Initial Community Composition Research Articles

Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations

BackgroundConnecting the composition and function of industrial microbiomes is a major aspiration in microbial biotechnology. Here, we address this question in wine fermentation, a model system where the diversity and functioning of fermenting yeast species are determinant of the flavor and quality of the resulting wines.ResultsFirst, we surveyed yeast communities associated with grape musts collected across wine appellations, revealing the importance of environmental (i.e., biogeography) and anthropic factors (i.e., farming system) in shaping community composition and structure. Then, we assayed the fermenting yeast communities in synthetic grape must under common winemaking conditions. The dominating yeast species defines the fermentation performance and metabolite profile of the resulting wines, and it is determined by the initial fungal community composition rather than the imposed fermentation conditions. Yeast dominance also had a more pronounced impact on wine meta-transcriptome than fermentation conditions. We unveiled yeast-specific transcriptomic profiles, leveraging different molecular functioning strategies in wine fermentation environments. We further studied the orthologs responsible for metabolite production, revealing modules associated with the dominance of specific yeast species. This emphasizes the unique contributions of yeast species to wine flavor, here summarized in an array of orthologs that defines the individual contribution of yeast species to wine ecosystem functioning.ConclusionsOur study bridges the gap between yeast community composition and wine metabolite production, providing insights to harness diverse yeast functionalities with the final aim to producing tailored high-quality wines.74dL8hDE5Rym1TqBfqxSSDVideo

Community Trait Variation Drives Selection on Species Diversity Through Feedback With Predator Density.

Identifying the processes underlying community assembly and dynamics remains a central goal in ecology. Although much research has been devoted to analyzing how environments affect species diversity, fewer studies have resolved the link between the fundamental process of ecological selection and species diversity. It has been suggested that identifying ecological selection by estimating changes in community-weighted variance (CWV) and mean (CWM) of functional traits may help to identify more general rules of community assembly. Here, we asked whether and how selection by predation and competition affect species diversity, and how this is determined by the initial CWV and CWM for traits governing species interactions, as in our case: Competitiveness and defense against a predator. We tracked experimental five-species phytoplankton communities in the presence and absence of a rotifer predator over time. We manipulated the initial community composition so that communities shared at least three of the five species but differed in CWV and CWM for defense against predation. We found that species diversity was highest with higher initial trait distributions and that temporal changes in diversity correlated with trait selection. The initial distributions determined the form of selection over time, with directional selection for defense and competitiveness, followed by reduced selection and an increase in niche availability when the initial trait distribution was low or high. For intermediate initial trait distributions, we observed directional selection in only one trait, followed by stabilizing selection. Differences and changes in selection for defense, competitiveness, and species diversity correlated with the changes in predator density over time. This suggests that the initial trait distribution determined species diversity through a feedback loop with changes in selection on traits and predator density. Overall, our study shows that identifying ecological selection on functional traits can provide a mechanistic understanding of community assembly.

Evidence for regional-scale declines in carabid beetles in old lowland beech forests following a period of severe drought

ContextEvidence for declines in insect populations is growing with climate change being one suspected driver. Forests, however, are still underrepresented in the relevant research. Recent droughts (2018–2020) have severely affected forests in Central Europe and have been linked to declines in carabid abundance, biomass as well as changes in species traits at the local scale.ObjectiveWe tested drought effects on forest carabids at regional scale. We additionally investigated whether variability in drought effects could be explained with the initial community composition and the local environmental context.MethodsWe used generalized linear mixed models to compare data from 1999 to 2001 and 2020 to 2022 across eleven old beech forest sites of high conservation interest in North-East Germany and investigated changes in carabid abundance, biomass, Hill numbers and selected species traits. We then tested additional community-related and environmental predictors to explain spatial variability in changes in biomass.ResultsWe found significant declines in biomass of 65% and in abundance of 51%. There were no significant changes in Hill numbers. We found consistent evidence that declines affected especially larger and less mobile species. Declines and changes in species traits also occurred in strictly protected old-growth beech forests. Among environmental predictors, landscape composition explained local variability in biomass declines best with stronger decline at forest sites with less forest area in their vicinity.ConclusionsOur findings reveal large-scale declines in forest carabids in the context of recent droughts and highlight the exceptional role of landscape composition in this regard. Future insect conservation strategies need to incorporate the landscape context and potential exposure to extreme weather.

Temporal and spatial dynamics within the fungal microbiome of grape fermentation.

Over 6 years, we conducted an extensive survey of spontaneous grape fermentations, examining 3105 fungal microbiomes across 14 distinct grape-growing regions. Our investigation into the biodiversity of these fermentations revealed that a small number of highly abundant genera form the core of the initial grape juice microbiome. Consistent with previous studies, we found that the region of origin had the most significant impact on microbial diversity patterns. We also discovered that certain taxa were consistently associated with specific geographical locations and grape varieties, although these taxa represented only a minor portion of the overall diversity in our dataset. Through unsupervised clustering and dimensionality reduction analysis, we identified three unique community types, each exhibiting variations in the abundance of key genera. When we projected these genera onto global branches, it suggested that microbiomes transition between these three broad community types. We further investigated the microbial community composition throughout the fermentation process. Our observations indicated that the initial microbial community composition could predict the diversity during the early stages of fermentation. Notably, Hanseniaspora uvarum emerged as the primary non-Saccharomyces species within this large collection of samples.

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review.

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium

Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.

Warming and trophic structure tightly control phytoplankton bloom amplitude, composition and succession.

To better identify the responses of phytoplankton blooms to warming conditions as expected in a climate change context, an in situ mesocosm experiment was carried out in a coastal Mediterranean lagoon (Thau Lagoon, South of France) in April 2018. Our objective was to assess both the direct and indirect effects of warming on phytoplankton, particularly those mediated by top-down control. Four treatments were applied: 1) natural planktonic community with ambient water temperature (C); 2) natural planktonic community at +3°C elevated temperature (T); 3) exclusion of larger zooplankton (> 200 μm; mesozooplankton) leaving microzooplankton predominant with ambient water temperature (MicroZ); and 4) exclusion of larger zooplankton (> 200 μm; mesozooplankton) at +3°C elevated temperature (TMicroZ). Warming strongly depressed the amplitude of the phytoplankton bloom as the chlorophyll a concentration was twice lower in the T treatment. This decline under warmer conditions was most likely imputed to increase top-down control by zooplankton. However, removal of mesozooplankton resulted in an opposite trend, with a higher bloom amplitude observed under warmer conditions (MicroZ vs. TMicroZ) pointing at a strong interplay between micro- and mesozooplankton and the effect of warming for the spring phytoplankton blooms. Furthermore, both warming and mesozooplankton exclusion induced shifts in phytoplankton community composition during bloom and post-bloom periods, favoring dinoflagellates and small green algae at the expense of diatoms and prymnesiophytes. Moreover, warming altered phytoplankton succession by promoting an early bloom of small green flagellates, and a late bloom of diatoms. Our findings clearly highlighted the sensitivity of phytoplankton blooms amplitudes, community composition and succession patterns to temperature increases, as well as the key role of initial zooplankton community composition to elicit opposite response in bloom dynamics. It also points out that warmer conditions might favor dinoflagellates and small green algae, irrespective of zooplankton community composition, with potential implications for food web dynamics and energy transfer efficiency under future ocean condition.

Organic amendments modulate the crop yield and rhizospheric bacterial community diversity: a 3-year field study with Cajanus cajan.

Excessive use of chemicals to enhance soil nutrient status and crop yield has resulted in a decline in soil health. Organic farming promotes organic amendments, which help to balance the ecosystem. Understanding the dynamic patterns of belowground microbial populations is essential for developing sustainable agricultural systems. Therefore, the study was designed to evaluate the effect of different agri-practices on rhizospheric bacterial diversity and crop yield in an Indian agricultural system. A 3-year field experiment was set up in a randomized block design using Cajanus cajan as a model crop, comparing conventional farming with organic practice (with animal manure and bio-compost as amendments). Plant and rhizospheric soil samples were collected at the harvest stage for assessing various growth attributes, and for characterizing rhizospheric bacterial diversity. Enhanced crop productivity was seen in conventional farming, with a 2.2-fold increase in grain yield over control. However, over the 3years, an overall positive impact was observed in the bio-compost-based organic amendment, in terms of bacterial abundance, over other treatments. At the harvest stage of the third cropping season, the bacterial diversity in the organic treatments showed little similarity to the initial bacterial community composition of the amendment applied, indicating stabilization along the growth cycles. The study emphasizes the significance of the choice of the amendment for ushering in agricultural sustainability.

The interacting influences of competition, composition and diversity determine successional community change

Abstract Community change is one of the few constants in nature, and the balance of mechanisms influencing this change is central for understanding the structure and functioning of communities and ecosystems. Newly established communities undergo succession and can change in diversity and composition as local environmental change, interspecific interactions and immigration play out over time. Understanding the influence of initial conditions and priority effects (long‐term consequences of the initial community composition and species identity) on community change is critically important for both evaluating ecological theory and predicting restoration outcomes. Here I evaluate how initial experimental conditions in 2012, like initial sown species richness, phylogenetic diversity and early biomass production, along with priority effects caused by the identity of sown species, influence subsequent herbaceous plant community composition and the number of colonizing species after 9 years of uninterrupted natural colonization. I found that sown phylogenetic diversity (measured as mean pairwise distance) indirectly affected the number of colonizing species by increasing biomass production early on and plots with more biomass in 2012 were colonized by fewer species. Individual species influenced the number of colonizing species with taller species reducing the number of colonists and some shorter species subject to a greater number of colonists. Synthesis. Taken together, these results indicate that initial composition influences the number of colonizing species via community‐wide competition. These findings suggest that restoration outcomes can be greatly influenced by decisions about sown species composition and early management practices.

Local environmental context drives heterogeneity of early succession dynamics in alpine glacier forefields

Abstract. Glacier forefields have long provided ecologists with a model to study patterns of plant succession following glacier retreat. While plant-survey-based approaches applied along chronosequences provide invaluable information on plant communities, the “space-for-time” approach assumes environmental uniformity and equal ecological potential across sites and does not account for spatial variability in initial site conditions. Remote sensing provides a promising avenue for assessing plant colonization dynamics using a so-called “real-time” approach. Here, we combined 36 years of Landsat imagery with extensive field sampling along chronosequences of deglaciation for eight glacier forefields in the southwestern European Alps to investigate the heterogeneity of early plant succession dynamics. Based on the two complementary and independent approaches, we found strong variability in the time lag between deglaciation and colonization by plants and in subsequent growth rates and in the composition of early plant succession. All three parameters were highly dependent on the local environmental context, i.e., neighboring vegetation cover and energy availability linked to temperature and snowmelt gradients. Potential geomorphological disturbance did not emerge as a strong predictor of succession parameters, which is perhaps due to insufficient spatial resolution of predictor variables. Notably, the identity of pioneer plant species was highly variable, and initial plant community composition had a much stronger influence on plant assemblages than elapsed time since deglaciation. Overall, both approaches converged towards the conclusion that early plant succession is not stochastic as previous authors have suggested but rather determined by local ecological context. We discuss the importance of scale in deciphering the complexity of plant succession in glacier forefields and provide recommendations for improving botanical field surveys and using Landsat time series in glacier forefield systems. Our work demonstrates complementarity between remote sensing and field-based approaches for both understanding and predicting future patterns of plant succession in glacier forefields.

Environmental factors contributing to the convergence of bacterial community structure during indigo reduction.

Indigo is solubilized through the reducing action of the microbiota that occurs during alkaline fermentation of composted leaves of Polygonum tinctorium L. (sukumo). However, the environmental effects on the microbiota during this treatment, as well as the mechanisms underlying the microbial succession toward stable state remain unknown. In this study, physicochemical analyses and Illumina metagenomic sequencing was used to determine the impact pretreatment conditions on the subsequent initiation of bacterial community transition and their convergence, dyeing capacity and the environmental factors critical for indigo reducing state during aging of sukumo. The initial pretreatment conditions analyzed included 60°C tap water (heat treatment: batch 1), 25°C tap water (control; batch 2), 25°C wood ash extract (high pH; batch 3) and hot wood ash extract (heat and high pH; batch 4), coupled with successive addition of wheat bran from days 5 to 194. High pH had larger impact than heat treatment on the microbiota, producing more rapid transitional changes from days 1 to 2. Although the initial bacterial community composition and dyeing intensity differed during days 2-5, the microbiota appropriately converged to facilitate indigo reduction from day 7 in all the batches, with Alkaliphilus oremalandii, Amphibacillus, Alkalicella caledoniensis, Atopostipes suicloalis and Tissierellaceae core taxa contributing to the improvement of when the dyeing intensity. This convergence is attributed to the continuous maintenance of high pH (day 1 ~) and low redox potential (day 2~), along with the introduction of wheat bran at day 5 (day 5~). PICRUSt2 predictive function profiling revealed the enrichment of phosphotransferease system (PTS) and starch and sucrose metabolism subpathways key toward indigo reduction. Seven NAD(P)-dependent oxidoreductases KEGG orthologs correlating to the dyeing intensity was also identified, with Alkalihalobacillus macyae, Alkalicella caledoniensis, and Atopostipes suicloalis contributing significantly toward the initiation of indigo reduction in batch 3. During the ripening period, the staining intensity was maintained by continuous addition of wheat bran and the successive emergence of indigo-reducing bacteria that also contributed to material circulation in the system. The above results provide insight into the interaction of microbial system and environmental factors in sukumo fermentation.

Species dynamics in natural bacterial communities over multiple rounds of propagation.

Our experimental work illustrates how microbial ecosystems can be shaped by selective pressures over long-term ecological time scales. Natural microbial ecosystems generally consist of various co-existing species, where community composition describes the frequency at which species or types are present. Overall functionality of the system is achieved by interacting species. Upon short-term selection, for instance by transfer to a novel environment, community composition and functionality may change in a process referred to as species sorting. Various factors, such as initial community composition and selective pressures from the environment, may influence this change. Mabisi is a traditional fermented food from Zambia that naturally contains a bacterial community of around twenty unique bacterial types. We used six comparable but different natural bacterial Mabisi communities, each split into five identical replicates, for 16 propagation cycles in a novel, common laboratory environment. Composition of the bacterial communities changed upon propagation. The influence of four main factors on community composition, i.e. initial composition (history), impact of the environment (adaptation), changes due to interaction between species and random processes (chance) in species dynamics, was tested using maximum likelihood ratios. Initial community composition seemed to determine the change in community composition, followed by random processes. Interestingly, we observed convergence at the level of ecosystem functionality, which was measured as profiles of metabolic output. This suggests different combinations of species or types can achieve similar eco-system functionality.

Initial community composition determines the long-term dynamics of a microbial cross-feeding interaction by modulating niche availability

Multi-step substrate consumption pathways can promote microbial biodiversity via cross-feeding. If one cell type preferentially consumes a primary substrate rather than the subsequently formed intermediates, then other cell types can specialize in consuming the intermediates. While this mechanism for promoting biodiversity is established, predicting the long-term persistence of such cross-feeding interactions remains challenging. Under what conditions will the interaction (and thus biodiversity) persist or disappear? To address this question, we propagated co-cultures of two isogenic strains of the bacterium Pseudomonas stutzeri. One completely reduces nitrate to nitrogen gas but preferentially reduces nitrate rather than nitrite (referred to as the generalist), while the other only reduces nitrite to nitrogen gas (referred to as the specialist). We found that the two strains coexist via nitrite cross-feeding when grown together, but the initial ratio of specialist-to-generalist (rS/G) determines the long-term dynamics of the co-culture. Co-cultures with large initial rS/Gs converge to the same rS/G and persist thereafter. Co-cultures with small initial rS/Gs also converge to the same rS/G but then become increasingly dominated by the generalist. The likely cause of these different dynamics is that the initial rS/G determines the initial environment, which in turn determines the initial selection pressures and phenotypes acquired by the generalist. Our results demonstrate that initial community composition controls the long-term dynamics and persistence of a cross-feeding interaction, and is therefore an important factor for community development and for engineering communities to achieve desired outcomes.

Tree species identity is the predominant modulator of the effects of soil fauna on leaf litter decomposition

Soil fauna is one of the key drivers of the litter decomposition at both local and global scales, yet the role of tree species in mediating the effects of soil fauna on litter decomposition remains elusive. We conducted a field experiment using litterbags with three different mesh sizes that allowed access of microfauna (0.1 mm), micro- and mesofauna (2 mm), and total soil fauna (5 mm) to evaluate the decomposition of foliar litter of two tree species associated with arbuscular mycorrhizal (AM) fungi and three tree species associated with ectomycorrhizal (ECM) fungi in six Danish common garden sites. We also assessed how differences in initial litter quality, soil properties, and microbial community composition among the tree species may affect litter decomposition as well as soil fauna effects on litter decomposition. Results showed that (1) litter mass loss varied significantly among different mesh sizes and tree species, with litter decomposition rates (k) ranging from 0.273 to 3.482; (2) the access of mesofauna significantly increased litter k of 0.658 for AM and 0.396 for ECM tree species with no access of soil fauna 255 and 92%, respectively, while the access of both meso- and macrofauna increased k by 265 and 108% for AM and ECM trees, respectively; (3) tree species identity, mycorrhizal association, initial litter quality, soil properties, microbial community composition, and ambient soil fauna biomass were all significantly influencing factors on litter decomposition, but tree species identity was the dominant factor regardless of litterbag mesh size; and (4) the effects of mesofauna on litter decomposition were predominantly controlled by tree species identity, initial litter Mg concentration and lignin:N ratio, while the small additional impact of macrofauna access was not well explained by any of the assessed factors. Overall, our results suggest that tree species affect litter decomposition via different stimulation of soil fauna functioning, and that AM and ECM associated tree species differ in the degree to which soil fauna stimulates litter decomposition. However, the pattern was not entirely consistent as litter decomposition rates for the ECM associated lime were stimulated to the same extent as rates for the AM associated tree species ash and maple. Overall, our results suggested that soil meso- and macrofauna communities may enhance tree species effects on litter decomposition as well as incorporation of litter C into mineral soil.

Methane production potential of pulp mill sludges: microbial community and substrate constraints.

Sludges from pulp and paper mills represent a major ecological and environmental cost, and anaerobic digestion represents a method of waste reduction and energy recovery for these mills. This study compared methane production potential and microbial communities across 11 primary- and biosludges from five pulp and paper mills using various mill processes. We measured methane production from sludges in anaerobic batch reactor experiments over 64 days. Sludges were incubated with and without added substrate to test for organic substrate limitation versus inhibition of methanogens. Initial microbial communities and changes to community composition were determined using Illumina MiSeq for metabarcoding of bacterial and archaeal 16S rRNA genes. Mean methane production potential varied greatly between sludges (0.002-79mL CH4 g-1 TS). Among primary sludges, kraft mill sludge produced more methane than other mill types. For these other mills, biosludge produced more methane than primary sludge, which had evidence of methanogen inhibition. Microbial communities and diversity were influenced by the initial community composition, and high methane production was only seen in sludges with high diversity. A number of sludges innately produced substantial methane and may be targets for further modelling and larger scale testing of anaerobic digestion.

Effect of Lowered pH on Community Composition, Growth and Cell Morphology of Freshwater Phytoplankton

This experiment studied the probable effects of lowered pH (6.5 to 5.0) on four freshwater phytoplankton species Chlorella vulgaris Beyerinck, Scenedesmus quadricauda (Turpin) Brebbison, Euglena granulata (Klebs) Schmitz and Gomphonema subtile Ehrenberg. The initial community composition was 2:2:1:1 for the four taxa respectively, which changed to 1.7:1.6:1:1 in pH 6.0, 1.6:2:1.6:1 in pH 5.5 and 1.2:2:1.8:1 in pH 5.0. The two chlorophytes showed almost gradual decreasing in growth rates and cell densities with the decreases in pH values, while diatom E. granulata showed more tolerance in a wide range of pH (6.5 to 5.5). Conspicuous changes in total biomass first observed in pH 6.0 and it reached the drastic level in pH 5.0. Moreover, significant changes in cell size of S. qaudricuada and E. granulata were found in pH 5.0 only. This lowered pH range has no effects on cell shape of the studied phytoplankton species.

Competition dynamics in long-term propagations of Schizosaccharomyces pombe strain communities.

Experimental evolution studies with microorganisms such as bacteria and yeast have been an increasingly important and powerful tool to draw long‐term inferences of how microbes interact. However, while several strains of the same species often exist in natural environments, many ecology and evolution studies in microbes are typically performed with isogenic populations of bacteria or yeast. In the present study, we firstly perform a genotypic and phenotypic characterization of two laboratory and eight natural strains of the yeast Schizosaccharomyces pombe. We then propagated, in a rich resource environment, yeast communities of 2, 3, 4, and 5 strains for hundreds of generations and asked which fitness‐related phenotypes—maximum growth rate or relative competitive fitness—would better predict the outcome of a focal strain during the propagations. While the strain's growth rates would wrongly predict long‐term coexistence, pairwise competitive fitness with a focal strain qualitatively predicted the success or extinction of the focal strain by a simple multigenotype population genetics model, given the initial community composition. Interestingly, we have also measured the competitive fitness of the ancestral and evolved communities by the end of the experiment (≈370 generations) and observed frequent maladaptation to the abiotic environment in communities with more than three members. Overall, our results aid establishing pairwise competitive fitness as good qualitative measurement of long‐term community composition but also reveal a complex adaptive scenario when trying to predict the evolutionary outcome of those communities.

Impacts of pH and salinity on community composition, growth and cell morphology of three freshwater phytoplankton

Impacts of climate change on phytoplankton species are very focusing issues nowadays. This research explored the probable impacts of different pH (pH 5.90 to 9.10) and salinity (0.60 to 3.0 ppt) concentrations on freshwater phytoplankton Chlorella vulgaris, Euglena granulata and Scenedesmus quadricauda. The initial community composition was 4:2:1 for the three taxa, which changed to 6:3:1, 6:2:1, 6:3.5:1 and 9:4:1 in pH 5.90, pH 9.10 and salinity 2.20 and 3.0 ppt respectively. E. granulata showed more tolerance in a wide range of pH (pH 5.90 to 8.30) based on growth rate studies. The other two species showed growth rates reduction gradually in changes with pH and salinity concentrations. Conspicuous changes of total biomass were seen in pH 5.90 and 9.10, and salinity 2.20 and 3.0 ppt conditions. Moreover, significant changes in cell morphology were found in pH 9.10 and 3.0 ppt salinity. The authors concluded that as group, the Chlorophytes were more susceptible than the diatom in these variable pH and salinity conditions, while S. quadricauda was comparatively more vulnerable as a single species.

Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors.

ABSTRACTRecent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors.IMPORTANCE The initial assembly of the plant microbiome may establish the trajectory of forthcoming microbiome states, which could determine the overall future health of the plant. However, while much is known about the initial microbiome assembly of grasses and agricultural crops, less is known about the initial microbiome of long-lived trees, such as poplar (Populus spp.). Thus, a greater understanding of initial plant microbiome assembly in an ecologically and economically important plant such as Populus is highly desirable. Here, we show that the initial microbiome community composition and assembly in the first growing season of Populus is temporally dynamic and is determined by a combination of both selective and stochastic factors. Our findings could be used to prescribe ecologically informed microbial inoculations and better predict the composition of the Populus microbiome into the future and to better understand its influence on plant health.

Substrate Pre-loading Influences Initial Colonization of GAC Biofilter Biofilms

Microbial community composition and stability affect pollutant removal for biological/granular activated carbon (BAC/GAC) processes. Here, we pre-loaded the organic carbon substrates sucrose, lactose, and Lysogeny Broth (LB) medium onto new GAC prior to use and then tested whether this substrate pre-loading promoted development of biofilms with high coverage that remained stable for prolonged operational periods. Temporal dynamics of the biomass and microbial community on the GAC were monitored via flow cytometry (FCM) and sequencing, respectively, in both batch and continuous-flow experiments. In comparison with the non-loaded GAC (control), the initial biofilm biomass on substrate-loaded GAC was 3–114 times higher, but the initial richness was considerably lower (only accounting for 13–28% of the control). The initial community compositions were significantly different between batch and continuous-flow column experiments, even when loaded with the same substrates. In the continuous-flow column experiments, both biomass and microbial community composition became remarkably similar to the control filters after 64 days of operation. From these findings, we conclude that substrate-loaded GAC could enhance initial colonization, affecting both biomass and microbial community composition. However, the biomass and composition did not remain stable during long-term operation due to continuous dispersal and competition from influent bacteria.