Microbial Ecology

Ecological effects on gut bacterial communities in wild bumble bee colonies.

by Hauke Koch

Koch, H., Cisarovsky, G., Schmid-Hempel, P. (in press) Journal of Animal Ecology

1. Animal hosts harbour diverse and often specific bacterial communities (“microbiota”) in their gut. These microbiota... more 1. Animal hosts harbour diverse and often specific bacterial communities (“microbiota”) in their gut. These microbiota can provide crucial services to the host, such as aiding in digestion of food and immune defence. However, the ecological factors correlating with and eventually shaping these microbiota under natural conditions are poorly understood.
2. Bumble bees have recently been shown to possess simple and highly specific microbiota. We here examine the dynamics of these microbiota in field colonies of the bumble bee Bombus terrestris over one season. The gut bacteria were assessed with culture-independent methods, i.e. with terminal restriction fragment length profiles (TRFLPs) of the 16S rRNA gene.
3. To further understand the factors that affect the microbiota, we experimentally manipulated field-placed colonies in a fully factorial experiment by providing additional food, or by priming the workers’ immune system by injecting heat killed bacteria. We furthermore looked at possible correlates of diversity and composition of the microbiota for a) natural infections with the microbial parasites Crithidia bombi and Nosema bombi; b) bumble bee worker size; c) colony identity, and d) colony age.
4. We found an increase in diversity of the microbiota in individuals naturally infected with either C. bombi or N. bombi. C. bombi infections, however, appear to be only indirectly linked with higher microbial diversity when comparing colonies. The treatments of priming the immune system with heat-killed bacteria, and additional food supply, as well as host body size had no effect on the diversity or composition of the microbiota. Host colony identity had only a weak effect on the composition of the microbiota at the level of resolution of our method. We found both significant increases and decreases in the relative abundance of selected bacterial taxa over the season.
5. We present the first study on the ecological dynamics of gut microbiota in bumble bees and identify parasite infections, colony identity and colony age as important factors influencing the diversity and composition of the bacterial communities. The
absence of an effect of our otherwise effective experimental treatments suggests a remarkable ability of the host to maintain a homeostasis in this community under widely different environments.

Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs

by deepak kumaresan

Patterns of elevational beta diversity in micro- and macroorganisms

by jianjun wang

Wang, Jianjun. Soininen, Janne. Zhang, Yong. Wang, Beixin. Yang, Xiangdong. Shen, Ji. Patterns of elevational beta diversity in micro- and macroorganisms, Global Ecology and Biogeography, In press

Keywords
Bacteria, beta diversity, Beta-sim, biogeography, China, diatoms, elevational gradient, human activities, macroecology, macroinvertebrates, species turnover, streams

Aim  While ecologists have long been interested in diversity in mountain regions, elevational patterns in beta... more Aim  While ecologists have long been interested in diversity in mountain regions, elevational patterns in beta diversity are still rarely studied across different life forms ranging from micro- to macroorganisms. Also, it is not known whether the patterns in turnover among organism groups are affected by the degree to which the environment is modified by human activities.

Location  Laojun Mountain, Yunnan Province, China.

Methods  The beta diversity patterns of benthic microorganisms (i.e. diatoms and bacteria) and macroorganisms (i.e. macroinvertebrates) in a stony stream were simultaneously investigated between elevations of 1820 and 4050 m. Data were analysed by using a distance-based approach and variation partitioning based on canonical redundancy analysis.

Results  Analyses of community dissimilarities between adjacent sampling sites showed comparable small-scale beta diversity along the elevational gradient for the organism groups. However, bacteria clearly showed the lowest elevational turnover when analyses were conducted simultaneously for all pairwise sites. Variation partitioning indicated that species turnover was mostly related to environmental heterogeneity and spatial gradients including horizontal distance and elevation, while purely human impacts were shown to be less important.

Main conclusions  The elevational beta diversity at large scales was lower for bacteria than for eukaryotic microorganisms or macroorganisms, perhaps indicative of high dispersal ability and good adaptability of bacteria to harsh environmental conditions. However, the small-scale beta diversity did not differ among the groups. Elevation was the major driver for the turnover of eukaryotic organisms, while the turnover of bacteria was correlated more with environmental variation.

Effects of flue gas desulphurization gypsum by-products on microbial biomass and community structure in alkaline-saline soils

by Paul Kardol

Ming Li, Lili Jiang, Zhaojun Sun, Jinzhi Wang, Yichao Rui, Lei Zhong, Yanfen Wang, Paul Kardol
Journal of Soils and Sediments, in press

Purpose: For an alkaline-saline region in Northwest China, we examined the responses of soil microbial communities to... more Purpose: For an alkaline-saline region in Northwest China, we examined the responses of soil microbial communities to flue gas desulphurization gypsum by-products (FGDB), a new ameliorant for alkaline-saline soils. In 2009 and 2010, we collected soils from 0-20 cm and 20-40 cm depth along an experimental FGDB gradient (0, 0.74, 1.49, 2.25, and 3.00 kg FGDB m-2).
Materials and methods: As a measure of microbial community composition and biomass, we analyzed phospholipid fatty acids (PLFAs). We used real-time quantitative polymerase chain reaction (qPCR) to measure abundance of bacterial 16S rRNA copy numbers. Additionally, physicochemical soil parameters were measured by common laboratory methods.
Results and discussion: Microbial community composition differed along the FGDB gradient; however, the microbial parameters did not follow a linear response. We found that in 2009 total PLFA concentrations, and concentrations of total bacterial, and Gram-negative bacterial PLFAs were slightly higher at intermediate FGDB concentrations. In 2010, total PLFA concentrations, and concentrations of total bacterial, Gram-positive bacterial, Gram-negative bacterial, and fungal PLFAs, as well as the fungal:bacterial PLFA ratio were highest at 1.49 kg FGDB m-2 and 3.00 kg FGDB m-2. PLFA concentrations often differed between 2009 and 2010; however, the patterns varied across the gradient and across microbial groups. For both years, PLFA concentrations were generally higher at 0-20 cm depth than at 20-40 cm depth. Similar results were obtained for the 16S rRNA copy numbers of bacteria at 0-20 cm depth. FGDB addition resulted in an increase in soil Ca2+, NO3--N and a decrease in pH, and electrical conductivity (EC). Shifts in PLFA-based microbial community composition and biomass could partly be explained by pH, soil organic carbon, total nitrogen, soil moisture, electrical conductivity, inorganic nitrogen, C/N, and Ca2+. Indirect effects via shifts in abiotic soil properties, therefore, seem to be an important pathway through which FGDB affect soil microbial communities.
Conclusions: Our results demonstrate that addition of FGDB leads to significant changes in soil physicochemical and microbial parameters. As such, addition of FGDB can have large impacts on the functioning of soil ecosystems, such as carbon and nitrogen cycling processes.

Bacterial Diversity Stabilizes Community Productivity

by Alexandre Jousset

Background

Stability is a crucial ecosystem feature gaining particular importance in face of increasing... more Background

Stability is a crucial ecosystem feature gaining particular importance in face of increasing anthropogenic stressors. Biodiversity is considered to be a driving biotic force maintaining stability, and in this study we investigate how different indices of biodiversity affect the stability of communities in varied abiotic (composition of available resources) and biotic (invasion) contexts.

Methodology/Principal Findings

We set up microbial microcosms to study the effects of genotypic diversity on the reliability of community productivity, defined as the inverse of the coefficient of variation of across-treatment productivity, in different environmental contexts. We established a bacterial diversity gradient ranging from 1 to 8 Pseudomonas fluorescens genotypes and grew the communities in different resource environments or in the presence of model invasive species. Biodiversity significantly stabilized community productivity across treatments in both experiments. Path analyses revealed that different aspects of diversity determined stability: genotypic richness stabilized community productivity across resource environments, whereas functional diversity determined stability when subjected to invasion.

Conclusions/Significance

Biodiversity increases the stability of microbial communities against both biotic and abiotic environmental perturbations. Depending on stressor type, varying aspects of biodiversity contribute to the stability of ecosystem functions. The results suggest that both genetic and functional diversity need to be preserved to ensure buffering of communities against abiotic and biotic stresses.

Increasing antagonistic interactions cause bacterial communities to collapse at high diversity

by Alexandre Jousset

Biodiversity is a major determinant of ecosystem functioning. Species-rich communities often use resourcesmore Biodiversity is a major determinant of ecosystem functioning. Species-rich communities often use resources
more  efficiently  thereby  improving  community  performance.  However,  high  competition  within  diverse
communities may also reduce community functioning. We manipulated the genotypic diversity of Pseudomonas
fluorescens communities, a plant mutualistic species inhibiting pathogens. We measured antagonistic interactions
in vitro, and related these interactions to bacterial community productivity (root colonisation) and ecosystem
service (host plant protection). Antagonistic interactions increased disproportionally with species richness.
Mutual poisoning between competitors lead to a negative complementarity effect, causing a decrease in
bacterial density by up to 98% in diverse communities and a complete loss of plant protection. The results
emphasize  that  antagonistic  interactions  may  determine  community  functioning  and  cause  negative
biodiversity–ecosystem functioning relationships. Interference competition may thus be an additional key for
predicting the dynamics and performance of natural assemblages and needs to be implemented in future
biodiversity models.

Pester_etal_2012_Frontiers

by Klaus-Holger Knorr

Freshwater wetlands are a major source of the greenhouse gas methane but at the same time can function as carbon sink.... more Freshwater wetlands are a major source of the greenhouse gas methane but at the same time can function as carbon sink. Their response to global warming and environmental pollution is one of the largest unknowns in the upcoming decades to centuries. In this review, we highlight the role of sulfate-reducing microorganisms (SRM) in the intertwined element cycles of wetlands. Although regarded primarily as methanogenic environments, biogeochemical studies have revealed a previously hidden sulfur cycle in wetlands that can sustain rapid renewal of the small standing pools of sulfate. Thus, dissimilatory sulfate reduction, which frequently occurs at rates comparable to marine surface sediments, can contribute up to 36–50% to anaerobic carbon mineralization in these ecosystems. Since sulfate reduction is thermodynamically favored relative to fermentative processes and methanogenesis, it effectively decreases gross methane production thereby mitigating the flux of methane to the atmosphere. However, very little is known about wetland SRM. Molecular analyses using dsrAB [encoding subunit A and B of the dissimilatory (bi)sulfite reductase] as marker genes demonstrated that members of novel phylogenetic lineages, which are unrelated to recognized SRM, dominate dsrAB richness and, if tested, are also abundant among the dsrAB-containing wetland microbiota. These discoveries point toward the existence of so far unknown SRM that are an important part of the autochthonous wetland microbiota. In addition to these numerically dominant microorganisms, a recent stable isotope probing study of SRM in a German peatland indicated that rare biosphere members might be highly active in situ and have a considerable stake in wetland sulfate reduction. The hidden sulfur cycle in wetlands and the fact that wetland SRM are not well represented by described SRM species explains their so far neglected role as important actors in carbon cycling and climate change.

Zooplankton interactions in an enclosure experiment: insights from stable isotope analyses

by Jonathan Grey

Freshwater Biology 2004

1. Density gradients of cladocerans and copepods were generated in an enclosure experiment to compare the impact on... more 1. Density gradients of cladocerans and copepods were generated in an enclosure experiment to compare the impact on the plankton of a filter feeder (Daphnia hyalina × galeata) with that of more selective feeders (calanoid and cyclopoid copepods). The experiment was conducted in situ over 25 days during spring in a mesotrophic lake, Schöhsee, Germany.

2. The plankton community was monitored regularly. Daphniids were able to graze on the phytoplankton present, which mainly consisted of small (<1000 μm3) species, whereas copepods did not show any impact on algae.

3. At the end of the experiment, Daphnia and remaining cyclopoid copepods were harvested and sorted manually, prior to analyses for stable isotopes of carbon and nitrogen. Daphniids from mesocosms stocked purely with differing densities of Daphnia showed little variability in stable isotope values, whereas those that thrived in enclosure bags together with copepods exhibited lower δ13C values.

4. The change in Daphniaδ13C indicates a change of food sources, modified by the presence of the copepods: the higher the mean abundance of copepods in the enclosures, the more 13C-depleted the daphniids. Increasing abundance of high nucleic acid (HNA) bacteria in the copepod bags may account for the trend in Daphniaδ13C via increased grazing on the bacteria themselves, or via grazing on phytoplankton utilising isotopically light CO2 from respiratory release.

5. Cyclopoid copepod stable isotope signatures were related to Daphnia and copepod abundances in copepod bags, suggesting that cyclopoids preyed on the available zooplankton.

Temporal Patterns of Protozooplankton Abundance and Their Food in Ellis Fjord, Princess Elizabeth Land, Eastern Antarctica

by Jonathan Grey

Estuarine, Coastal & Shelf Science 1997

The abundance and biomass of ciliates, dinoflagellates and heterotrophic and phototrophic nanoflagellates were... more The abundance and biomass of ciliates, dinoflagellates and heterotrophic and phototrophic nanoflagellates were determined at three sites along an ice-covered Antarctic fjord between January and November 1993. The water column showed little in the way of temperature and salinity gradients during the study period. In general, the protozooplankton exhibited a seasonal variation which closely mirrored that of chlorophyll a and bacterioplankton. The fjord mouth, which was affected by the greatest marine influences, consistently had the highest densities of ciliates and the most diverse community, with up to 18 species during the sampling period. Small aloricate ciliates were present throughout the year with Strobilidium spp. being dominant during the winter. Larger loricate and aloricate ciliates became more prominent during January and November, along with the autotrophic ciliate Mesodinium rubrum and two mixotrophic species (Strombidium wulffi and a type resembling Tontonia) suggesting evidence of species successions. Data on dinoflagellates were less extensive, but these protists showed greatest species diversity in the middle reaches of the fjord. A total of 13 species of dinoflagellate was recorded.
Ciliates made a significant contribution to the biomass of the microbial community in summer, particularly in the middle and at the seaward end of the fjord. In winter, heterotrophic flagellates (HNAN) and phototrophic nanoflagellates (PNAN) were the dominant component of protistan biomass. In terms of percentage contribution to the microbial carbon pool, bacteria dominated during winter and spring. To the authors’ knowledge, this is the first seasonal study of an Antarctic fjord. The Ellis Fjord is very unproductive compared to lower latitude systems, and supports low biomass of phytoplankton and microbial plankton during most of the year. This relates to severe climatic and seasonal conditions, and the lack of allochthonous carbon inputs to the system. Thus, high latitude estuaries may differ significantly from lower latitude systems, which generally rank among the most productive aquatic systems in the world.

Microbial dynamics in coastal waters of East Antarctica: bacterial production and nanoflagellate bacterivory.

by Jonathan Grey

Marine Ecology Progress Series 1996

Bacterial production and heterotrophic nanoflagellate (HNAN) bacterivory were determined concurrently with... more Bacterial production and heterotrophic nanoflagellate (HNAN) bacterivory were determined concurrently with measurements of abundance and biomass at weekly intervals between 30 December 1993 and 11 February 1994 at a shallow, coastal location in Prydz Bay, eastern Antarctica. Bacterial production was measured by [3H]thymidine incorporation and HNAN bacterivory by the uptake of fluorescently labelled bacteria. Bacterial abundance, biomass and production ranged from 2 to 8 x 108 l-1, 13 to 64 µg C l-1 and 8 to 14 µg C l-1 d-1, respectively, with maximum values recorded in mid January. The HNAN community comprised choanoflagellate, non-collared and colonial taxa, with non-collared forms dominating abundance and biomass in late January and early February. Total HNAN abundance and biomass ranged from 1.6 to 4.2 x 106 l-1 and 8 to 16 µg C l-1, respectively. HNAN cellular ingestion and clearance rates differed between taxa with maximum rates of 8.28 particles cell-1 h-1 and 9.32 nl cell-1 h-1 recorded for large non-collared forms. During the study period the HNAN community grazed 0.9 to 4.7 µg bacterial C l-1 d-1, equivalent to 3 and 12% of bacterial biomass, and 10 and 36% of daily bacterial production; however, these values are likely to be minimal estimates and grazing impact may have been higher on occasion. Choanoflagellates were responsible for much of the grazing impact at the beginning of the study period, while non-collared HNAN were the dominant grazers in late January and early February. The HNAN community therefore appears to graze substantial bacterial production in Antarctic coastal waters during the austral summer, although alternative sources of bacterial mortality are likely to be of importance.

Methane cycling in lake sediments and its influence on chironomid larval δ13C

by Jonathan Grey

FEMS Microbiology Ecology 2005

Stable carbon isotope analysis of chironomid larvae gave rise to the hypothesis that methane-oxidizing bacteria can... more Stable carbon isotope analysis of chironomid larvae gave rise to the hypothesis that methane-oxidizing bacteria can provide an important food source for higher trophic levels in lakes. To investigate the importance of the methane cycle for the larval stable carbon signatures, isotope analysis and microbiological and biogeochemical investigations were combined. The study was based on comparison of a dimictic lake (Holzsee) and a polymictic, shallow lake (Großer Binnensee), both located in northern Germany. Both lakes are inhabited by Chironomus plumosus larvae, which exhibited a stronger 13C-depletion in Holzsee than in Großer Binnensee, indicating a greater contribution of methane–carbon in the former. Indeed, the processes involved in the microbial methane cycle were found to be more active in Holzsee, showing higher potential methane production and methane oxidation rates. Consistently, cell numbers of methane-oxidizing bacteria were with 0.5 − 1.7× 106 cells inline image about one order of magnitude higher in Holzsee than in Großer Binnensee. Molecular analysis of the microbial community structure revealed no differences in the methanotrophic community between the two lakes, with a clear dominance of type I methanotrophs. The methanogenic population seemed to be adapted to the prevailing substrate in the respective lake (H2/CO2 in Holzsee and acetate in Großer Binnensee), even though differences were minor.

In conclusion, the stronger larval 13C-depletion in Holzsee was not reflected in differences in the microbial community structure, but in the activity and size of the methanogenic and methanotrophic populations in the lake sediment.

Experimental δ13C evidence for a contribution of methane to pelagic food webs in lakes

by Jonathan Grey

Limnology & Oceanography 2006

We tested the hypothesis that low stable carbon isotope (d13C) values commonly observed for zooplankton in humic lakes... more We tested the hypothesis that low stable carbon isotope (d13C) values commonly observed for zooplankton in humic lakes are due to their feeding on isotopically light methane-oxidizing microbes, and thus that methanederived carbon is important in the food webs of these lakes. In replicate laboratory cultures, Daphnia longispina, a common crustacean zooplankter in humic lakes, were fed microbial suspensions with or without enrichment by biogenic methane. The d13C values of Daphnia indicated consumption of 13C-depleted methanotrophic bacteria,
while growth rates, survival, and reproduction of Daphnia in cultures enriched with methane were equal to or greater than those in nonenriched cultures. Results from lake enclosures during the autumn overturn period revealed a decrease in d13C of adult Daphnia from -40.5% to -50.3%, reflecting extensive consumption of 13Cdepleted methanotrophic bacteria. Methane-derived carbon is a more important contribution to carbon flux
through lake pelagic food webs than has previously been suspected.

Utilisation of dissolved organic carbon from different sources by pelagic bacteria in an acidic mining lake

by Jonathan Grey

Archive Für Hydrobiologie 2006

We compared growth rates and efficiencies of pelagic bacteria from an extremely acidic mining lake (pH 2.6, mean depth... more We compared growth rates and efficiencies of pelagic bacteria from an extremely acidic mining lake (pH 2.6, mean depth 4.6 m) supplied with different sources of carbon: (1) excreted by phytoplankton, (2) derived from benthic algae, (3) entering the lake via ground water, and (4) leached from leaf litter. Bacteria exhibited high growth rate and efficiency on exudates of pelagic and benthic algae. In contrast, they showed a lower growth rate and efficiency with organic carbon from ground water, and grew at a very high rate but a very low efficiency on leaf leachate. Results from stable isotope analyses indicate a greater importance of benthic exudates and leaf leachate for bacteria in the epilimnion, and a higher impact of ground water sources in the hypolimnion. Given the magnitude of differential source inputs into the lake, we suggest that benthic primary production was the most important carbon source for pelagic bacteria. The benthic-pelagic coupling seems to be more relevant in this shallow acidic lake with low pelagic carbon dioxide concentrations than in neutral lakes.

Linking larval chironomids to methane: seasonal variation of the microbial methane cycle and chironomid d13C

by Jonathan Grey

Aquatic Microbial Ecology 2007

Methane-derived carbon has been shown to be an important carbon source for macroinvertebrates in several studies of... more Methane-derived carbon has been shown to be an important carbon source for macroinvertebrates in several studies of lake ecosystems using stable isotopes. Furthermore, season and lake morphology appear to influence the importance of methane as a carbon source. However, rarely have the dynamics of the methane cycle been measured concurrently with the isotope signatures of chironomid larvae. We examined the methane dynamics in 2 lakes with contrasting mixing regimes (polymictic and dimictic), while monitoring corresponding changes in chironomid larval δ13C throughout an annual cycle. Both methane turnover rates and abundance of methane-oxidising bacteria were higher in the dimictic lake, where correspondingly lower mean larval δ13C values of –44.2 to –61.7‰ were recorded. In contrast, potential methane production and oxidation rates, as well as cell numbers of methane-oxidising bacteria were always lower in the polymictic lake; corresponding
larval δ13C values ranged from –32.3 to –29.6‰. Furthermore, seasonal variation in larval δ13C was more pronounced in the dimictic lake (–50.1 ± 5.9‰) compared to the polymictic lake (–31.1 ± 1.2‰), reflecting the amplitude of turnover rates. This suggests strongly that lake characteristics have an influence on methane turnover rates and, in conjunction with season, affect the subsequent incorporation of methane-derived carbon into freshwater food webs via macroinvertebrates.

Unravelling complexities in benthic food webs using a dual stable isotope (hydrogen and carbon) approach

by Jonathan Grey

Freshwater Biology 2009

1. Stable carbon isotope studies have been an essential component of research regarding the contribution of methane... more 1. Stable carbon isotope studies have been an essential component of research regarding the contribution of methane (CH4)-derived carbon to freshwater food webs and results
have suggested that benthic macroinvertebrates in billabongs, streams and lakes may be partially, and in some instances, significantly ‘fuelled’ by methanotrophic biomass. However, the singular use of carbon isotopes can lead to ambiguous interpretations concerning the origin of carbon, especially in systems where phototrophs are likely to be using carbon respired sources and hence show more 13C-depleted values.
2. These uncertainties can be further resolved by the inclusion of additional isotopic data. Stable hydrogen isotopes are being increasingly used in food web studies with a marked advantage that sources may be isotopically distinct by one or two orders of magnitude greater than stable carbon or nitrogen, the isotopes most commonly used to delineate trophic interactions. By using hydrogen as a second biogeochemical tracer we provide further supportive evidence for the assimilation of methanotrophic microbial biomass by chironomid larvae.
3. Moreover, the hydrogen and carbon isotope values we found in chironomid tissues appear to reflect the original substrate used during methanogenesis; either acetate fermentation or carbonate reduction. Use of the former tends to result in relatively heavy
carbon and light hydrogen isotope values due to kinetic isotope effects, whereas use of the latter results in relatively lighter carbon and heavier hydrogen isotope values.
4. We provide preliminary evidence to suggest that hydrogen and carbon isotope values in macroinvertebrates may be used to distinguish between CH4 formation pathways and help to explain inter-depth and inter-specific differences between co-existing chironomid species found in the same lake.

Differential assimilation of methanotrophic and chemoautotrophic bacteria by lake chironomid larvae

by Jonathan Grey

Aquatic Microbial Ecology 2005

Bacteria play an important role in the nutrition of many lake-dwelling detritivorous macroinvertebrates, yet few... more Bacteria play an important role in the nutrition of many lake-dwelling detritivorous macroinvertebrates, yet few studies have investigated the roles of differing groups of bacteria in freshwater systems. Recent stable carbon isotope analyses have revealed that methanotrophic bacteria help fuel lake food webs. We analysed individual larvae of co-existing Chironomus plumosus and C. anthracinus for stable sulphur isotopes as an alternative tracer for bacterial assimilation, and compared them with existing stable carbon isotope data. The combination of these 2 isotopes suggests that there are large inter- and intraspecific differences in the incorporation of bacteria rather than algae in the diet of both species. C. anthracinus appears to assimilate a greater proportion of chemoautotrophs relative to its congener, which is consistent with classical descriptions of C. anthracinus feeding mode relative to bacterial stratigraphy in the sediments. The higher intraspecific isotope variability of C. plumosus indicates variable proportions of methanotrophs, chemoautotrophs and phytoplankton to the diets of individuals.

Phylogenetic clustering increases with elevation for microbes

by jianjun wang

Jianjun Wang, Janne Soininen, Jizheng He, Ji Shen, Phylogenetic clustering increases with elevation in microbes, Environmental Microbiology Reports 4: 217-226.

Summary
Although phylogenetic approaches are useful for providing insights into the processes underlying... more Summary
Although phylogenetic approaches are useful for providing insights into the processes underlying biodiversity patterns, the studies of microbial phylogenetic relatedness are rare, especially for elevational gradients. Using high-throughput pyrosequencing, we examined the biodiversity patterns for biofilm bacterial communities that were scraped from stream stones along an elevational gradient from 1820 to 4050 m in China. The patterns of bacterial species richness and phylogenetic diversity were hollow towards higher elevations. The bacterial communities consisted of closer relatives than expected and displayed increasing terminal phylogenetic clustering towards mountain top. The increasing phylogenetic clustering with elevation contrasts reports for macroorganisms that revealed phylogenetic overdispersion at low or intermediate elevations. Because water temperature showed the strongest correlation with phylogenetic relatedness (r2 = 0.516), the elevational pattern in the bacterial phylogenetic structure indicated that environmental filtering possibly due to lower temperature or more frequent temperature fluctuations increased towards higher elevations. Evidence supporting the environmental filtering on bacteria was also reflected by the orderly succession in the relative abundance of different bacterial phyla along the elevational gradient and in the high evenness of bacterial taxa at higher elevations. Overall, our results indicated that ecological processes possibly related to temperature may play a dominant role in structuring bacterial biodiversity along the elevational gradient.

Keywords: Bacteria, Elevational gradient, Phylogenetic diversity, Phylogenetic relatedness, Species diversity pattern, Streams

mean nearest taxon distances: MNTD
mean nearest neighbor distance: MNND
standardized effect size of mean nearest taxon distances: ses.MNTD
nearest taxon index: NTI

Another new reference:
Stegen, J.C., Lin, X., Konopka, A.E., and Fredrickson, J.K. (2012) Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. In press.

Predators promote defence of rhizosphere bacterial populations by selective feeding on non-toxic cheaters

by Alexandre Jousset

Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities

by Alexandre Jousset

Predator-prey chemical warfare determines the expression of biocontrol genes by rhizosphere-associated Pseudomonas fluorescens

by Alexandre Jousset