Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

Background

Bacteriophages are known to be one of the driving forces of bacterial evolution. Besides promoting horizontal transfer of genes between cells, they may induce directional selection of cells (for instance, according to more or less resistance to phage infection). Switching between lysogenic and lytic pathways results in various types of (co)evolution in host-phage systems. Spatial (more generally, ecological) organization of the living environment is another factor affecting evolution. In this study, we have simulated and analyzed a series of computer models of microbial communities evolving in spatially distributed environments under the pressure of phage infection.

Results

We modeled evolving microbial communities living in spatially distributed flowing environments. Non-specific nutrient supplied in the only spatial direction, resulting in its non-uniform distribution in environment. We varied the time and the location of initial phage infestation of cells as well as switched chemotaxis on and off. Simulations were performed with the Haploid evolutionary constructor software (http://evol-constructor.bionet.nsc.ru/).

Conclusion

Simulations have shown that the spatial location of initial phage invasion may lead to different evolutionary scenarios. Phage infection decreases the speciation rate by more than one order as far as intensified selection blocks the origin of novel viable populations/species, which could carve out potential ecological niches. The dependence of speciation rate on the invasion node location varied on the time of invasion. Speciation rate was found to be lower when the phage invaded fully formed community of sedentary cells (at middle and late times) at the species-rich regions. This is especially noticeable in the case of late-time invasion.Our simulation study has shown that phage infection affects evolution of microbial community slowing down speciation and stabilizing the system as a whole. This influencing varied in its efficiency depending on spatially-ecological factors as well as community state at the moment of phage invasion.

     

The bacterial community associated with rose-scented geranium (<Emphasis Type="Italic">Pelargonium graveolens</Emphasis>) leaves responds to anthracnose symptoms

Background

The fungus Colletotrichum is a plant pathogen that causes the anthracnose disease, resulting in huge losses in various crops including the rose-scented geranium (Pelargonium graveolens). Although the bacterial community associated with plants has an important role in the establishment of plant diseases, little is known about what happens in P. graveolens.

Aims

To increase the knowledge about the bacterial community associated with P. graveolens and its relationship with anthracnose disease symptoms.

Methods

Quantitative PCR and high-throughput sequencing were combined to determine the presence of the fungus Colletotrichum and to reveal the bacterial communities associated with different plant parts – root, stem and leaf – and in the rhizosphere and bulk soil, and also to determine the respective bacterial communities associated with P. graveolens leaves symptomatic and asymptomatic for anthracnose disease.

Results

The fungus Colletotrichum was detected in all plant parts and in the surrounding soil. Bacterial communities varied spatially in plants, and the disease symptoms also influenced the composition of the bacterial community. Abundances of operational taxonomic units (OTUs) assigned to the phylum Actinobacteria and to the genus Streptococcus were greatly increased in asymptomatic leaves.

Conclusions

The bacterial community associated to geranium leaves responds to anthracnose symptoms.

     

Assembly of seed-associated microbial communities within and across successive plant generations

Background and aims

Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.

Methods

Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model.

Results

Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota.

Conclusions

These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.

     

Dynamics of plant nutrient uptake as affected by biopore-associated root growth in arable subsoil

Background and aims

Soil microbial communities influence nutrient cycling, chemistry and structure of soil, and plant productivity. In turn, agronomic practices such as fertilization and crop rotation alter soil physical and chemical properties and consequently soil microbiomes. Understanding the long-term effects of agronomic practices on soil microbiomes is essential for improving agronomic practices to optimize these microbial communities for agricultural sustainability. We examine the composition and substrate-utilization profiles of microbial communities at the Morrow Plots in Illinois.

Methods

Microbial community composition is assessed with 16S rRNA gene sequencing and subsequent bioinformatic analyses. Community- level substrate utilization is characterized with the BIOLOG EcoPlate.

Results

Fertilizer and rotation treatments significantly affected microbial community structure, while substrate utilization was affected by fertilizer, but not crop-rotation treatments. Differences in relative abundance and occurrence of bacterial taxa found in fertilizer treatments can explain the observed differences in community level substrate utilization.

Conclusion

Long-term fertilization and crop-rotation treatments affect soil microbial community composition and physiology, specifically through chronic nutrient limitation, long-term influx of microbes and organic matter via manure application, as well as through changes in soil chemistry. Relatively greater abundance of Koribacteraceae and Solibacterales taxa in soils might prove useful as indicators of soil degradation.

     

Heterogeneity in arbuscular mycorrhizal fungal communities may contribute to inconsistent plant-soil feedback in a Neotropical forest

Background and aims

Plant-soil feedback may vary across host species and environmental gradients. The relative importance of these biotic versus abiotic drivers of feedback will determine the stability of plant and microbial communities across environments. If plant hosts are the main driver of soil microbial communities, plant-soil feedback may be stable across changing environments. However, if microbial communities vary with environmental gradients, feedback may also vary, limiting its capacity to predict plant distributions.

Methods

We characterized arbuscular mycorrhizal (AM) fungi across tree plantations and a primary Neotropical rainforest. We then performed a plant-soil feedback pot experiment of AM fungi from these plantations on three plant species and related feedback and AM fungal communities in the field.

Results

In the field, temporal and spatial variation in AM fungal composition was similar in magnitude to variation across plant host species. Composition of AM fungi in the pot experiment significantly differed from the field plots. Furthermore, differential feedback was explained by shifts in AM fungal composition only for one plant host species (Hyeronima alchorneoides) in the pot experiment.

Conclusions

Natural AM fungal communities were temporally and spatially heterogeneous and AM fungal communities in the greenhouse did not reflect natural soils. These factors led to heterogeneous and unpredictable feedback responses, which suggests that applying greenhouse derived plant-soil feedback trends to predict plant coexistence in natural systems may be misleading.

     

“Preferential” ammonium uptake by sugarcane does not increase the <Superscript>15</Superscript>N recovery of fertilizer sources

Aims

Human activities can dramatically alter natural plant communities which, after disturbance cessation, undergo secondary succession. In arid environments plant succession is quite slow, and its link to the carbon (C) cycle is not well known. We assessed changes in C balance on a semiarid plant community along a chronosequence spanning ca. 100 years after land abandonment in an arid environment in SE Spain to examine temporal changes in C following human disturbance.

Methods

We selected 5 individuals of the dominant plant species along five plant community stages differing in the time since land abandonment occurred, and we used a closed-chamber infrared gas analyzer method to estimate the contribution of whole plants and bare soil to community C exchange. We estimated CO₂ fluxes for each plant community stage and calculated temporal differences along the chronosequence.

Results

Plant community composition and plant cover changed throughout the chronosequence. Carbon balance was related to changes in plant photosynthesis and plant and soil respiration along the chronosequence. Overall, community C exchange shifted from source to sink as plant colonization progressed. It took 65 years for the system to recover the equivalent C sink capacity of the undisturbed site.

Conclusions

Recovery of arid plant communities after land abandonment may enhance long-term C sequestration and significantly contribute to C balance at the global level.

     

Total and active microbial communities and <Emphasis Type="Italic">phoD</Emphasis> as affected by phosphate depletion and pH in soil

Background and Aims

Soil microbial communities contribute to organic phosphorus cycling in a variety of ways, including secretion of the PhoD alkaline phosphatase. We sampled a long-term grassland fertilization trial in Switzerland characterized by a natural pH gradient. We examined the effects of phosphate depletion and pH on total and active microbial community structures and on the structure and composition of the total and active phoD-harboring community.

Methods

Archaeal, bacterial and fungal communities were investigated using T-RFLP and phoD-harboring members of these communities were identified by 454-sequencing.

Results

Phosphate depletion decreased total, resin-extractable and organic phosphorus and changed the structure of all active microbial communities, and of the total archaeal and phoD-harboring communities. Organic carbon, nitrogen and phosphorus increased with pH, and the structures of all total and active microbial communities except the total fungal community differed between the two pH levels. phoD-harboring members were affiliated to Actinomycetales, Bacilliales, Gloeobacterales, Planctomycetales and Rhizobiales.

Conclusions

Our results suggest that pH and associated soil factors are important determinants of microbial and phoD-harboring community structures. These associated factors include organic carbon and total nitrogen, and to a lesser degree phosphorus status, and active communities are more responsive than total communities. Key players in organic P mineralization are affiliated to phyla that are known to be important in organic matter decomposition.

     

Dynamic succession of chickpea rhizobia over years and sampling sites in Xinjiang,China

Aims

Cyanobacterial and algal communities have a large effect on biocrust formation and development. Biocrust species and abundance vary spatially and temporally due to different environmental factors. The relationships among cyanobacterial and algal communities, and biocrust function have been studied extensively. Lacking, however, are studies of temporal changes in a similar landscape where environmental conditions are similar, but where biocrust formation is different.

Methods

Biocrusts of different ages were located in the Loess Plateau in an area that had experienced a landslide. We examined changes in cyanobacterial and algal communities, carbon, nutrients, and the composition of dissolved organic matter in the topsoil, and the relationships among the community and soil characteristics using redundancy analysis.

Results

Phormidium tenue (Cyanophyta) dominated in all biocrusts, and co-dominated in a newly formed crust with Euglena sp. (Euglenophyta). Oscillatoria sp. (Cyanophyta) increased with biocrust age. Oscillatoria was positively correlated with carbon fixation and nutrient (nitrogen and phosphorus) accumulation in topsoils.

Conclusions

While incubation of Phormidium tenue and Euglena sp. is suggested for rapid biocrust formation at an early stage, increasing the abundance of Phormidium tenue and Oscillatoria sp. can promote carbon fixation and nutrient (nitrogen and phosphorus) accumulation, thereby accelerating biocrusts into a later stage.

     

Spring to autumn changes in the arbuscular mycorrhizal fungal community composition in the different propagule types associated to a Mediterranean shrubland

Background and aims

Arbuscular mycorrhizal fungi (AMF) appear differentially represented among propagule forms [intraradical mycelium (IRM) in colonized roots, spores and extraradical mycelium (ERM)]. However, spring to autumn changes in the AMF communities harboured in the different propagule forms has not been studied, being this the aim of the present study.

Methods

A terminal restriction fragment length polymorphism approach was used to monitor, in spring and autumn, the AMF community composition present in the three propagule types associated to five shrub species in a semi-arid Mediterranean environment.

Results

The AMF community composition in roots was significantly different between spring and autumn; however, no significant differences were detected in soil propagules (spores and ERM). Different trends were identified according to the preferential biomass allocation patterns of AMF phylotypes, suggesting different life strategies: those allocating mainly into IRM (belonging to the Glomeraceae), ERM (Diversisporaceae and Gigasporaceae) or spores (Pacisporaceae and Paraglomeraceae).

Conclusions

Differences of AMF taxa in the biomass allocation patterns among propagules are maintained throughout the year. Progress in the knowledge of functional features of AMF communities and their responses to seasonal variations are important for the AMF application in Mediterranean ecosystems.

     

Halophytic plant community patterns in Mediterranean saltmarshes: shedding light on the connection between abiotic factors and the distribution of halophytes

Aims

Establishing a vegetation-soil model in Mediterranean saltmarshes based on the relationships between the plant communities and the abiotic factors, considering temporary variation.

Methods

Relationships between perennial plant species abundances and plant communities were analysed by DCAs. A CCA was performed to study the relationships between floristic composition and edaphic variables. Sixteen soil variables and Pearson correlations between them were considered. Marginal and conditional effects were supported by mixed ANOVA. Statistical analyses were performed to check temporary variation.

Results

DCAs results showed eight vegetation types. CCA showed E.C. as the main gradient, with the succulent halophyte communities growing in high E.C. soils. SAR and percentage of sand were considered as secondary gradients. Finally, the highest values of the edaphic variables were observed, in general, during the cold period.

Conclusions

The main gradient of salinity, together with sodicity and texture gradients, would markedly influence the plant distribution in Mediterranean saltmarshes. Two principal plant zones were observed: succulent zone vs. non-succulent zone, with a specific edaphic distribution for each plant community and for the proposed Limonium morphotypes treatment. A plant-soil model based on these three gradients is here proposed. Our results would complement the previous knowledge about plant-soil relationships in Mediterranean saltmarshes.

     

Interaction between contrasting rice genotypes and soil physical conditions induced by hydraulic stresses typical of alternate wetting and drying irrigation of soil

Background and aims

Drought events, agricultural practices and plant communities influence microbial and soil abiotic parameters which can feedback to fodder production. This study aimed to determine which soil legacies influence plant biomass production and nutritional quality, and its resistance and recovery to extreme weather events.

Methods

In a greenhouse experiment, soil legacy effects on Lolium perenne were examined, first under optimal conditions, and subsequently during and after drought. We used subalpine grassland soils previously cultivated for two years with grass communities of distinct functional composition, and subjected to combinations of climatic stress and simulated management.

Results

The soil legacy of climatic stress increased biomass production of Lolium perenne and its resistance and recovery to a new drought. This beneficial effect resulted from higher nutrient availability in soils previously exposed to climatic stresses due to lower competitive abilities and resistance of microbial communities to a new drought. This negative effect on microbial communities was strongest in soils from previously cut and fertilized grasslands or dominated by conservative grasses.

Conclusion

In subalpine grasslands more frequent climatic stresses could benefit fodder production in the short term, but threaten ecosystem functioning and the maintenance of traditional agricultural practices in the long term.

     

Differential signal sensitivities can contribute to the stability of multispecies bacterial communities

Background

Bacterial species present in multispecies microbial communities often react to the same chemical signal but at vastly different concentrations. The existence of different response thresholds with respect to the same signal molecule has been well documented in quorum sensing which is one of the best studied inter-cellular signalling mechanisms in bacteria. The biological significance of this phenomenon is still poorly understood, and cannot be easily studied in nature or in laboratory models. The aim of this study is to establish the role of differential signal response thresholds in stabilizing microbial communities.

Results

We tested binary competition scenarios using an agent-based model in which competing bacteria had different response levels with respect to signals, cooperation factors or both, respectively. While in previous scenarios fitter species outcompete slower growing competitors, we found that stable equilibria could form if the fitter species responded to a higher chemical concentration level than the slower growing competitor. We also found that species secreting antibiotic could form a stable community with other competing species if antibiotic production started at higher response thresholds.

Conclusions

Microbial communities in nature rely on the stable coexistence of species that necessarily differ in their fitness. We found that differential response thresholds provide a simple and elegant way for keeping slower growing species within the community. High response thresholds can be considered as self-restraint of the fitter species that allows metabolically useful but slower growing species to remain within a community, and thereby the metabolic repertoire of the community will be maintained.

Reviewers

This article was reviewed by Michael Gromiha, Sebastian Maurer-Stroh, István Simon and L. Aravind.

     

Grass vs. tree origin of soil organic carbon under different land-use systems in the Brazilian Cerrado

Aims

This study aimed at assessing whether patch type (i.e., under-shrub soil patch and inter-shrub soil patch) has an effect on soil microbes and how different shrub species altered the soil microbes through understanding soil microbial activity, biomass, and community structure.

Methods

We characterized the soil microbes in under-shrub and inter-shrub soil patches in three shrublands (Artemisia ordosica, Salix psammophila, and Caragana microphylla), respectively, in the Mu Us Desert, China, using microbial activity indicators, chloroform fumigation-extraction analysis, and high-throughput 16S rRNA gene sequencing.

Results

Members of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, Firmicutes, and Gemmatimonadetes were dominant. Inter-shrub soil patch differed from under-shrub soil patch in soil bacterial composition, microbial enzyme activity, and biomass, but not in diversity. Soil collected in A. ordosica shrubland exhibited the highest microbial enzyme activity, biomass, and diversity. Shrub species had significant effects on community structure, primarily the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes.

Conclusions

The results indicated that both shrub species and patch type had effects on soil microbial communities. In shrub-dominated desert ecosystems, spatial heterogeneity of soil nutrients and moisture might not be the main factors underlying variations in bacterial diversity. The different compositions of microbial communities in various shrublands provide a foundation for further research into the mechanisms of soil organic carbon accumulation.

     

Insolation and disturbance history drive biocrust biodiversity in Western Montana rangelands

Background and Aims

Biological soil crust (biocrust) communities, though common and important in the intermountain west, have received little research attention. There are gaps in understanding what influences biocrust species’ abundance and distributions in this ecoregion. Climatic, edaphic, topographic, and biotic forces, in addition to anthropogenic disturbance can all influence the biocrust.

Methods

We determined the relative influence of several possible environmental filters in biocrust communities of western Montana (USA) grasslands at two spatial scales. The larger scale exploited strong topographically-dictated climatic variation across >60km², while the smaller scale focused on differences among distinct microsites within ~700m² plots.

Results

We detected a total of 96 biocrust taxa, mostly lichens. Biocrust richness at each site ranged from 0 to 39 species, averaging 14 species. Insolation, aspect, and disturbance history were the strongest predictors of biocrust richness, abundance, and species turnover across the landscape; soil texture was influential for some biocrust community properties. Steep, north-facing slopes that receive longer periods of shade harbored higher diversity and cover of biocrust than south-facing sites. At a small scale, interspaces among native herbaceous communities supported the greatest diversity of biocrust species, but microsites under shrub canopies supported the greatest cover.

Conclusions

We found that, among the variables investigated, tillage, insolation, soil texture and the associated vegetation community were the most important drivers of biocrust abundance and species richness. This study can inform the practice of restoration and conservation, and also guide future work to improve predictions of biocrust properties.

     

Litter fingerprint on microbial biomass,activity, and community structure in the underlying soil

Aims

Little is known about how plant leaf litter decomposing on the soil surface is affecting microbial communities in the underlying soil. Here we examined the effects of decomposing leaf litter of different initial chemistry on biomass, stoichiometry, community structure and activity of microorganisms in the soil underneath the decaying litter layer.

Methods

Leaf litter from six different neotropical tree species with contrasted quality decomposed on top of a common tropical soil in a laboratory microcosm experiment over 98 days. At the end of the experiment we determined microbial biomass C, N, and P, microbial community structure (PLFA), and community level physiological profiles (CLPP) from the top soil.

Results

Despite growing in a common soil substrate, soil microorganisms were strongly affected by litter species, especially by the soluble litter fraction. While litters with low soluble C content did not affect the soil microbial community, litters with high soluble C content led to an increase of microbial biomass and to a structural shift to relatively more Gram-negative bacteria. Changing community structure resulted in changes of catabolic capacity of microorganisms to metabolize a range of different C substrates. The large differences in leachate N and P among litter species, in contrast, had no effect on soil microbial parameters.

Conclusions

Our data suggest that plant litter decomposing on the soil surface exhibit a strong and predictable leachate C-control over microbial community biomass, structure and function in the underlying soil.

     

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics

Introduction

Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.

Objectives

In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.

Methods

The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.

Results

A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.

Conclusion

The workflow generated repeatable and informative fingerprints for robust metabolome characterization.

     

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys

Background

Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis.

Results

Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion.

Conclusions

RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs.

     

Performance and diversity of polyvinyl alcohol-degrading bacteria under aerobic and anaerobic conditions

Objectives

To compare the degradation performance and biodiversity of a polyvinyl alcohol-degrading microbial community under aerobic and anaerobic conditions.

Results

An anaerobic–aerobic bioreactor was operated to degrade polyvinyl alcohol (PVA) in simulated wastewater. The degradation performance of the bioreactor during sludge cultivation and the microbial communities in each reactor were compared. Both anaerobic and aerobic bioreactors demonstrated high chemical oxygen demand removal efficiencies of 87.5 and 83.6 %, respectively. Results of 16S rDNA sequencing indicated that Proteobacteria dominated in both reactors and that the microbial community structures varied significantly under different operating conditions. Both reactors obviously differed in bacterial diversity from the phyla Planctomycetes, Chlamydiae, Bacteroidetes, and Chloroflexi. Betaproteobacteria and Alphaproteobacteria dominated, respectively, in the anaerobic and aerobic reactors.

Conclusions

The anaerobic–aerobic system is suitable for PVA wastewater treatment, and the microbial genetic analysis may serve as a reference for PVA biodegradation.

     

Community structure and diversity of endophytic bacteria in seeds of three consecutive generations of <Emphasis Type="Italic">Crotalaria pumila</Emphasis> growing on metal mine residues

Aims

We investigated the possible transgenerational transfer of bacterial seed endophytes across three consecutive seed generations of Crotalaria pumila growing on a metal mining site in Mexico.

Methods

Seeds were collected during three successive years in the semi-arid region of Zimapan, Mexico. Total communities of seed endophytes were investigated using DNA extraction from surface sterilized seeds and 454 pyrosequencing of the V5-V7 hypervariable regions of the 16S rRNA gene.

Results

The communities consisted of an average of 75 operational taxonomic units (OTUs); richness and diversity did not change across years. Methylobacterium, Staphylococcus, Corynebacterium, Propionibacterium and eight other OTUs constituted >60% of the community in each generation. The microbiome was dominated by Methylobacterium (present in >80% of samples). Functions associated with the microbiome were C and N fixation, oxidative phosphorylation and photosynthesis activity.

Conclusions

The bacterial endophytic communities were similar across three consecutive seed generations. Among the core microbiome Methylobacterium strains were the most abundant and they can contribute to nutrient acquisition, plant growth promotion and stress resilience to their host in metal contaminated mine residues. Identification of the seed microbiome of C. pumila may lead to novel and more efficient inoculants for microbe-assisted phytoremediation.

     

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

Introduction

Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.

Objectives

(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.

Methods

A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.

Results

Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.

Conclusion

Further efforts are required to improve data sharing in metabolomics.