Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation.

Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (ß-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment.IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs' ß-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.

Three keys to the radiation of angiosperms into freezing environments.

Early flowering plants are thought to have been woody species restricted to warm habitats. This lineage has since radiated into almost every climate, with manifold growth forms. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species' traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile, but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold.

Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities.

Because biodiversity is multidimensional and scale-dependent, it is challenging to estimate its change. However, it is unclear (1) how much scale-dependence matters for empirical studies, and (2) if it does matter, how exactly we should quantify biodiversity change. To address the first question, we analysed studies with comparisons among multiple assemblages, and found that rarefaction curves frequently crossed, implying reversals in the ranking of species richness across spatial scales. Moreover, the most frequently measured aspect of diversity - species richness - was poorly correlated with other measures of diversity. Second, we collated studies that included spatial scale in their estimates of biodiversity change in response to ecological drivers and found frequent and strong scale-dependence, including nearly 10% of studies which showed that biodiversity changes switched directions across scales. Having established the complexity of empirical biodiversity comparisons, we describe a synthesis of methods based on rarefaction curves that allow more explicit analyses of spatial and sampling effects on biodiversity comparisons. We use a case study of nutrient additions in experimental ponds to illustrate how this multi-dimensional and multi-scale perspective informs the responses of biodiversity to ecological drivers.

Functional biogeography of angiosperms: life at the extremes.

Nonlinear relationships between species and their environments are believed common in ecology and evolution, including during angiosperms' rise to dominance. Early angiosperms are thought of as woody evergreens restricted to warm, wet habitats. They have since expanded into numerous cold and dry places. This expansion may have included transitions across important environmental thresholds. To understand linear and nonlinear relationships between angiosperm structure and biogeographic distributions, we integrated large datasets of growth habits, conduit sizes, leaf phenologies, evolutionary histories, and environmental limits. We consider current-day patterns and develop a new evolutionary model to investigate processes that created them. The macroecological pattern was clear: herbs had lower minimum temperature and precipitation limits. In woody species, conduit sizes were smaller in evergreens and related to species' minimum temperatures. Across evolutionary timescales, our new modeling approach found conduit sizes in deciduous species decreased linearly with minimum temperature limits. By contrast, evergreen species had a sigmoidal relationship with minimum temperature limits and an inflection overlapping freezing. These results suggest freezing represented an important threshold for evergreen but not deciduous woody angiosperms. Global success of angiosperms appears tied to a small set of alternative solutions when faced with a novel environmental threshold.

Vessel diameter is related to amount and spatial arrangement of axial parenchyma in woody angiosperms.

Parenchyma represents a critically important living tissue in the sapwood of the secondary xylem of woody angiosperms. Considering various interactions between parenchyma and water transporting vessels, we hypothesize a structure-function relationship between both cell types. Through a generalized additive mixed model approach based on 2,332 woody angiosperm species derived from the literature, we explored the relationship between the proportion and spatial distribution of ray and axial parenchyma and vessel size, while controlling for maximum plant height and a range of climatic factors. When factoring in maximum plant height, we found that with increasing mean annual temperatures, mean vessel diameter showed a positive correlation with axial parenchyma proportion and arrangement, but not for ray parenchyma. Species with a high axial parenchyma tissue fraction tend to have wide vessels, with most of the parenchyma packed around vessels, whereas species with small diameter vessels show a reduced amount of axial parenchyma that is not directly connected to vessels. This finding provides evidence for independent functions of axial parenchyma and ray parenchyma in large vesselled species and further supports a strong role for axial parenchyma in long-distance xylem water transport.

Dehalococcoides and general bacterial ecology of differentially trichloroethene dechlorinating flow-through columns.

The diversity of Dehalococcoides mccartyi (Dhc) and/or other organohalide respiring or associated microorganisms in parallel, partial, or complete trichloroethene (TCE) dehalogenating systems has not been well described. The composition of Dhc populations and the associated bacterial community that developed over 7.5 years in the top layer (0-10 cm) of eight TCE-fed columns were examined using pyrosequencing. Columns biostimulated with one of three carbon sources, along with non-stimulated controls, developed into complete (ethene production, whey amended), partial (cis-dichloroethene (DCE) and VC, an emulsified oil with nonionic surfactant), limited (<5 % cis-DCE and 95 % TCE, an emulsified oil), and non- (controls) TCE dehalogenating systems. Bioaugmentation of one column of each treatment with Bachman Road enrichment culture did not change Dhc populations nor the eventual degree of TCE dehalogenation. Pyrosequencing revealed high diversity among Dhc strains. There were 13 OTUs that were represented by more than 1000 sequences each. Cornell group-related populations dominated in complete TCE dehalogenating columns, while Pinellas group related Dhc dominated in all other treatments. General microbial communities varied with biostimulation, and three distinct microbial communities were established: one each for whey, oils, and control treatments. Bacterial genera, including Dehalobacter, Desulfitobacterium, Sulfurospirillum, Desulfuromonas, and Geobacter, all capable of partial TCE dehalogenation, were abundant in the limited and partial TCE dehalogenating systems. Dhc strain diversity was wider than previously reported and their composition within the community varied significantly depending on the nature of the carbon source applied and/or changes in the Dhc associated partners that fostered different biogeochemical conditions across the columns.

Mutualism Persistence and Abandonment during the Evolution of the Mycorrhizal Symbiosis.

Mutualistic symbioses with mycorrhizal fungi are widespread in plants. The majority of plant species associate with arbuscular mycorrhizal (AM) fungi. By contrast, the minority associate with ectomycorrhizal (EM) fungi, have abandoned the symbiosis and are nonmycorrhizal (NM), or engage in an intermediate, weakly AM symbiosis (AMNM). To understand the processes that maintain the mycorrhizal symbiosis or cause its loss, we reconstructed its evolution using a ∼3,000-species seed plant phylogeny integrated with mycorrhizal state information. Reconstruction indicated that the common ancestor of seed plants most likely associated with AM fungi and that the EM, NM, and AMNM states descended from the AM state. Direct transitions from the AM state to the EM and NM states were infrequent and generally irreversible, implying that natural selection or genetic constraint could promote stasis once a particular state evolved. However, the evolution of the NM state was more frequent via an indirect pathway through the AMNM state, suggesting that weakening of the AM symbiosis is a necessary precursor to mutualism abandonment. Nevertheless, reversions from the AMNM state back to the AM state were an order of magnitude more likely than transitions to the NM state, suggesting that natural selection favors the AM symbiosis over mutualism abandonment.

A global analysis of parenchyma tissue fractions in secondary xylem of seed plants.

Parenchyma is an important tissue in secondary xylem of seed plants, with functions ranging from storage to defence and with effects on the physical and mechanical properties of wood. Currently, we lack a large-scale quantitative analysis of ray parenchyma (RP) and axial parenchyma (AP) tissue fractions. Here, we use data from the literature on AP and RP fractions to investigate the potential relationships of climate and growth form with total ray and axial parenchyma fractions (RAP). We found a 29-fold variation in RAP fraction, which was more strongly related to temperature than with precipitation. Stem succulents had the highest RAP values (mean ± SD: 70.2 ± 22.0%), followed by lianas (50.1 ± 16.3%), angiosperm trees and shrubs (26.3 ± 12.4%), and conifers (7.6 ± 2.6%). Differences in RAP fraction between temperate and tropical angiosperm trees (21.1 ± 7.9% vs 36.2 ± 13.4%, respectively) are due to differences in the AP fraction, which is typically three times higher in tropical than in temperate trees, but not in RP fraction. Our results illustrate that both temperature and growth form are important drivers of RAP fractions. These findings should help pave the way to better understand the various functions of RAP in plants.

A strong test of the maximum entropy theory of ecology.

The maximum entropy theory of ecology (METE) is a unified theory of biodiversity that predicts a large number of macroecological patterns using information on only species richness, total abundance, and total metabolic rate of the community. We evaluated four major predictions of METE simultaneously at an unprecedented scale using data from 60 globally distributed forest communities including more than 300,000 individuals and nearly 2,000 species.METE successfully captured 96% and 89% of the variation in the rank distribution of species abundance and individual size but performed poorly when characterizing the size-density relationship and intraspecific distribution of individual size. Specifically, METE predicted a negative correlation between size and species abundance, which is weak in natural communities. By evaluating multiple predictions with large quantities of data, our study not only identifies a mismatch between abundance and body size in METE but also demonstrates the importance of conducting strong tests of ecological theories.

Scale dependence in species turnover reflects variance in species occupancy.

Patterns of species turnover may reflect the processes driving community dynamics across scales. While the majority of studies on species turnover have examined pairwise comparison metrics (e.g., the average Jaccard dissimilarity), it has been proposed that the species-area relationship (SAR) also offers insight into patterns of species turnover because these two patterns may be analytically linked. However, these previous links only apply in a special case where turnover is scale invariant, and we demonstrate across three different plant communities that over 90% of the pairwise turnover values are larger than expected based on scale-invariant predictions from the SAR. Furthermore, the degree of scale dependence in turnover was negatively related to the degree of variance in the occupancy frequency distribution (OFD). These findings suggest that species turnover diverges from scale invariance, and as such pairwise turnover and the slope of the SAR are not redundant. Furthermore, models developed to explain the OFD should be linked with those developed to explain species turnover to achieve a more unified understanding of community structure.

How does variation in total and relative abundance contribute to gradients of species diversity?

Patterns of biodiversity provide insights into the processes that shape biological communities around the world. Variation in species diversity along biogeographical or ecological gradients, such as latitude or precipitation, can be attributed to variation in different components of biodiversity: changes in the total abundance (i.e., more-individual effects) and changes in the regional species abundance distribution (SAD). Rarefaction curves can provide a tool to partition these sources of variation on diversity, but first must be converted to a common unit of measurement. Here, we partition species diversity gradients into components of the SAD and abundance using the effective number of species (ENS) transformation of the individual-based rarefaction curve. Because the ENS curve is unconstrained by sample size, it can act as a standardized unit of measurement when comparing effect sizes among different components of biodiversity change. We illustrate the utility of the approach using two data sets spanning latitudinal diversity gradients in trees and marine reef fish and find contrasting results. Whereas the diversity gradient of fish was mostly associated with variation in abundance (86%), the tree diversity gradient was mostly associated with variation in the SAD (59%). These results suggest that local fish diversity may be limited by energy through the more-individuals effect, while species pool effects are the larger determinant of tree diversity. We suggest that the framework of the ENS-curve has the potential to quantify the underlying factors influencing most aspects of diversity change.

Local biodiversity change reflects interactions among changing abundance, evenness, and richness.

Biodiversity metrics often integrate data on the presence and abundance of multiple species. Yet our understanding of covariation between changes to the numbers of individuals, the evenness of species relative abundances, and the total number of species remains limited. Using individual-based rarefaction curves, we show how expected positive relationships among changes in abundance, evenness and richness arise, and how they can break down. We then examined interdependencies between changes in abundance, evenness and richness in more than 1100 assemblages sampled either through time or across space. As predicted, richness changes were greatest when abundance and evenness changed in the same direction, and countervailing changes in abundance and evenness acted to constrain the magnitude of changes in species richness. Site-to-site differences in abundance, evenness, and richness were often decoupled, and pairwise relationships between these components across assemblages were weak. In contrast, changes in species richness and relative abundance were strongly correlated for assemblages varying through time. Temporal changes in local biodiversity showed greater inertia and stronger relationships between the component changes when compared to site-to-site variation. Overall, local variation in assemblage diversity was rarely due to repeated passive samples from an approximately static species abundance distribution. Instead, changing species relative abundances often dominated local variation in diversity. Moreover, how changing relative abundances combined with changes to total abundance frequently determined the magnitude of richness changes. Embracing the interdependencies between changing abundance, evenness and richness can provide new information to better understand biodiversity change in the Anthropocene.

A multiscale framework for disentangling the roles of evenness, density, and aggregation on diversity gradients.

Disentangling the drivers of diversity gradients can be challenging. The Measurement of Biodiversity (MoB) framework decomposes scale-dependent changes in species diversity into three components of community structure: species abundance distribution (SAD), total community abundance, and within-species spatial aggregation. Here we extend MoB from categorical treatment comparisons to quantify variation along continuous geographic or environmental gradients. Our approach requires sites along a gradient, each consisting of georeferenced plots of abundance-based species composition data. We demonstrate our method using a case study of ants sampled along an elevational gradient of 28 sites in a mixed deciduous forest of the Great Smoky Mountains National Park, USA. MoB analysis revealed that decreases in ant species richness along the elevational gradient were associated with decreasing evenness and total number of species, which counteracted the modest increase in richness associated with decreasing spatial aggregation along the gradient. Total community abundance had a negligible effect on richness at all but the finest spatial grains, SAD effects increased in importance with sampling effort, and the aggregation effect had the strongest effect at coarser spatial grains. These results do not support the more-individuals hypothesis, but they are consistent with a hypothesis of stronger environmental filtering at coarser spatial grains. Our extension of MoB has the potential to elucidate how components of community structure contribute to changes in diversity along environmental gradients and should be useful for a variety of assemblage-level data collected along gradients.

Modeling the sampling effect in the species-time-area relationship.

Recent empirical work in numerous systems has demonstrated the interdependence of spatial and temporal accumulation of species in the species-time-area relationship (STAR). The purpose of this study was to develop a process-based stochastic model for the STAR that assumes species neutrality and to compare the model's expectations to data collected on plant species in a tallgrass prairie. We varied two important aspects of the neutral species assemblage: evenness in the species pool and individual replacement rate (R). When R is larger than approximately 0.5 and evenness is intermediate to high, the neutral STAR generates patterns qualitatively similar to the empirical STAR. Our model also indicates that space and time were not symmetrical in their effects on species accumulation, except in the special case of R = 1.0. We observed both positive and negative time-by-area interactions in the sampling model, which indicates that nonzero interactions are not necessarily evidence of ecological processes. Furthermore, as accumulated richness approaches the size of the species pool, the time-by-area interaction becomes increasingly negative in our model. This suggests that negative time-by-area interactions should be expected a priori in empirical systems if rates of species accumulation decrease due to increasing rarity of unique species. Given the wide range of STARs that the sampling model generated, the difficulty in estimating key parameters, and the complexity of assessing the relative abundance distribution and scale of the species pool, we cannot refute the sampling effect, and we suggest caution in accepting ecologically oriented explanations of empirical STARs.

Examining the assumptions of heterogeneity-based management for promoting plant diversity in a disturbance-prone ecosystem.

BACKGROUND: Patch-burn management approaches attempt to increase overall landscape biodiversity by creating a mosaic of habitats using a patchy application of fire and grazing. We tested two assumptions of the patch-burn approach, namely that: (1) fire and grazing drive spatial patch differentiation in community structure and (2) species composition of patches change through time in response to disturbance. METHODS: We analyzed species cover data on 100 m2 square quadrats from 128 sites located on a 1 × 1 km UTM grid in the grassland habitats of the Tallgrass Prairie Preserve. A total of 20 of these sites were annually sampled for 12 years. We examined how strongly changes in species richness and species composition correlated with changes in management variables relative to independent spatial and temporal drivers using multiple regression and direct ordination, respectively. RESULTS: Site effects, probably due to edaphic differences, explained the majority of variation in richness and composition. Interannual variation in fire and grazing management was relatively unimportant relative to inherent site and year drivers with respect to both richness and composition; however, the effects of fire and grazing variables were statistically significant and interpretable, and bison management was positively correlated with plant richness. CONCLUSIONS: There was some support for the two assumptions of patch-burn management we examined; however, in situ spatial and temporal environmental heterogeneity played a much larger role than management in shaping both plant richness and composition. Our results suggest that fine-tuning the application of fire and grazing may not be critical for maintaining landscape scale plant diversity in disturbance-prone ecosystems.

Indices for detecting differences in species composition: some simplifications of RDA and CCA.

We provide algebraic simplifications for the redundancy analysis (RDA) eigenvalue and the canonical correspondence analysis (CCA) eigenvalue in the special case of permanent plots sampled twice. The indices for RDA and CCA are interrelated and are intuitively interpretable. These simplifications also apply to simple split-plot designs and to a balanced design with two independent samples.

Determinants of taxonomic composition of plant viruses at the Nature Conservancy's Tallgrass Prairie Preserve, Oklahoma.

The role of biotic and abiotic factors in shaping the diversity and composition of communities of plant viruses remain understudied, particularly in natural settings. In this study, we test the effects of host identity, location, and sampling year on the taxonomic composition of plant viruses in six native plant species [Ambrosia psilostachya (Asteraceae), Vernonia baldwinii (Asteraceae), Asclepias viridis (Asclepiadaceae), Ruellia humilis (Acanthaceae), Panicum virgatum (Poaceae) and Sorghastrum nutans (Poaceae)] from the Nature Conservancy's Tallgrass Prairie Preserve in northeastern Oklahoma. We sampled over 400 specimens of the target host plants from twenty sites (plots) in the Tallgrass Prairie Preserve over 4 years and tested them for the presence of plant viruses applying virus-like particle and double-stranded RNA enrichment methods. Many of the viral sequences identified could not be readily assigned to species, either due to their novelty or the shortness of the sequence. We thus grouped our putative viruses into operational viral taxonomic units for further analysis. Partial canonical correspondence analysis revealed that the taxonomic composition of plant viruses in the target species had a significant relationship with host species (P value: 0.001) but no clear relation with sampling site or year. Variation partitioning further showed that host identity explained about 2-5 per cent of the variation in plant virus composition. We could not interpret the significant relationship between virus composition and host plants with respect to host taxonomy or ecology. Only six operational viral taxonomic units had over 5 per cent incidence over a 4-year period, while the remainder exhibited sporadic infection of the target hosts. This study is the first of its kind to document the dynamics of the entire range of viruses in multiple plant species in a natural setting.

An empirical evaluation of four variants of a universal species-area relationship.

The Maximum Entropy Theory of Ecology (METE) predicts a universal species-area relationship (SAR) that can be fully characterized using only the total abundance (N) and species richness (S) at a single spatial scale. This theory has shown promise for characterizing scale dependence in the SAR. However, there are currently four different approaches to applying METE to predict the SAR and it is unclear which approach should be used due to a lack of empirical comparison. Specifically, METE can be applied recursively or non-recursively and can use either a theoretical or observed species-abundance distribution (SAD). We compared the four different combinations of approaches using empirical data from 16 datasets containing over 1000 species and 300,000 individual trees and herbs. In general, METE accurately downscaled the SAR (R (2) > 0.94), but the recursive approach consistently under-predicted richness. METE's accuracy did not depend strongly on using the observed or predicted SAD. This suggests that the best approach to scaling diversity using METE is to use a combination of non-recursive scaling and the theoretical abundance distribution, which allows predictions to be made across a broad range of spatial scales with only knowledge of the species richness and total abundance at a single scale.