Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere. This revised version was published online in August 2006 with corrections to the Cover Date.     

Diversity of microbial communities colonizing the walls of a Karstic cave in Slovenia

Karstic cave systems in Slovenia receive substantial amounts of organic input from adjacent forest and freshwater systems. These caves host microbial communities that consist of distinct small colonies differing in colour and shape. Visible to the naked eye, the colonies cover cave walls and are strewn with light-reflecting water droplets. In this study, the diversity of prokaryotes constituting these unusual microbial communities in Pajsarjeva jama cave was examined. A molecular survey based on small subunit rRNA diversity showed a high diversity within the Bacteria , while members of Archaea were not recovered. A total of eight bacterial phyla were detected. The application of various species richness estimators confirmed the diverse nature of the microbial community sample. Members of Gammaproteobacteria were most abundant in the clone libraries constructed and were followed in abundance by members of Actinobacteria and Nitrospira . In addition, members of Alphaproteobacteria, Betaproteobacteria and Deltaproteobacteria as well as Acidobacteria, Verrucomicrobia, Planctomycetes, Chloroflexi and Gemmatimonadetes were identified in clone libraries. The high number of clones most closely related to environmental 16S rRNA gene clones showed the broad spectrum of unknown and yet to be cultivated microorganisms inhabiting these cave systems.     

Diversity of endophytic bacterial communities in poplar grown under field conditions

Bacterial endophytes may be important for plant health and other ecologically relevant functions of poplar trees. The composition of endophytic bacteria colonizing the aerial parts of poplar was studied using a multiphasic approach. The terminal restriction fragment length polymorphism analysis of 16S rRNA genes demonstrated the impact of different hybrid poplar clones on the endophytic community structure. Detailed analysis of endophytic bacteria using cultivation methods in combination with cloning of 16S rRNA genes amplified from plant tissue revealed a high phylogenetic diversity of endophytic bacteria with a total of 53 taxa at the genus level that included Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The community structure displayed clear differences in terms of the presence and relative proportions of bacterial taxa between the four poplar clones studied. The results showed that the genetic background of the hybrid poplar clones corresponded well with the endophytic community structure. Out of the 513 isolates and 209 clones identified, Actinobacteria, in particular the family Microbacteriaceae, made up the largest fraction of the isolates, whereas the clone library was dominated by Alpha- and Betaproteobacteria. The most abundant genera among the isolates were Pseudomonas and Curtobacterium, while Sphingomonas prevailed among the clones.     

Soil parent material is a key determinant of the bacterial community structure in arable soils

The bacterial community composition in soil and rhizosphere taken from arable field sites, differing in soil parent material and soil texture, was analyzed using terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. Nine sandy to silty soils from North-East Germany could clearly be distinguished from each other, with a relatively low heterogeneity in the community structure within the field replicates. There was a relationship between the soil parent material, i.e. different glacial and aeolian sediments, and the clustering of the profiles from different sites. A site-specific grouping of T-RFLP profiles was also found for the rhizosphere samples of the same field sites that were planted with potatoes. The branching of the rhizosphere profiles corresponded partly with the soil parent material, whereas the effect of the plant genotype was negligible. Selected terminal restriction fragments differing in their relative abundance within the nine soils were analyzed based on the cloning of the 16S rRNA genes of one soil sample. A high phylogenetic diversity observed to include Acidobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, and Gemmatimonadetes. The assignment of three out of the seven selected terminal restriction fragments to members of Acidobacteria suggested that this group seems to participate frequently in the shifting of community structures that result from soil property changes.     

Response of 1,2-dichloroethane-adapted microbial communities to ex-situ biostimulation of polluted groundwater

The microbial community of a groundwater system contaminated by 1,2-dichloroethane (1,2-DCA), a toxic and persistent chlorinated hydrocarbon, has been investigated for its response to biostimulation finalized to 1,2-DCA removal by reductive dehalogenation. The microbial population profile of samples from different wells in the aquifer and from microcosms enriched in the laboratory with different organic electron donors was analyzed by ARISA (Amplified Ribosomal Intergenic Spacer Analysis) and DGGE (Denaturing Gradient Gel Electrophoresis) of 16S rRNA genes. 1,2-DCA was completely removed with release of ethene from most of the microcosms supplemented with lactate, acetate plus formate, while cheese whey supported 1,2-DCA dehalogenation only after a lag period. Microbial species richness deduced from ARISA profiles of the microbial community before and after electron donor amendments indicated that the response of the community to biostimulation was heterogeneous and depended on the well from which groundwater was sampled. Sequencing of 16S rRNA genes separated by DGGE indicated the presence of bacteria previously associated with soils and groundwater polluted by halogenated hydrocarbons or present in consortia active in the removal of these compounds. A PCR assay specific for Desulfitobacterium sp. showed the enrichment of this genus in some of the microcosms. The dehalogenation potential of the microbial community was confirmed by the amplification of dehalogenase-related sequences from the most active microcosms. Cloning and sequencing of PCR products indicated the presence in the metagenome of the bacterial community of a new dehalogenase potentially involved in 1,2-DCA reductive dechlorination.     

Bacterial community composition over a dry winter in meso- and eutrophic Portuguese water bodies

In order to investigate the bacterial diversity in a number of rivers, reservoirs and lakes in northern and central Portugal during the winter of 2004/5 (atypically dry), we applied molecular methodologies, namely denaturing gradient gel electrophoresis with primers targeting fractions of the bacterial 16S rRNA gene. Environmental parameters such as pH, conductivity, inorganic nutrients, total suspended solids and chlorophyll a were determined in order to characterize the trophic status of the studied water bodies. We found water bodies with oligotrophic to hypereutrophic characteristics. Organisms belonging to the Bacteroidetes and Alphaproteobacteria were found at the highest pH environment. Bacteroidetes were also related to high nutrient concentrations. Verrucomicrobia were associated with the most oligotrophic reservoir and low pH values. Actinobacteria were present in all samples from lakes and reservoirs, indicating its preference for lentic water bodies. Cyanobacteria dominance was related to high pH and conductivity levels. In general the conductivity values recorded in winter 2005 were the highest over recent years and chlorophyll a also reached very high levels. The data emphasize an enhanced risk of eutrophication for the studied water bodies, especially in the subsequent months when the temperature rises.     

Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies.     

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge of above-ground plant and animal diversity, the biodiversity found in soils remains largely uncharacterized. Here, we present an assessment of soil biodiversity and biogeographic patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system harbours large amounts of undescribed soil biodiversity. Despite high variability across the Park, below-ground diversity patterns were predictable based on soil characteristics, with prokaryotic and eukaryotic communities exhibiting overlapping biogeographic patterns. Further, Central Park soils harboured nearly as many distinct soil microbial phylotypes and types of soil communities as we found in biomes across the globe (including arctic, tropical and desert soils). This integrated cross-domain investigation highlights that the amount and patterning of novel and uncharacterized diversity at a single urban location matches that observed across natural ecosystems spanning multiple biomes and continents.     

Characterization of the depth-related changes in the microbial communities in Lake Hovsgol sediment by 16S rRNA gene-based approaches

The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it represents a record of the environmental changes that took place between the Holocene (the present age) and Pleistocene (the last ice age; 12,000 14C years before present day). Here, we investigated how the current microbial communities change as the depth increases by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes of the microbial communities. The microbial diversity, as estimated by the Shannon index, decreased as the depth increased. In particular, significant changes in archaeal diversity were observed in the middle depth (at 39-42 cm depth of total 60 cm depth) that marks the border between the Holocene and Pleistocene. Phylotype belonging to Beta-and Gamma-Proteobacteria were the predominant bacteria and most of these persisted throughout the depth examined. However, as the depth increased, some bacteria (some genera belonging to Beta-Proteobacteria, Nitrospira, and OP8-9) were not detectable while others (some genera belonging to Alpha-, Beta-, Gamma-Proteobacteria) newly detected by DGGE. Crenarchaea were the predominant archaea and only one phylotype belonging to Euryarchaea was found. Both the archaeal and bacterial profiles revealed by the DGGE band patterns could be grouped into four and three subsets, respectively, subsets that were largely divided by the border between the Holocene and Pleistocene. Thus, the diversity of the current microbial communities in Lake Hovsgol sediments decreases with increasing depth. These changes probably relate to the environmental conditions in the sediments, which were shaped by the paleoclimatic events taking place between the Holocene and Pleistocene.     

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species

A silica sands-based method has been developed to isolate high quality genomic DNAs from cells of animals, plants and microorganisms, such as Hemisalanx prognathus, Spinacia oleracea, Pichia pastoris, Bacillus licheniformis and Escherichia coli. To the best of our knowledge, no DNA isolation method has so wide application until now. In addition, this method and a commercially available kit were compared in analysis of microbial communities using high-throughput 16s rDNA sequencing. As a result, the silica sands-based method was found to be even more efficient in isolating genomic DNA from gram-positive bacteria than the kit, indicating that it would become a very valuable choice to faithfully reflect the composition of microbial communities.     

Predominance of Roseobacter, Sulfitobacter, Glaciecola and Psychrobacter in seawater collected off Ushuaia, Argentina, Sub-Antarctica

Bacterial diversity in sub-Antarctic seawater, collected off Ushuaia, Argentina, was examined using a culture independent approach. The composition of the 16S rRNA gene libraries from seawater and seawater contaminated with the water soluble fraction of crude oil was statistically different (P value 0.001). In both libraries, clones representing the Alphaproteobacteria, Gammaproteobacteria, the Cytophaga-Flavobacterium-Bacteroidetes group and unculturable bacteria were dominant. Clones associated with the genera Roseobacter, Sulfitobacter, Staleya, Glaciecola, Colwellia, Marinomonas, Cytophaga and Cellulophaga were common to both the libraries. However, clones associated with Psychrobacter, Arcobacter, Formosa algae, Polaribacter, Ulvibacter and Tenacibaculum were found only in seawater contaminated with hydrocarbons (Table 1). Further, the percentage of clones of Roseobacter, Sulfitobacter and Glaceicola was high in seawater (43%, 90% and 12% respectively) compared to seawater contaminated with hydrocarbons (35%, 4% and 9% respectively). One of the clones F2C63 showed 100% similarity with Marinomonas ushuaiensis a bacterium identified by us from the same site.     

Biodiversity and seasonal variation of the cyanobacterial assemblage in a rice paddy field in Fujian, China

Cyanobacteria are one of the main components of the microbiota in rice paddy fields and significantly contribute to its fertilization. The diversity and changes of the cyanobacterial assemblage were investigated during a rice growth season and after harvest in a paddy field located in Fujian Province, China. The cyanobacterial populations were analyzed by a semi-nested PCR, followed by denaturing gradient gel electrophoresis analysis. Twenty-four phylotypes were identified from the denaturing gradient gel electrophoresis profiles. The number of cyanobacterial phylotypes showed a seasonal variation and reached a peak in September, both in the upper (0-5 cm) and the deeper (10-15 cm) soil fractions. Some cyanobacterial sequences were only present during the rice growth season, while others were only found after harvest.     

内蒙草原不同植物功能群及物种对土壤微生物组成的影响

为了分析不同植物群落组成对内蒙古典型草原土壤微生物群落组成的影响,本研究利用植物功能群剔除处理实验平台,采用荧光定量PCR(real-timePCR)和自动核糖体间隔区基因分析(automated ribosomal intergenic spacer analysis,ARISA)技术,对不同植物功能群组成的非根际土壤和常见物种的根际土壤中细菌和真菌的数量及群落结构进行了分析。结果表明,在非根际土壤中,不同植物功能群组成对细菌数量有显著影响,而对真菌数量及细菌和真菌的群落结构影响不明显;在根际土壤中,不同植物物种对细菌、真菌的数量都有显著影响。此外,聚类分析表明,不同物种的根际土中细菌和真菌的群落结构也有所不同,尤其以细菌的群落结构变化较为明显。研究结果表明不同植物物种可以通过根系影响土壤微生物群落组成。     

Analysis of the composition of bacterial communities in oil reservoirs from a southern offshore Brazilian basin

The aim of this study was to characterize and compare the bacterial community structure of two distinct oil samples from a petroleum field in Brazil by using both molecular, based on the construction of 16S rRNA gene libraries, and cultivation methods. Statistical comparisons of libraries based on Amplified Ribosomal DNA Restriction Analysis (ARDRA) data revealed no significant differences between the communities recovered in the non-biodegraded (NBD) and highly biodegraded oils (HBD). BlastN analysis of the 16S rRNA gene sequences representative of distinct ribotypes from both oils showed the presence of nine different bacterial genera in these samples, encompassing members of the genera Arcobacter, Halanaerobium, Marinobacter, Propionibacterium, Streptomyces, Leuconostoc, Acinetobacter, Bacillus and Streptococcus. Enrichments obtained using oil as inoculum and sole carbon source yielded bacterial isolates showing high 16S rRNA gene sequence similarity with Achromobacter xylosoxidans, Bacillus subtilis, Brevibacillus sp., Dietzia sp. and Methylobacterium sp. Comparison between the data obtained using cultivation-independent and enrichment cultures suggests that different selection of community members may occur when using distinct approaches. All the organisms found, except for Leuconostoc sp. and Streptococus sp., have been previously reported in the literature as hydrocarbon degraders and/or associated to oil field environments.     

Shift in microbial population in response to crystalline cellulose degradation during enrichment with a semi-desert soil

Addition of crystalline cellulose to semi-desert soil shifts the microbial population; this was assessed by following the 16S rRNA gene, glycosyl hydrolase, and measuring its functional diversity in the bacterial population. Quantification of the glycosyl hydrolase gene showed an increase from 1 × 10⁴ g⁻¹ of unamended soil to 3 × 10⁴ g⁻¹ of crystalline-cellulose-amended soil by the 15th day of crystalline cellulose utilization. The indigenous glycosyl hydrolase community in unamended soil was dominated by the clone families that were closely related to the glycosyl hydrolases from Betaproteobacteria and Firmicutes. The addition of crystalline cellulose induced a shift in the glycosyl hydrolase population toward an increase in the relative abundance of the glycosyl hydrolase that was consistent with those of Bacteroidetes and Flavobacteria. The population shift of glycosyl hydrolase was also supported by the comparison of the 16S rRNA gene families in unamended and crystalline-cellulose-amended soil libraries. The most abundant 16S rRNA gene sequences retrieved in the unamended soil were identical to Pseudomonas, Massilia, Paenibacillus, and Bacillus spp., while Cytophaga and Flavobacterium spp. dominated in crystalline-cellulose-amended soil.     

Structure and function of denitrifying and nitrifying bacterial communities in relation to the plant species in a constructed wetland

The community structure and potential activities of nitrifying and denitrifying bacteria were studied in the rhizosphere of Typha latifolia and Phragmites australis present in a free water system constructed wetland (CW). Potential nitrate reduction and nitrification activities were shown to be significantly higher in the rhizosphere when compared with the nonvegetated sediment. Higher rates were generally obtained for P. australis . The community structure of denitrifying bacteria in the rhizosphere differed from that found at the bulk sediment, as revealed by PCR-denaturing gradient gel electrophoresis (DGGE) of the nitrous oxide reductase encoding gene nosZ . Results also show a greater nosZ genotype diversification and suggest a plant species effect in rhizosphere samples obtained during events of low hydraulic retention times. Ammonia-oxidizing communities were less complex on the basis of PCR-DGGE analysis of the 16S rRNA gene. Retrieved sequences were all related to Nitrosomonas marina and Nitrosomonas ureae , being both present in rhizosphere and bulk sediment regardless of environmental changes. The results demonstrate the effect of vegetation on the functioning and structure of bacterial communities involved in the removal of nitrogen in the treatment cells of a CW and point to the use of vegetation coverage to promote nitrification or denitrification in particular areas.     

Stability and microbial community structure of a partial nitrifying fixed-film bioreactor in long run

A partial nitrification system was investigated for 471 days under DO varying concentrations for assessing its stability and population dynamics. Within 130 days of operation at feed DO concentration of 1.0 ± 0.1 mg/L, more than 85% of nitrite was accumulated. Efficiency deteriorated when the feed DO concentration was increased to 4.2 ± 0.3 mg/L. Nitrite accumulation could not be re-established on decreasing feed DO to 1.0 ± 0.1 mg/L. Even at DO concentration of <0.05 mg/L, nitrate production was observed; a condition termed as anoxic nitrification. NOB was detected in the biomass even under this condition by Fluorescence in-situ hybridization (FISH) analysis. Through 16S rRNA gene sequencing a major fraction of unknown bacterial sequences closely resembling haloalkalophilic bacteria of marine origin were detected. The study indicated that these bacterial species might play a role in anoxic nitrification and that NOB could survive extreme low DO condition.     

Microbial communities and processes within a hypersaline gypsum crust in a saltern evaporation pond (Eilat,Israel)

Gypsum crusts containing multicolored, stratified microbial communities develop in the evaporation ponds of a commercial saltern in Eilat, Israel at salt concentrations between 190 and 240 g l⁻¹. The upper 0.5–2 cm of the crust is densely populated by orange-brown unicellular cyanobacteria. Below, a layer of green-colored filamentous cyanobacteria is found. Underneath, a bright purple layer of anoxygenic phototrophs is present, below which a reduced black layer is found. We have investigated the biological properties of this crust using a wide variety of techniques, and we here review the results of these interdisciplinary studies. The tests performed included microscopic examination of the biota, phylogenetic analyses based on 16S rRNA gene clone libraries and denaturing gradient gel electrophoresis, fatty acid analysis, light intensity and light quality measurements, microelectrode studies of oxygen profiles and oxygen evolution, determination of sulfate reduction using radioisotope methods, and measurement of methane evolution. The stable vertical stratification in the system enabled separate analyses of the different layers with a high spatial resolution. It was therefore possible to combine the different approaches and obtain information on the activities of the different types of oxygenic and anoxygenic phototrophs, dissimilatory sulfate reducers and methanogens in the different layers, as well as phylogenetic information on the nature of the microorganisms responsible for these processes. The gypsum crust thus becomes a paradigm for the study of a wide variety of microbial processes and their interrelationships in the presence of high salt concentrations. Guest Editors: J. John & B. Timms Salt Lake Research: Biodiversity and Conservation—Selected papers from the 9th Conference of the International Society for Salt Lake Research     

Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development

The origins of the biological complexity and the factors that regulate the development of community composition, diversity and richness in soil remain largely unknown. To gain a better understanding of how bacterial communities change during soil ecosystem development, their composition and diversity in soils that developed over c. 77 000 years of intermittent aeolian deposition were studied. 16S rRNA gene clone libraries and fatty acid methyl ester (FAME) analyses were used to assess the diversity and composition of the communities. The bacterial community composition changed with soil age, and the overall diversity, richness and evenness of the communities increased as the soil habitat matured. When analysed using a multivariate Bray-Curtis ordination technique, the distribution of ribotypes showed an orderly pattern of bacterial community development that was clearly associated with soil and ecosystem development. Similarly, changes in the composition of the FAMEs across the chronosequence were associated with biomarkers for fungi, actinomycetes and Gram-positive bacteria. The development of the soil ecosystem promoted the development of distinctive microbial communities that were reminiscent of successional processes often evoked to describe change during the development of plant communities in terrestrial ecosystems.