Whole-community Level Research Articles

Climate Justice and Climate Adaptation in California: Indigenous Community Climate Adaptation Leadership and Opportunities for Scientific Collaboration

Abstract Climate and weather-related disasters in California illustrate the need for immediate climate change action—both mitigation to reduce impacts and adaptation to protect our communities, relatives, and the ecosystems we depend upon. Indigenous frontline communities face even greater threats from climate impacts due to historical and political legacies of environmental injustice. Climate change adaptation actions have proven challenging to implement as communities struggle to access necessary climate data at appropriate scales, identify effective strategies that address community priorities, and obtain resources to act at a whole-community level. In this paper, we present three examples of Indigenous communities in California that have used a climate justice approach to climate change adaptation. These communities are drawing upon community knowledge and expertise to address the challenges of adaptation planning and taking actions that center community priorities. The three cases address emergency preparation and response, cultural burning and fire management, and community organizing and social cohesion. Across these spheres, they illustrate the ways in which a community-based and climate justice-focused approach to adaptation can be effective in addressing current threats while also addressing the legacy of imposed, socially constructed vulnerability and environmental injustices. Because we recognize the need for multiple knowledges and skills in adaptation actions, we include recommendations that have emerged based on what has been learned through these long-standing and engaged participatory research collaborations for climate scientists who wish to contribute to climate justice-focused adaptation efforts by using scientific data to support—not supplant—community efforts, target funding toward genuine community engagement and adaptation actions, and become aware of the historical and political legacies that created the climate vulnerabilities and injustices evident today.

Evaluating a potential model to analyze the function of the gut microbiota of the giant panda.

To contribute to the conservation of endangered animals, the utilization of model systems is critical to analyze the function of their gut microbiota. In this study, the results of a fecal microbial transplantation (FMT) experiment with germ-free (GF) mice receiving giant panda or horse fecal microbiota showed a clear clustering by donor microbial communities in GF mice, which was consistent with the results of blood metabolites from these mice. At the genus level, FMT re-established approximately 9% of the giant panda donor microbiota in GF mice compared to about 32% for the horse donor microbiota. In line with this, the difference between the panda donor microbiota and panda-mice microbiota on whole-community level was significantly larger than that between the horse donor microbiota and the horse-mice microbiota. These results were consistent with source tracking analysis that found a significantly higher retention rate of the horse donor microbiota (30.9%) than the giant panda donor microbiota (4.0%) in GF mice where the microbiota remained stable after FMT. Further analyzes indicated that the possible reason for the low retention rate of the panda donor microbiota in GF mice was a low relative abundance of Clostridiaceae in the panda donor microbiota. Our results indicate that the donor microbiota has a large effect on GF mice microbiota after FMT.

Reconstruction of a Soil Microbial Network Induced by Stress Temperature.

ABSTRACTThe microbial community is viewed as a network of diverse microorganisms connected by various interspecific interactions. While the stress gradient hypothesis (SGH) predicts that positive interactions are favored in more stressful environments, the prediction has been less explored in complex microbial communities due to the challenges of identifying interactions. Here, by applying a nonlinear time series analysis to the amplicon-based diversity time series data of the soil microbiota cultured under less stressful (30°C) or more stressful (37°C) temperature conditions, we show how the microbial network responds to temperature stress. While the genera that persisted only under the less stressful condition showed fewer positive effects, the genera that appeared only under the more stressful condition received more positive effects, in agreement with SGH. However, temperature difference also induced reconstruction of the community network, leading to an increased proportion of negative interactions at the whole-community level. The anti-SGH pattern can be explained by the stronger competition caused by increased metabolic rate and population densities.IMPORTANCE By combining amplicon-based diversity survey with recently developed nonlinear analytical tools, we successfully determined the interaction networks of more than 150 natural soil microbial genera under less or more temperature stress and explored the applicability of the stress gradient hypothesis to soil microbiota, shedding new light on the well-known hypothesis.

Weed germinable seedbanks of rice-wheat systems in the Eastern Indo-Gangetic Plains: Do tillage and edaphic factors explain community variation?

Zero tillage (ZT) is widely promoted throughout India's Eastern Indo‐Gangetic Plains (IGP) because of its potential to increase wheat productivity and resilience to abiotic stresses. Weeds remain a major barrier to ZT adoption, yet it remains unclear how ZT will influence weed communities in the Eastern‐IGP. The primary objective of this study was to characterise the composition of the germinable weed seedbank sampled just prior to the wheat phase of rice–wheat farms in Bihar and Eastern Uttar Pradesh, and examine whether adoption of ZT wheat has shifted weed community composition compared to conventional tillage (CT). Additionally, we examined whether edaphic properties and topography (upland vs. lowland) explain variation in germinable weed seedbank communities. In December 2014, we evaluated the germinable seedbank from 72 fields differing in their historic (>=3 year) tillage practices (ZT vs. CT) in three regions: Samastipur–Vaishali–Muzaffarpur (SVM), Ara–Buxar and Maharajgunj–Kushinagar. Weed community composition and species richness varied by region and topography. ZT adoption was associated with lower relative density of Chenopodium album in the germinable seedbank and lower emergence of Phalaris minor seedlings within farmers’ fields. In upland topographies of the SVM region, ZT adoption was also associated with greater relative abundance of Solanum nigrum in the weed seedbank. However, differences between tillage systems in individual species were not large enough to result in detection of differences at the whole‐community level. Variation in edaphic properties, most notably soil texture and pH, explained 51% of the variation in the weed seedbank community. Our work suggests several frequent but poorly understood species (e.g. Mazus pumilus and Grangea maderaspatana) in Eastern IGP for which future research should quantify their effects on crop yields. Finally, future work surveying weed species abundance at harvest could further determine the dominant problematic species in these regions.

Tree-size dimension inequality shapes aboveground carbon stock across temperate forest strata along environmental gradients

It is generally well-explored that overstorey stratum regulates understorey stratum through the dominant role over the available resources in forests. However, the relationships amongst topography, soil nutrients, species diversity, tree-size dimension inequality and aboveground carbon (AGC) stock across forest strata remain debated in forest ecosystems. Here, we assumed that soil nutrients, species diversity and tree-size dimension inequality promote AGC stock in overstorey stratum, which in turn regulate AGC stock in understorey stratum in natural temperate forests. To do so, using several structural equation models (SEMs) on the data from 104 temperate forest plots in Northern Iran, we assessed the effects of tree-size dimension inequality as well as the individual effects of either inequality in tree diameter, height, basal area, crown volume, or crown area, species diversity, soil nutrients and topographic factors on AGC in each forest stratum and at whole-community level as well as the effects of overstorey on understorey (i.e., joint SEMs). Results show that AGC stock in overstorey stratum was mainly determined by tree-size dimension inequality rather than by species diversity on nutrient-rich soils but controlled by topographic factors related to light availability. In understorey stratum, only basal area inequality was the strong driver of AGC stock, but overstorey overruled the effects of understorey drivers on understorey AGC stock. Specifically, overstorey tree-size dimension inequality increased but AGC stock decreased the AGC stock of understorey. The observed mechanism and effects at overstorey stratum were nearly similar to whole-community level. This study shows that overstorey stratum regulates understorey through dominant occupancy on the light availability and soil nutrients. We suggest that integrative modeling of overstorey and understorey strata based on tree height, diameter and crown inequality may better enhance our understanding and extend the existing debate based on multiple drivers of forest functioning, which may help to provide specific guidelines for forest management.

Patterns of Relative and Quantitative Abundances of Marine Bacteria in Surface Waters of the Subtropical Northwest Pacific Ocean Estimated With High-Throughput Quantification Sequencing.

Bacteria play a pivotal role in shaping ecosystems and contributing to elemental cycling and energy flow in the oceans. However, few studies have focused on bacteria at a trans-basin scale, and studies across the subtropical Northwest Pacific Ocean (NWPO), one of the largest biomes on Earth, have been especially lacking. Although the recently developed high-throughput quantitative sequencing methodology can simultaneously provide information on relative abundance, quantitative abundance, and taxonomic affiliations, it has not been thoroughly evaluated. We collected surface seawater samples for high-throughput, quantitative sequencing of 16S rRNA genes on a transect across the subtropical NWPO to elucidate the distribution of bacterial taxa, patterns of their community structure, and the factors that are potentially important regulators of that structure. We used the quantitative and relative abundances of bacterial taxa to test hypotheses related to their ecology. Total 16S rRNA gene copies ranged from 1.86 × 108 to 1.14 × 109 copies L−1. Bacterial communities were distributed in distinct geographical patterns with spatially adjacent stations clustered together. Spatial considerations may be more important determinants of bacterial community structures than measured environmental variables. The quantitative and relative abundances of bacterial communities exhibited similar distribution patterns and potentially important determinants at the whole-community level, but inner-community connections and correlations with variables differed at subgroup levels. This study advanced understanding of the community structure and distribution patterns of marine bacteria as well as some potentially important determinants thereof in a subtropical oligotrophic ocean system. Results highlighted the importance of considering both the quantitative and relative abundances of members of marine bacterial communities.

Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin.

Dietary composition and antibiotic use have major impacts on the structure and function of the gut microbiome, often resulting in dysbiosis. Despite this, little research has been done to explore the role of host diet as a determinant of antibiotic-induced microbiome disruption. Here, we utilize a multi-omic approach to characterize the impact of Western-style diet consumption on ciprofloxacin-induced changes to gut microbiome structure and transcriptional activity. We found that Western diet consumption dramatically increased Bacteroides abundances and shifted the community toward the metabolism of simple sugars and mucus glycoproteins. Mice consuming a Western-style diet experienced a greater expansion of Firmicutes following ciprofloxacin treatment than those eating a control diet. Transcriptionally, we found that ciprofloxacin reduced the abundance of tricarboxylic acid (TCA) cycle transcripts on both diets, suggesting that carbon metabolism plays a key role in the response of the gut microbiome to this antibiotic. Despite this, we observed extensive diet-dependent differences in the impact of ciprofloxacin on microbiota function. In particular, at the whole-community level we detected an increase in starch degradation, glycolysis, and pyruvate fermentation following antibiotic treatment in mice on the Western diet, which we did not observe in mice on the control diet. Similarly, we observed diet-specific changes in the transcriptional activity of two important commensal bacteria, Akkermansia muciniphila and Bacteroides thetaiotaomicron, involving diverse cellular processes such as nutrient acquisition, stress responses, and capsular polysaccharide (CPS) biosynthesis. These findings demonstrate that host diet plays a role in determining the impacts of ciprofloxacin on microbiome composition and microbiome function.IMPORTANCE Due to the growing incidence of disorders related to antibiotic-induced dysbiosis, it is essential to determine how our "Western"-style diet impacts the response of the microbiome to antibiotics. While diet and antibiotics have profound impacts on gut microbiome composition, little work has been done to examine their combined effects. Previous work has shown that nutrient availability, influenced by diet, plays an important role in determining the extent of antibiotic-induced disruption to the gut microbiome. Thus, we hypothesize that the Western diet will shift microbiota metabolism toward simple sugar and mucus degradation and away from polysaccharide utilization. Because of bacterial metabolism's critical role in antibiotic susceptibility, this change in baseline metabolism will impact how the structure and function of the microbiome are impacted by ciprofloxacin exposure. Understanding how diet modulates antibiotic-induced microbiome disruption will allow for the development of dietary interventions that can alleviate many of the microbiome-dependent complications of antibiotic treatment.

Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes.

It is a central ecological goal to explore the effects of global change factors on soil microbial communities. The vast functional gene repertoire of soil microbial communities is composed of both core and accessory genes, which may be governed by distinct drivers. This intuitive hypothesis, however, remains largely unexplored. We conducted a 5-year nitrogen and water addition experiment in the Eurasian steppe and quantified microbial gene diversity via shotgun metagenomics. Nitrogen addition led to an 11-fold increase in the abundance (based on quantitative PCR [qPCR]) of ammonia-oxidizing bacteria, which have mainly core community genes and few accessory community genes. Thus, nitrogen addition substantially increased the relative abundance of many core genes at the whole-community level. Water addition stimulated both plant diversity and microbial respiration; however, increased carbon/energy resources from plants did not counteract increased respiration, so soil carbon/energy resources became more limited. Thus, water addition selected for microorganisms with genes responsible for degrading recalcitrant soil organic matter. Accordingly, many other microorganisms without these genes (but likely with other accessory community genes due to relatively stable average microbial genome size) were selected against, leading to the decrease in the diversity of accessory community genes. In summary, nitrogen addition primarily affected core community genes through nitrogen-cycling processes, and water addition primarily regulated accessory community genes through carbon-cycling processes. Although both gene components may significantly respond as the intensity of nitrogen/water addition increases, our results demonstrated how these common global change factors distinctly impact each component.IMPORTANCE Our results demonstrated increased ecosystem nitrogen and water content as the primary drivers of the core and accessory components of soil microbial community functional diversity, respectively. Our findings suggested that more attention should be paid to certain components of community functional diversity under specific global change conditions. Our findings also indicated that microbial communities have adapted to nitrogen addition by strengthening the function of ammonia oxidization to deplete the excess nitrogen, thus maintaining ecosystem homeostasis. Because community gene richness is primarily determined by the presence/absence of accessory community genes, our findings further implied that strategies such as maintaining the amount of soil organic matter could be adopted to effectively improve the functional gene diversity of soil microbial communities subject to global change factors.

Redbiom: a Rapid Sample Discovery and Feature Characterization System.

Meta-analyses at the whole-community level have been important in microbiome studies, revealing profound features that structure Earth's microbial communities, such as the unique differentiation of microbes from the mammalian gut relative to free-living microbial communities, the separation of microbiomes in saline and nonsaline environments, and the role of pH in driving soil microbial compositions. However, our ability to identify the specific features of a microbiome that differentiate these community-level patterns have lagged behind, especially as ever-cheaper DNA sequencing has yielded increasingly large data sets. One critical gap is the ability to search for samples that contain specific features (for example, sub-operational taxonomic units [sOTUs] identified by high-resolution statistical methods for removing amplicon sequencing errors). Here we introduce redbiom, a microbiome caching layer, which allows users to rapidly query samples that contain a given feature, retrieve sample data and metadata, and search for samples that match specified metadata values or ranges (e.g., all samples with a pH of >7), implemented using an in-memory NoSQL database called Redis. By default, redbiom allows public anonymous sample access for over 100,000 publicly available samples in the Qiita database. At over 100,000 samples, the caching server requires only 35 GB of resident memory. We highlight how redbiom enables a new type of characterization of microbiome samples and provide tutorials for using redbiom with QIIME 2. redbiom is open source under the BSD license, hosted on GitHub, and can be deployed independently of Qiita to enable search of proprietary or clinically restricted microbiome databases.IMPORTANCE Although analyses that combine many microbiomes at the whole-community level have become routine, searching rapidly for microbiomes that contain a particular sequence has remained difficult. The software we present here, redbiom, dramatically accelerates this process, allowing samples that contain microbiome features to be rapidly identified. This is especially useful when taxonomic annotation is limited, allowing users to identify environments in which unannotated microbes of interest were previously observed. This approach also allows environmental or clinical factors that correlate with specific features, or vice versa, to be identified rapidly, even at a scale of billions of sequences in hundreds of thousands of samples. The software is integrated with existing analysis tools to enable fast, large-scale microbiome searches and discovery of new microbiome relationships.

Community structural differences shape microbial responses to high molecular weight organic matter.

The extent to which differences in microbial community structure result in variations in organic matter (OM) degradation is not well understood. Here, we tested the hypothesis that distinct marine microbial communities from North Atlantic surface and bottom waters would exhibit varying compositional succession and functional shifts in response to the same pool of complex high molecular weight (HMW-OM). We also hypothesized that microbial communities would produce a broader spectrum of enzymes upon exposure to HMW-OM, indicating a greater potential to degrade these compounds than reflected by initial enzymatic activities. Our results show that community succession in amended mesocosms was congruent with cell growth, increased bacterial production and most notably, with substantial shifts in enzymatic activities. In all amended mesocosms, closely related taxa that were initially rare became dominant at time frames during which a broader spectrum of active enzymes were detected compared to initial timepoints, indicating a similar response among different communities. However, succession on the whole-community level, and the rates, spectra and progression of enzymatic activities, reveal robust differences among distinct communities from discrete water masses. These results underscore the crucial role of rare bacterial taxa in ocean carbon cycling and the importance of bacterial community structure for HMW-OM degradation.

Consequences of phylogenetic conservativeness and functional trait similarity on aboveground biomass vary across subtropical forest strata

Phylogenetically close and/or functionally similar species are generally assumed to compete more strongly than phylogenetically distant and functionally dissimilar species in a community. However, how coexisting species with different extents of variation in their phylogeny and functional traits determine community function such as aboveground biomass across forest strata remains an unresolved question. We hypothesize that phylogenetically close and functionally similar species of overstorey, but phylogenetically distant and functionally dissimilar species of understorey drive high aboveground biomass in structurally-complex subtropical forests. Multiple linear regression models were used to test the consequences of phylogenetic distances and functional traits of tree species, and environmental factors on aboveground biomass in a subtropical forest in Eastern China. Overstorey aboveground biomass was driven by functional evenness (β = −0.21), phylogenetic species evenness (β = −0.27) and phylogenetic diversity (β = 0.31). Understorey aboveground biomass was driven by functional richness (β = 0.25), functional dispersion (β = −0.21), soil nutrients (β = −0.17) and topography (β = 0.36). Whole-community aboveground biomass was best predicted by functional divergence (β = 0.36), functional dispersion (β = −0.38), phylogenetic diversity (β = 0.24) and soil nutrients (β = −0.20). Our results suggest that understorey aboveground biomass is great for groups of phylogenetically distant species having high functional richness due to specific functional strategy shared by all the species. By contrast, high overstorey aboveground biomass is related with groups of phylogenetically close species having low functional trait diversity (i.e. high functional trait similarity) due to the evolutionary relatedness. The mechanism at the whole-community level might result from the mixed effects of overstorey evolutionary relatedness and understorey functional trait diversity. This study highlights that disentangling the effects of evolutionary diversity and functional trait diversity across forest strata may be helpful for better understanding of ecological mechanisms for predicting aboveground biomass in a subtropical forest.

The mediation roles of intraspecific and interspecific functional trait diversity for linking the response of aboveground biomass to species richness across forest strata in a subtropical forest

Intraspecific functional trait diversity (FTD) has improved our understandings about the key mechanisms of species coexistence in plant communities. Yet, little is known about whether and how intraspecific and interspecific FTD mediate the response of aboveground biomass to species richness across forest strata (i.e. overstorey and understorey) and at whole-community in forests. To address this question, we tested the direct and indirect responses of aboveground biomass to species richness via intraspecific and interspecific FTD based on specific leaf area (FTDSLA) and leaf dry matter content (FTDLDMC) using structural equation modeling, in addition to the effects of soil nutrients, across 125 plots in a 5-ha subtropical forest in Eastern China. Results showed that intraspecific FTD mediates the response of aboveground biomass to species richness at overstorey and understorey strata, and whole-community level, while interspecific FTD did so at understorey strata only. At overstorey strata, 14% of the variation in aboveground biomass was accounted by the strong direct positive effect of species richness only. At understorey strata, soil nutrients had a strong negative direct effect followed by positive effects of species richness and FTDLDMC on aboveground biomass with 44–45% of the variation in both intraspecific and interspecific FTD models. At whole community level, 14% of the variation in aboveground biomass was explained by the strong positive direct effect of species richness followed by negative direct effect of intraspecific FTDSLA. Intraspecific and interspecific FTDLDMC had positively mediated the response of aboveground biomass to species richness at understorey strata through niche differentiation. Intraspecific FTD had negligible mediation role, whereas interspecific FTD had no role, for linking the response of aboveground biomass to species richness at overstorey strata, indicating that only dominant species with a specific functional strategy may largely determine community trait space. Intraspecific FTDSLA had negative relationship with aboveground biomass at the whole-community, probably due to the presence of a few large trees occupying larger niche space in a community. We conclude that intraspecific versus interspecific FTD plays a central role for linking the direct and indirect responses of aboveground biomass to species richness, but these relationships depend on the forest strata of a community.

Abiotic and biotic drivers of aboveground biomass in semi-steppe rangelands

Rangelands play an important role in the biodiversity conservation and ecosystem functions. Yet, few studies have assessed the effects of biotic and abiotic factors on aboveground biomass across plant growth forms and at whole-community level in rangelands. Here, we hypothesized that aboveground biomass is driven by both biotic (plant coverage, species richness and evenness) and abiotic factors (soil textural properties and topographic factors) but biotic factors may best predict aboveground biomass, probably due to small spatial scale. To test this hypothesis, we performed multiple linear mixed model by including abiotic and biotic factors as fixed effects while sites aspects and plant community types across sites, and disturbance intensities as random effects, using data from 735 quadrats across 35 sites in semi-steppe rangelands in Iran. The optimal model for shrubs showed that aboveground biomass was positively related to plant coverage, species richness, elevation, sand, silt and clay. Aboveground biomass of forbs and grasses was positively related to plant coverage, species richness, elevation and slope. Whole-community aboveground biomass was positively related to plant coverage, species richness and elevation, but negatively to species evenness and slope. We conclude that higher aboveground biomass is related to high species richness and plant coverage, and located on high elevation and/or slope across plant growth forms while having medium-coarse-textured to fine-textured soils for adaptation of shrubs only. Few dominant species or niche overlap in whole-community may also drive high aboveground biomass, and located on high elevation with gentle slope. Therefore, we found support for both the niche complementarity and selection effects across plant growth forms and at whole-community. In addition, this study shows that plant coverage is the best proxy for aboveground biomass in the studied rangelands.

Functional identity of overstorey tree height and understorey conservative traits drive aboveground biomass in a subtropical forest

The niche complementarity hypothesis has received empirical support but species differ in functional strategies for their contribution to ecosystem function, as predicted by the mass ratio hypothesis. Our understanding of how functional identity of conservative and acquisitive strategies of trees predicts aboveground biomass across forest strata (i.e. overstorey and understorey) remains unclear. Aboveground biomass, community-weighted mean (CWM − functional identity) of trait values (6 leaf and 2 stem traits), and soil physicochemical properties were estimated for 125 plots in a 5-ha subtropical forest in Eastern China. We used multiple linear regressions models to relate aboveground biomass to CWM indices at overstorey and understorey strata separately, and whole-community level. We finally employed the structural equation model to test for the effects of overstorey on understorey strata, in addition to the effects of soil physicochemical properties. Forest strata optimal models showed that overstorey strata had high aboveground biomass when they are dominated by functional identity of tree height, whereas high aboveground biomass in understorey strata was driven by functional identity of dense-wooded conservative strategy. Whole-community optimal model showed that communities dominated by functional identity of leaf dry matter content and mean leaf area had high aboveground biomass. Aboveground biomass was negatively related to soil nutrients across forest strata and whole-community level. The structural equation model showed that CWM of overstorey tree height did not affect understorey functional identity and aboveground biomass, when soil physicochemical properties were accounted. Soil nutrients had positive effect on functional identity of overstorey tree height whereas negative effect on functional identity of understorey dense-wooded strategy. This study highlights the fundamental roles of forest strata where overstorey and understorey strata contribute to their corresponding aboveground biomass with contrasting functional strategies across a range of soil nutrients. High aboveground biomass was potentially driven by functional identity of tree height through making use of plentiful soil nutrients at overstorey strata, whereas by conservative strategy at understorey strata through enduring nutrient-poor soils. To better understand the roles of functional identity of conservative and acquisitive strategies in driving ecosystem functions, it is worth to analyse forest strata separately.

The forest strata-dependent relationship between biodiversity and aboveground biomass within a subtropical forest

The relationships between biodiversity and aboveground biomass in forest ecosystems have been intensively studied in recent decades. Still, the mechanisms that underlie it remain highly debated. We hypothesized that overstorey species diversity and individual tree size variation contribute to aboveground biomass and understorey species diversity through the niche complementarity effect, while weaken the relationship between understorey aboveground biomass and individual tree size variation due to the mixed effects of tree development, biotic interaction and reduced available resources by overstorey strata. The integrative relationships of species diversity and tree size variation (variation in diameter at breast height-DBH) with aboveground biomass were analysed at overstorey and understorey strata across 125 plots in a 5-ha subtropical forest in Eastern China. For comparison, we tested these relationships at individual strata (isolation modelling), and whole-community level, by using linear structural equation model while accounting for the effects of soil nutrients. The integrative modelling accounted for 35, 31, 16, 12, 4, and 0% of the variation in understorey aboveground biomass, overstorey aboveground biomass, overstorey DBH variation, overstorey species diversity, understorey species diversity, and understorey DBH variation, respectively. Overstorey DBH variation and species diversity had the positive direct effects on overstorey aboveground biomass. Overstorey species diversity significantly promoted the understorey species diversity, but DBH variation and aboveground biomass of overstorey strata had negligible effects on the diversity and aboveground biomass of understorey strata. Soil nutrients had positive direct effect on overstorey DBH variation, but negative direct effects on overstorey and understorey aboveground biomass and overstorey species diversity. These results provide strong evidence for the niche complementarity effect for driving positive relationships of species diversity and individual tree size variation with aboveground biomass at overstorey strata. The strong and consistent negative effects of soil nutrients on overstorey aboveground biomass and species diversity suggest an important mechanism that high species diversity of overstorey strata with great tree size variation on nutrient-poor soils is crucial for driving high aboveground biomass in subtropical forest ecosystems. In conclusion, this study suggests that no sole and ubiquitous relationship between biodiversity and aboveground biomass exists in a structurally complex forest, but rather that the magnitude and direction of this relationship is greatly dependent on the forest strata where available resources shift substantially. We argue that ecological models for predicting aboveground biomass would be improved by including separate effects of overstorey and understorey diversity.

Which plant traits respond to aridity? A critical step to assess functional diversity in Mediterranean drylands

Aridity acts as a strong environmental filter to plants, limiting major ecosystem processes. Climate change models predict an overall increase of aridity in drylands. This could lead to changes in plant communities, particularly in the dominance and range of plant functional traits, which largely determine ecosystem functioning. However, to study how changes in aridity may affect plant functional metrics, a critical decision needs to be taken: the choice of the functional traits to be studied. Previous studies related plant functional traits and aridity, however mostly focusing on a single facet of functional diversity and primarily on perennial species. Hence, the response of plant traits to aridity quantifying different functional metrics at the whole-community level (considering also annual species) is not well established in drylands.Here, we use a high-resolution aridity gradient along a Mediterranean dryland ecosystem of Holm-oak woodlands to identify plant functional traits responding to aridity at the community-level (comprising annual and perennial species). We studied how the community-weighted-mean and functional dispersion of 13 traits related to plant establishment, growth, reproduction, dispersal and persistence changed with aridity.Nine plant functional traits varied with aridity. Aridity acted as an environmental filter on community-weighted-means, increasing the dominance of annual species, particularly rosettes, and plants with lower maximum height, shorter flowering duration, and increased anemochorous dispersal. Higher aridity was associated to an overall decrease in functional dispersion, particularly for life cycle, specific leaf area, onset of flowering, dispersal strategy and seed persistence traits, probably due to a lower niche differentiation under more arid conditions. The changes in community-weighted-means and in functional dispersion due to aridity are likely to negatively affect major ecosystem functions such as biomass production and nutrient cycling.Our results fill an important knowledge gap by quantifying how the functional structure and dispersion of 13 plant traits change with aridity at the whole-community level, providing an important basis for the selection of key functional traits to be used in trait-based studies in drylands.

The relationship between microbial community evenness and function in slow sand filters.

ABSTRACTTwo full-scale slow sand filters (SSFs) were sampled periodically from April until November 2011 to study the spatial and temporal structures of the bacterial communities found in the filters. To monitor global changes in the microbial communities, DNA from sand samples taken at different depths and locations within the SSFs and at different filters ages was used for Illumina 16S rRNA gene sequencing. Additionally, 15 water quality parameters were monitored to assess filter performance, with functionally relevant microbial members being identified by using multivariate statistics. The bacterial diversity in the SSFs was found to be much larger than previously documented, with community composition being shaped by the characteristics of the SSFs (filter age and depth) and sampling characteristics (month, side, and distance from the influent and effluent pipes). We found that several key genera (Acidovorax, Halomonas, Sphingobium, and Sphingomonas) were associated with filter performance. In addition, at the whole-community level, a strong positive correlation was found between species evenness and filter performance. This study is the first to comprehensively characterize the microbial community of SSFs and link specific microbes to water quality parameters. In doing so, we reveal key patterns in microbial community structure that relate to overall community function.

Distribution and Interaction Patterns of Bacterial Communities in an Ornithogenic Soil of Seymour Island, Antarctica

Next-generation, culture-independent sequencing offers an excellent opportunity to examine network interactions among different microbial species. In this study, soil bacterial communities from a penguin rookery site at Seymour Island were analyzed for abundance, structure, diversity, and interaction networks to identify interaction patterns among the various taxa at three soil depths. The analysis revealed the presence of eight phyla distributed in different proportions among the surface layer (0-8cm), middle layer (20-25cm), and bottom (35-40cm). The bottom layer presented the highest values of bacterial richness, diversity, and evenness when compared to surface and middle layers. The network analysis revealed the existence of a unique pattern of interactions in which the soil microbial network formed a clustered topology, rather than a modular structure as is usually found in biological communities. In addition, specific taxa were identified as important players in microbial community structure. Furthermore, simulation analyses indicated that the loss of potential keystone groups of microorganisms might alter the patterns of interactions within the microbial community. These findings provide new insights for assessing the consequences of environmental disturbances at the whole-community level in Antarctica.

Extinction and invasion do not add up in noisy dynamic ecological networks

Species extinction and invasion concurrently affect the composition and properties of ecological communities, yet their effects have largely been studied separately, and with more focus on species and ecological functional groups than the whole-community level. We adopted a dynamic ecological network approach to compare the effects of simultaneous single-species primary extinction and invasion on a set of ecosystem metrics to the effects of extinction and invasion in isolation. We also investigated the relationship between the impact and reversibility of extinction or invasion through reintroduction or eradication, respectively. We used Monte Carlo simulations of bioenergetic ecological network models that combined trophic and mutualistic interactions, contained either prey-dependent or ratio-dependent trophic functional responses, and incorporated either white or pink environmental stochasticity. As the separate extinction or invasion impact increased, the simultaneous extinction–invasion impact increased but was decreasingly additive of the two separate impacts, across all ecosystem metrics. Greater extinction or invasion impact was associated with lower reversibility for most model types and ecosystem metrics. There were also systematic differences between models with prey- and ratio-dependent functional responses. These results highlight the importance of considering the combined effects of extinction and invasion in ecological studies, management and restoration.

Coherent ecological dynamics induced by large-scale disturbance

Aggregate community-level response to disturbance is a principle concern in ecology because post-disturbance dynamics are integral to the ability of ecosystems to maintain function in an uncertain world. Community-level responses to disturbance can be arrayed along a spectrum ranging from synchronous oscillations where all species rise and fall together, to compensatory dynamics where total biomass remains relatively constant despite fluctuations in the densities of individual species. An important recent insight is that patterns of synchrony and compensation can vary with the timescale of analysis and that spectral time series methods can enable detection of coherent dynamics that would otherwise be obscured by opposing patterns occurring at different scales. Here I show that application of wavelet analysis to experimentally manipulated plankton communities reveals strong synchrony after disturbance. The result is paradoxical because it is well established that these communities contain both disturbance-sensitive and disturbance-tolerant species leading to compensation within functional groups. Theory predicts that compensatory substitution of functionally equivalent species should stabilize ecological communities, yet I found at the whole-community level a large increase in seasonal biomass variation. Resolution of the paradox hinges on patterns of seasonality among species. The compensatory shift in community composition after disturbance resulted in a loss of cold-season dominants, which before disturbance had served to stabilize biomass throughout the year. Species dominating the disturbed community peaked coherently during the warm season, explaining the observed synchrony and increase in seasonal biomass variation. These results suggest that theory relating compensatory dynamics to ecological stability needs to consider not only complementarity in species responses to environmental change, but also seasonal complementarity among disturbance-tolerant and disturbance-sensitive species.