Phylogenetic Patterns in the Microbial Response to Resource Availability: Amino Acid Incorporation in San Francisco Bay

Aquatic microorganisms are typically identified as either oligotrophic or copiotrophic, representing trophic strategies adapted to low or high nutrient concentrations, respectively. Here, we sought to take steps towards identifying these and additional adaptations to nutrient availability with a quantitative analysis of microbial resource use in mixed communities. We incubated an estuarine microbial community with stable isotope labeled amino acids (AAs) at concentrations spanning three orders of magnitude, followed by taxon-specific quantitation of isotopic incorporation using NanoSIMS analysis of high-density microarrays. The resulting data revealed that trophic response to AA availability falls along a continuum between copiotrophy and oligotrophy, and high and low activity. To illustrate strategies along this continuum more simply, we statistically categorized microbial taxa among three trophic types, based on their incorporation responses to increasing resource concentration. The data indicated that taxa with copiotrophic-like resource use were not necessarily the most active, and taxa with oligotrophic-like resource use were not always the least active. Two of the trophic strategies were not randomly distributed throughout a 16S rDNA phylogeny, suggesting they are under selective pressure in this ecosystem and that a link exists between evolutionary relatedness and substrate affinity. The diversity of strategies to adapt to differences in resource availability highlights the need to expand our understanding of microbial interactions with organic matter in order to better predict microbial responses to a changing environment.     

Water Content Differences Have Stronger Effects than Plant Functional Groups on Soil Bacteria in a Steppe Ecosystem

Many investigations across natural and artificial plant diversity gradients have reported that both soil physicochemical factors and plant community composition affect soil microbial communities. To test the effect of plant diversity loss on soil bacterial communities, we conducted a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia (China). We found that the number and composition type of plant functional groups had no effect on bacterial diversity and community composition, or on the relative abundance of major taxa. In contrast, bacterial community patterns were significantly structured by soil water content differences among plots. Our results support researches that suggest that water availability is the key factor structuring soil bacterial communities in this semi-arid ecosystem.     

Hypolithic community shifts occur as a result of liquid water availability along environmental gradients in China's hot and cold hyperarid deserts

Hypolithic cyanobacterial communities occur in hot and cold hyperarid environments but the physical factors determining their diversity are not well understood. Here we report hypolithic diversity and colonization of a common quartz substrate at several hyperarid locations in the ancient deserts of north-western China, that experience varying mean annual temperature, rainfall and concomitant availability of liquid water in soil. Microscopy and enrichment culture resulted only in Chroococcidiopsis morphotypes which were ubiquitous, but community phylogenetic analysis revealed considerable cyanobacterial and heterotrophic bacterial diversity. Species Richness and Shannon's Diversity Index displayed a significant positive linear correlation with availability of liquid water but not temperature or rainfall alone. Several taxonomic groups occurred only in specific climatically defined locations, while for Chroococcidiopsis, Deinococcus and Phormidium location specific lineages within these genera were also evident. Multivariate analysis was used to illustrate pronounced community shifts due to liquid water availability, although these did not significantly affect the predicted functional relationships within any given assemblage in either hot or cold, wet or dry hyperarid deserts. This study clearly demonstrates that availability of liquid water, rather than temperature or rainfall per se is the key determinant of hypolithic diversity in hyperarid locations, and furthermore that functionally similar yet taxonomically distinct communities occur, characterized by the presence of taxa that are specific to defined levels of aridity.     

Soil resource availability is much more important than soil resource heterogeneity in determining the species diversity and abundance of karst plant communities

Resource availability and heterogeneity are recognized as two essential environmental aspects to determine species diversity and community abundance. However, how soil resource availability and heterogeneity determine species diversity and community abundance in highly heterogeneous and most fragile karst landscapes is largely unknown. We examined the effects of soil resource availability and heterogeneity on plant community composition and quantified their relative contribution by variation partitioning. Then, a structural equation model (SEM) was used to further disentangle the multiple direct and indirect effects of soil resource availability on plant community composition. Species diversity was significantly influenced by the soil resource availability in shrubland and woodland but not by the heterogeneity in woodland. Abundance was significantly affected by both soil resource availability and heterogeneity, whereas variation partitioning results showed that soil resource availability explained the majority of the variance in abundance, and the contribution of soil resource heterogeneity was marginal. These results indicated that soil resource availability plays a more important role in determining karst plant community composition than soil resource heterogeneity. Our SEMs further found that the multiple direct and indirect processes of soil resource availability in determining karst species diversity and abundance were different in different vegetation types. Soil resource availability and heterogeneity both played a certain role in determining karst plant community composition, while the importance of soil resource availability far exceeded soil resource heterogeneity. We propose that steering community restoration and reconstruction should be highly dependent on soil resource availability, and multiple direct and indirect pathways of soil resource availability for structuring karst plant communities need to be taken into account.     

Concentration-dependent patterns of leucine incorporation by coastal picoplankton

Coastal pelagic environments are believed to feature concentration gradients of dissolved organic carbon at a microscale, and they are characterized by pronounced seasonal differences in substrate availability for the heterotrophic picoplankton. Microbial taxa that coexist in such habitats might thus differ in their ability to incorporate substrates at various concentrations. We investigated the incorporation patterns of leucine in four microbial lineages from the coastal North Sea at concentrations between 0.1 and 100 nM before and during a spring phytoplankton bloom. Community bulk incorporation rates and the fraction of leucine-incorporating cells in the different populations were analyzed. Significantly fewer bacterial cells incorporated the amino acid before (13 to 35%) than during (23 to 47%) the bloom at all but the highest concentration. The incorporation rate per active cell in the prebloom situation was constant above 0.1 nM added leucine, whereas it increased steeply with substrate concentration during the bloom. At both time points, a high proportion of members of the Roseobacter clade incorporated leucine at all concentrations (55 to 80% and 86 to 94%, respectively). In contrast, the fractions of leucine-incorporating cells increased substantially with substrate availability in bacteria from the SAR86 clade (8 to 31%) and from DE cluster 2 of the Flavobacteria-Sphingobacteria (14 to 33%). The incorporation patterns of marine Euryarchaeota were between these extremes (30 to 56% and 48 to 70%, respectively). Our results suggest that the contribution of microbial taxa to the turnover of particular substrates may be concentration dependent. This may help us to understand the specific niches of coexisting populations that appear to compete for the same resources.     

Competition and predation as possible causes of bacterial rarity

We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria.     

Soil substrate utilization pattern and relation of functional evenness of plant groups and soil microbial community in five low mountain NATURA 2000

Background and aims

Species rich, semi-natural grassland systems provide several ecosystem functions. The goal was to assess how aboveground composition and evenness affects soil substrate utilization pattern and soil microbial functional evenness.

Methods

At five German NATURA 2000 grassland sites, the interactions of plant functional groups (graminoids, forbs and legumes) and belowground microbial functional evenness were investigated in relation to soil properties and sampling date. Functional evenness of soil microorganisms was measured with high spatial resolution by community level physiological profiling (CLPP) using multi-SIR (substrate-induced respiration) at three sampling dates during the vegetation period. Evenness indices were used to compare plant functional group diversity and soil microbial functional diversity.

Results

All sites differed in the consistently high soil microbial functional evenness, which was strongly predicted by soil pH, but not by plant functional groups or aboveground plant dry matter production. However, soil microbial functional evenness was particularly decreased by an increasing legume proportion and showed seasonal changes, probably driven by shifts in resource availability and soil water content.

Conclusions

Our results suggest that changes in soil chemical properties or in a single key plant functional group may have stronger effects on soil microbial functional evenness than changes in plant functional group evenness.     

Concentration-Dependent Patterns of Leucine Incorporation by Coastal Picoplankton

Coastal pelagic environments are believed to feature concentration gradients of dissolved organic carbon at a microscale, and they are characterized by pronounced seasonal differences in substrate availability for the heterotrophic picoplankton. Microbial taxa that coexist in such habitats might thus differ in their ability to incorporate substrates at various concentrations. We investigated the incorporation patterns of leucine in four microbial lineages from the coastal North Sea at concentrations between 0.1 and 100 nM before and during a spring phytoplankton bloom. Community bulk incorporation rates and the fraction of leucine-incorporating cells in the different populations were analyzed. Significantly fewer bacterial cells incorporated the amino acid before (13 to 35%) than during (23 to 47%) the bloom at all but the highest concentration. The incorporation rate per active cell in the prebloom situation was constant above 0.1 nM added leucine, whereas it increased steeply with substrate concentration during the bloom. At both time points, a high proportion of members of the Roseobacter clade incorporated leucine at all concentrations (55 to 80% and 86 to 94%, respectively). In contrast, the fractions of leucine-incorporating cells increased substantially with substrate availability in bacteria from the SAR86 clade (8 to 31%) and from DE cluster 2 of the Flavobacteria-Sphingobacteria (14 to 33%). The incorporation patterns of marine Euryarchaeota were between these extremes (30 to 56% and 48 to 70%, respectively). Our results suggest that the contribution of microbial taxa to the turnover of particular substrates may be concentration dependent. This may help us to understand the specific niches of coexisting populations that appear to compete for the same resources.     

Plant functional traits along environmental gradients in seasonally dry and fire‐prone ecosystem

Questions: How does the abundance and richness of plant assemblages with different functional (regeneration and nutrient acquisition) traits vary with fire regime, moisture availability and substrate fertility? What is the role of different functional traits in maintaining plant diversity under changing environmental conditions in seasonally dry and fire‐prone environments? Location: Southwest Western Australia. Methods: Plant species abundance and soil nutrients were determined at 16 forest sites with variable fire histories across an aridity gradient. All plant species were classified based on their functional traits as (1) perennial or annual, (2) ectomycorrhizal, arbuscular mycorrhizal, ericoid mycorrhizal, orchid mycorrhizal, proteoid or other non‐mycorrhizal, (3) resprouters or seeder, and (4) nitrogen fixer or non‐fixer. We used a multivariate (fourth‐corner) technique to simultaneously test the significance and direction of the relationship between each of these traits and fire frequency, fire interval length, aridity, and soil N, P and C fractions. Results: The functional response of the vegetation to fire regime was minor and restricted to annual species, which comprised only ～4% of taxa. Proteoid and ectomycorrhizal species dominated over species with arbuscular and orchid mycorrhizal roots, N‐fixers dominated over non‐fixers, and seeders dominated over resprouters when N fertility was low but organic labile P was high. Further, proteoid and ectomycorrhizal species richness increased with aridity, while arbuscular mycorrhizal species richness decreased. Conclusions: While the functional composition of southwest Australian vegetation is largely insensitive to changes in fire regime, nutrient acquisition and, to a lesser extent, regeneration traits provide mechanisms for the vegetation community to adjust to changes in resource availability. Thus, diversity responses to environmental change in seasonally dry and fire‐prone ecosystems are likely to be primarily mediated by the composition of nutrient acquisition traits in the vegetation community.     

Relationships among site characteristics,taxonomical structure and functional trait distribution of arthropods in forest,urban and agricultural soils of Southern Italy

Urbanization and agriculture cause alterations in soil biodiversity. As arthropods quickly respond to soil changes, they have been recognized as good indicators of soil quality. This study aimed to evaluate if (1) soil physico-chemical properties act as environmental filters of the functional trait distribution of soil arthropod community; (2) the abundance of certain functional traits is linked to different land uses; (3) the taxonomical and functional approaches provide complementary information about the evaluation of biological soil quality. The study was performed at forest, agricultural and urban sites in downtown and surroundings of Naples. The soils were characterized for texture, pH, organic matter content, water content, total Cd, Cr, Cu, Ni, Pb and Zn concentrations. The forest soils showed the highest organic matter and water contents, and the lowest metal concentrations; the agricultural soils showed the lowest organic matter and water contents and high Cd and Cu concentrations, whereas the urban soils showed high Pb and Zn concentrations. The forest soils showed the highest arthropod density, taxa richness and diversity. The distribution of the functional traits in the arthropod communities of the different land uses highlighted similarity only for the preference to occupy soil and for the percentage contribution of detritivores. The abundance of arthropods living above litter and omnivores were positively correlated to Pb and Zn concentrations, whereas predators were positively correlated to Cu concentrations. The findings suggest that the arthropod identification at order level could be enough to detect differences in functional traits among forest, urban, and agricultural soils.     

Shifts in desulfonating bacterial communities along a soil chronosequence in the forefield of a receding glacier

Forefields of receding glaciers are unique and sensitive environments representing natural soil chronosequences, where sulfate availability is assumed to be a limiting factor. Bacterial mineralization of organosulfur is an important sulfate-providing process in soils. We analyzed the diversity of sulfonate-desulfurizing (desulfonating) bacteria in the Damma glacier forefield on the basis of the key gene asfA by terminal restriction fragment length polymorphism and clone libraries. The community structure and sequence diversity of desulfonating bacteria differed significantly between forefield soils deglaciated in the 1990s and the 1950s. Soil age had a strong effect on the desulfonating rhizosphere communities of Agrostis rupestris , but only a slight impact on the ones from Leucanthemopsis alpina . AsfA affiliated to Polaromonas sp. was predominantly found in the more recent ice-free soils and the corresponding rhizospheres of A. rupestris , while a group of unidentified sequences was found to be dominating the matured soils and the corresponding rhizospheres of A. rupestris . The desulfonating bacterial diversity was not affected by varying levels of sulfate concentrations. The level of asfA diversity in recently deglaciated soils suggests that desulfonating bacteria are a critical factor in sulfur cycling, with defined groups dominating at different stages of soil formation.     

贺兰山不同海拔典型植被带土壤微生物多样性

土壤微生物多样性在海拔梯度的分布格局研究近年来受到和植物动物一样的重视程度,但是干旱风沙区微生物多样性在海拔梯度上的多样性分布规律尚未揭示。本研究以处于干旱风沙区的贺兰山不同海拔的六个典型植被带（荒漠草原带、山地旱生灌丛带、温性针叶林带、针阔混交林带、寒温性针叶林带和亚高山草甸带）土壤为研究对象,利用Biolog微平板法和磷脂脂肪酸甲酯法(FAMEs)系统研究微生物多样性群落特征以及在不同植被带分布规律。结果表明：土壤微生物功能多样性随海拔增加发生变化,且微生物群落结构存在显著差异。Biolog分析显示土壤微生物群落代谢活性依次是：亚高山草甸>寒温性针叶林>针阔混交林>温性针叶林>山地旱生灌丛>荒漠草原,随海拔的升高土壤微生物群落物种丰富度指数（H）和均匀度指数（E）总体上均表现出增大的趋势,差异显著（P＜0.05）;FAMEs分析表明不同海拔的微生物区系发生了一定程度的变化,寒温性针叶林土壤微生物磷酸脂肪酸生物标记的数量和种类均最高,且细菌、真菌特征脂肪酸相对含量也最高;土壤微生物群落结构多样性次序是：寒温性针叶林带>针阔混交林带>温性针叶林带>亚高山草甸>山地旱生灌丛>荒漠草原。本研究结果表明贺兰山海拔梯度的微生物多样性分布规律不同于已有的植物多样性“中部膨胀”研究结果,这说明在高海拔地区有更多的适合该生境的微生物存在,这对维持干旱风沙区的生态系统功能稳定性具有重要意义。     

Plant community responses to resource availability and heterogeneity during restoration

Availability and heterogeneity of resources have a strong influence on plant community structure in undisturbed systems, as well as those recovering from disturbance. Less is known about the role of resource availability and heterogeneity in restored communities, although restoration provides a valuable opportunity to test our understanding of factors that influence plant community assembly. We altered soil nitrogen (N) availability and soil depth during a prairie restoration to determine if the availability and/or heterogeneity of soil resources influenced plant community composition in restored grassland communities. Plant community responses to three levels of N availability (ambient, enriched by fertilization, and reduced by carbon amendment) and two levels of soil depth (deep and shallow) were evaluated. In addition, we evaluated plant community responses to four whole plot heterogeneity treatments created from the six possible combinations of soil N availability and soil depth. The soil depth treatment had little influence on community structure during the first 3 years of restoration. Total diversity and richness declined over time under annual N enrichment, whereas diversity was maintained and richness increased over time in soil with reduced N availability. Non-native species establishment was lowest in reduced-N soil in the initial year, but their presence was negligible in all of the soil N treatments by the second year of restoration. Panicum virgatum, a native perennial C₄ grass, was the dominant species in all soil N treatments by year three, but the magnitude of its dominance was lowest in the reduced-N soil and highest in enriched-N soil. Consequently, the relative cover of P. virgatum was strongly correlated with community dominance and inversely related to diversity. The differential growth response of P. virgatum to soil N availability led to a higher degree of community similarity to native prairie in the reduced-N treatment than in the enriched-N treatment. There were no differences in plant community structure among the four whole plot-level heterogeneity treatments, which all exhibited the same degree of similarity to native prairie. Diversity and community heterogeneity in the whole-plot treatments appeared to be regulated by the dominant species effect on light availability, rather than soil N heterogeneity per se. Our results indicate that a strong differential response of a dominant species to resource availability in a restored community can regulate community structure, diversity, and similarity to the native (or target) community, but the importance of resource heterogeneity in restoring diversity may be dampened in systems where a dominant species can successfully establish across a range of resource availability.     

Unimodal productivity–diversity relationships among bacterial communities in a simple polar soil ecosystem

Unlike other macroecological principles, relationships between productivity and diversity have not been effectively tested for microbial communities. Here we describe an experiment in which the availability of resources to soil bacterial communities was manipulated in a model system, the McMurdo Dry Valleys of Antarctica. Mannitol additions were used to simulate a productivity gradient such that a response in bacterial biomass production, taxonomic diversity and functioning (e.g., enzyme activity) were induced. Resource amendment induced a positive linear response in microbial productivity (P < 0.001) but a unimodal (hump-shaped) response in microbial diversity at multiple taxonomic scales (P = 0.035). Putative oligotrophic (e.g., phyla Nitrospirae and Cyanobacteria) and copiotrophic (e.g., phylum Proteobacteria) taxa were apparent through substantial community turnover along the resource gradient. Soil enzyme activity was inversely related to bacterial biomass but positively related to diversity, suggesting the latter may be a stronger control over enzyme-mediated decomposition. The mechanisms behind this pattern are consistent with macroecological theory of a shift from environmental (e.g., stress tolerance) to biotic (e.g., competition) drivers with increasing resource availability. This evidence is among the first of its kind to document a significant unimodal productivity–diversity relationship for soil bacteria.     

The bacterial biogeography of British soils

Despite recognition of the importance of soil bacteria to terrestrial ecosystem functioning there is little consensus on the factors regulating belowground biodiversity. Here we present a multi-scale spatial assessment of soil bacterial community profiles across Great Britain (> 1000 soil cores), and show the first landscape scale map of bacterial distributions across a nation. Bacterial diversity and community dissimilarities, assessed using terminal restriction fragment length polymorphism, were most strongly related to soil pH providing a large-scale confirmation of the role of pH in structuring bacterial taxa. However, while α diversity was positively related to pH, the converse was true for β diversity (between sample variance in α diversity). β diversity was found to be greatest in acidic soils, corresponding with greater environmental heterogeneity. Analyses of clone libraries revealed the pH effects were predominantly manifest at the level of broad bacterial taxonomic groups, with acidic soils being dominated by few taxa (notably the group 1 Acidobacteria and Alphaproteobacteria). We also noted significant correlations between bacterial communities and most other measured environmental variables (soil chemistry, aboveground features and climatic variables), together with significant spatial correlations at close distances. In particular, bacterial and plant communities were closely related signifying no strong evidence that soil bacteria are driven by different ecological processes to those governing higher organisms. We conclude that broad scale surveys are useful in identifying distinct soil biomes comprising reproducible communities of dominant taxa. Together these results provide a baseline ecological framework with which to pursue future research on both soil microbial function, and more explicit biome based assessments of the local ecological drivers of bacterial biodiversity.     

Soil fertility increases with plant species diversity in a long-term biodiversity experiment

Most explanations for the positive effect of plant species diversity on productivity have focused on the efficiency of resource use, implicitly assuming that resource supply is constant. To test this assumption, we grew seedlings of Echinacea purpurea in soil collected beneath 10-year-old, experimental plant communities containing one, two, four, eight, or 16 native grassland species. The results of this greenhouse bioassay challenge the assumption of constant resource supply; we found that bioassay seedlings grown in soil collected from experimental communities containing 16 plant species produced 70% more biomass than seedlings grown in soil collected beneath monocultures. This increase was likely attributable to greater soil N availability, which had increased in higher diversity communities over the 10-year-duration of the experiment. In a distinction akin to the selection/complementarity partition commonly made in studies of diversity and productivity, we further determined whether the additive effects of functional groups or the interactive effects of functional groups explained the increase in fertility with diversity. The increase in bioassay seedling biomass with diversity was largely explained by a concomitant increase in N-fixer, C4 grass, forb, and C3 grass biomass with diversity, suggesting that the additive effects of these four functional groups at higher diversity contributed to enhance N availability and retention. Nevertheless, diversity still explained a significant amount of the residual variation in bioassay seedling biomass after functional group biomass was included in a multiple regression, suggesting that interactions also increased fertility in diverse communities. Our results suggest a mechanism, the fertility effect, by which increased plant species diversity may increase community productivity over time by increasing the supply of nutrients via both greater inputs and greater retention.     

Spatial Patchiness of Litter, Nutrients and Macroinvertebrates during Secondary Succession in a Tropical Montane Cloud Forest in Mexico

We test the hypothesis that secondary succession in Tropical Montane Cloud Forest (TMCF) in Mexico is accompanied by an increase in the spatial structuring of litter resources, soil nutrient concentrations and the soil macroinvertebrate community at a within-plot scale (5–25 m). This increased spatial structuring is expected because secondary succession in these forests is associated with an increase in the diversity of trees that dominate the canopy. If each tree species generates a particular soil environment under its canopy, then under a diverse tree community, soil properties will be spatially very heterogeneous. Tree censuses and grid sampling were performed in four successional stages of a secondary chronosequence of TMCF. Variography was used to analyse spatial patterns in continuous variables such as nutrient concentrations, while Spatial Analysis by Distance Indices (SADIE) was applied to determine patchiness in the distribution of soil macroinvertebrate taxa. Secondary succession was found to be accompanied by the predicted increase in the spatial structuring of litter resources and the macroinvertebrate community at the within-plot scale. Spatial patterns in the macroinvertebrate community only became evident for all taxa in the oldest forest (100 years old). Patches with low Ca and Mg concentrations in early successional soils were associated with patches where pine litter was most abundant while those with low P concentrations in late successional stages were associated with patches where oak litter was most abundant. Results suggest that anthropogenic disturbance aboveground promotes a more homogeneous resource environment in the surface soil, which compared to older forests, sustains a less diverse and less spatially structured macroinvertebrate community.     

Response of fungal, bacterial and ureolytic communities to synthetic sheep urine deposition in a grassland soil

In grazed pastures, soil pH is raised in urine patches, causing dissolution of organic carbon and increased ammonium and nitrate concentrations, with potential effects on the structure and functioning of soil microbial communities. Here we examined the effects of synthetic sheep urine (SU) in a field study on dominant soil bacterial and fungal communities associated with bulk soil and plant roots (rhizoplane), using culture-independent methods and a new approach to investigate the ureolytic community. A differential response of bacteria and fungal communities to SU treatment was observed. The bacterial community showed a clear shift in composition after SU treatment, which was more pronounced in bulk soil than on the rhizoplane. The fungal community did not respond to SU treatment; instead, it was more affected by the time of sampling. Redundancy analysis of data indicated that the variation in the bacterial community was related to change in soil pH, while fungal community was more responsive to dissolution of organic carbon. Like the universal bacterial community, the ureolytic community was influenced by the SU treatment. However, different taxa within the ureolytic bacterial community responded differentially to the treatment. The ureolytic community comprised of members from a range of phylogenetically different taxa and could be used to measure the effect of environmental perturbations on the functional diversity of natural ecosystems.     

Bacterial diversity in deep Mediterranean sediments: relationship with the active bacterial fraction and substrate availability

We investigated vertical distribution and depth-related patterns (from 670 to 2,570 metres) of bacterial diversity in sediment samples collected along a transect in the warm deep Mediterranean sea. Analyses of bacterial diversity were compared with the abundance of benthic bacteria, their metabolically active fraction and the substrates potentially available for their growth. The number of active bacteria was dependent upon the availability of organic substrate in the sediment deriving from phytopigment inputs from the photic layer. The T-RFLP analysis revealed that the surface layers of all sediments analysed were dominated by the same ribotypes, but clear shifts in bacterial community structure were observed in deeper sediment layers. High values of bacterial diversity (expressed as D, H') and evenness (as J) were observed at all stations (a total of 61 ribotypes was identified), and as a result of the large fraction of rare ribotypes (c. 35%), the overall bacterial diversity in the deep sea region investigated was among the highest reported so far in literature. Biodiversity parameters did not display any relationship with water depth, but ribotype richness was related with the number and percentage of active bacteria, suggesting a coupling between organic inputs stimulating bacterial growth and deep-sea bacterial diversity.     

The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria

We developed a novel method, the filtration-acclimatization method (FAM), which enables the isolation and cultivation of an important fraction of the bacterial diversity, which is not cultivable by standard methods. The method consists of a filtration step, which removes most of the readily cultivable bacteria able to overgrow slowly growing bacteria, and an acclimatization procedure that provides a slow transition from the low environmental substrate concentrations to the high concentration of standard microbial media. So far, we isolated in total 65 strains from surface freshwater habitats by utilizing FAM. The isolates are affiliated with Actinobacteria, Alpha-, Betaproteobacteria, Bacteroidetes, and Spirochaeta. All isolates are pure cultures and form visible colonies on agar plates with high substrate concentrations. For further analysis, strains sharing more than a 97% 16S rRNA gene sequence similarity were grouped into one taxon. Based on sequence similarities, 88% of the obtained taxa can be considered to be undescribed species (<97% similarity to closest species). The highest similarity value of the taxa to the respective closest related species ranged from 87.7% to 99.8%, and was on average 94.5%. For comparison we isolated, by direct plating of water samples on a rich agar medium, a similar number of taxa. Amongst these taxa the percentage of taxa, which can be considered to be undescribed species, was only half of the percentage found for the taxa isolated by FAM. More importantly, it was amongst the taxa obtained by the standard method no taxon that was closer related to an uncultured bacterium than to an isolate, while 56% of the taxa isolated by FAM were closely related to uncultured bacteria.