天然区与非天然区(种间)及天然区(种内)之间食用日中花入侵后的变化，发现了一种与众不同的碳底物利用模式，食用日中花入侵对群落功能的影响因地而异，而与之相辅相成的是，PCR-DGGE结果表明原沙地的菌落结构不同于食用日中花入侵后沙地的菌落结构。     

Microbial Communities Involved in Fe Reduction and Mobility During Soil Organic Matter (SOM) Mineralization in Two Contrasted Paddy Soils

Lowland rice fields of West Africa (Ivory Coast) and South Asia (Thailand) are affected by ferrous toxicity or salinity, respectively, and their soil waters contain large amounts of ferrous iron, depending on reducing irrigation condition and suggesting occurrence of bacterial reducing processes. To determine the involvement, dynamic and activities of bacterial communities in Fe(III) reduction and mobilization during anaerobic degradation and mineralization of soil organic matter (SOM), different experiments and analyses have been performed. Results demonstrated that the utilization of SOM as sole carbon, nutrient and energy sources favored the presence of large bacterial communities: facultative anaerobic and anaerobic bacteria, Fe(III)-reducing bacteria (FeRB) (fermentative and Fe respiring), sulfate reducing bacteria (SRB) which are involved in carbon, nitrogen, iron and sulfur cycling. The larger functional diversity is observed in the Ivory Coast paddy soils containing larger amounts of organic matter and sulfur compounds. These communities contained complementary populations (chemoorganotrophic, chemolitotrophic, aerobic, facultative anaerobic and anaerobic) that can be active at different steps of iron solubilization with simultaneous organic matter mineralization. Our results indicate that the pH controlled by bacterial activity, the nature much more than the content of organic matter, and consequently the structure and activity of bacterial communities influence significantly the availability and dynamic of iron in paddy fields which affect the soil quality.     

Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities

The cold-adapted bacterial communities in petroleum hydrocarbon-contaminated and non-impacted soils from two northern Canadian environments, Kuujjuaq, Que., and Alert, Nunavut, were analyzed using a polyphasic approach. Denaturing gradient gel electrophoresis (DGGE) separation of 16S rDNA PCR fragments from soil total community DNA revealed a high level of bacterial diversity, as estimated by the total number of bands visualized. Dendrogram analysis clustered the sample sites on the basis of geographical location. Comparison of the overall microbial molecular diversity suggested that in the Kuujjuaq sites, contamination negatively impacted diversity whereas in the Alert samples, diversity was maintained or increased as compared to uncontaminated controls. Extraction and sequencing analysis of selected 16S rDNA bands demonstrated a range of similarity of 86-100% to reference organisms, with 63.6% of the bands representing high G+C Gram-positive organisms in the order Actinomycetales and 36.4% in the class Proteobacteria. Community level physiological profiles generated using Biolog GN plates were analyzed by cluster analysis. Based on substrate oxidation rates, the samples clustered into groups similar to those of the DGGE dendrograms, i.e. separation based upon geographic origin. The coinciding results reached using culture-independent and -dependent analyses reinforces the conclusion that geographical origin of the samples, rather than petroleum contamination level, was more important in determining species diversity within these cold-adapted bacterial communities.     

Microcosm-based analyses of Scots pine seedling growth, ectomycorrhizal fungal community structure and bacterial carbon utilization profiles in boreal forest humus and underlying illuvial mineral horizons

We report on the identity of indigenous mycorrhiza forming fungi and rhizosphere/mycorrhizosphere bacterial community carbon source utilization profiles of Scots pine (Pinus sylvestris L.) seedlings grown in boreal forest humus (O) or illuvial (B) mineral horizon containing microcosm growth systems. Based on rDNA (ITS)-RFLP analyses, a total of 10 fungal RFLP taxa were identified from pre-morphotyped mycorrhizas on 7-month-old seedling roots. Hierarchical cluster analysis, including corresponding RFLPs of known fungal species, confirmed root colonization by eight mycorrhizal species. In the O horizon, roots were colonized by e.g. Suillus bovinus, Suillus variegatus, Cenococcum geophilum, Piloderma croceum, Thelephora terrestris and Russula vinicolor. Mycobiont diversity in the mineral B horizon was lower but included Piceirhiza bicolorata and both Suillus species which produced extensive extramatrical mycelium. In comparison to non-colonized soils, rhizosphere and mycorrhizosphere compartments supported significantly higher numbers of bacteria (mean range 10(8)-10(11) cells g(-1) fresh weight (fw)). Specific rhizosphere/mycorrhizosphere 'niche'-linked bacterial communities were detected following multivariate analyses (PCA and CA) of bacterial carbon utilization profiles (Biolog(R) GN microplate). Distinct preferences for amino and carboxylic acids were identified in mineral B horizon rhizospheres whereas a wider range of carbon sources were utilized in the fungal-dominated mycorrhizospheres irrespective of soil types.     

Species Diversity and Substrate Utilization Patterns of Thermophilic Bacterial Communities in Hot Aerobic Poultry and Cattle Manure Composts

This study investigated the species diversity and substrate utilization patterns of culturable thermophilic bacterial communities in hot aerobic poultry and cattle manure composts by coupling 16S rDNA analysis with Biolog data. Based on the phylogenetic relationships of 16S rDNA sequences, 34 thermophilic (grown at 60 degrees C) bacteria isolated during aerobic composting of poultry manure and cattle manure were classified as Bacillus licheniformis, B. atrophaeus, Geobacillus stearothermophilus, G. thermodenitrificans, Brevibacillus thermoruber, Ureibacillus terrenus, U. thermosphaericus, and Paenibacillus cookii. In this study, B. atrophaeus, Br. thermoruber, and P. cookii were recorded for the first time in hot compost. Physiological profiles of these bacteria, obtained from the Biolog Gram-positive (GP) microplate system, were subjected to principal component analysis (PCA). All isolates were categorized into eight different PCA groups based on their substrate utilization patterns. The bacterial community from poultry manure compost comprised more divergent species (21 isolates, seven species) and utilized more diverse substrates (eight PCA groups) than that from cattle manure compost (13 isolates, five species, and four PCA groups). Many thermophilic bacteria isolated in this study could use a variety of carboxylic acids. Isolate B110 (from poultry manure compost), which is 97.6% similar to U. terrenus in its 16S rDNA sequence, possesses particularly high activity in utilizing a broad spectrum of substrates. This isolate may have potential applications in industry.     

Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment

The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR) and C. floccosa-transformed DOR (CORDOR) on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.     

The impact of zinc and lead concentrations and seasonal variation on bacterial and actinobacterial community structure in a metallophytic grassland soil

The diversity and structure of bacterial and actinobacteral diversity and communities were determined in a metallophytic grassland soil from an upland site in northern England. The community profiles were subjected to multivariate analyses using correspondence and cluster analyses. The total bacterial community diversities and structures were not significantly affected by Pb and Zn concentration in the soil. However, the community structure did show changes between winter and summer samples. Raup and Crick analysis indicated that deterministic selection lead to winter profiles exhibiting significant similarity. The actinobacterial community was also unaffected by Pb and Zn concentration. However, seasonal changes were apparent as diversity were significantly lower in winter compared to summer profiles. Moreover, the community structure showed evidence of changes of structure based on the seasonal samples with winter samples showing significant similarity to each other.     

Comparison of API 20NE and Biolog GN identification systems assessed by techniques of multivariate analyses.

The increasing use of commercial multitest systems for identification of environmental bacteria creates the problem of how to compare the identification results obtained from different systems. The limited use of species designations in such comparisons is caused by low usage of environmental bacteria in the development of commercial identification schemes. Two multivariate statistical methods, the Mantel's test and the co-inertia analysis, were applied to analyze data derived from the Biolog GN and the API 20NE systems of identification for 50 environmental bacterial strains. We found these two methods to be useful for revealing the relationship between the two sets of numerical taxonomic traits. Both of these methods showed that the distances according to the Biolog GN results between the studied strains were related to those derived from the API 20NE results, despite the differences in the test sets of the two systems. In addition, the co-inertia analysis allowed us to visualise the relationships between classifications of strains derived from the two identification systems and, simultaneously, to estimate the contribution of particular tests to the differentiation of bacterial strains.