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Plant productivity varies due to environmental heterogeneity, and theory suggests that plant diversity can reduce this variation. While there is strong evidence of diversity effects on temporal variability of productivity, whether this mechanism extends to variability across space remains elusive. Here we determine the relationship between plant diversity and spatial variability of productivity in 83 grasslands, and quantify the effect of experimentally increased spatial heterogeneity in environmental conditions on this relationship. We found that communities with higher plant species richness (alpha and gamma diversity) have lower spatial variability of productivity as reduced abundance of some species can be compensated for by increased abundance of other species. In contrast, high species dissimilarity among local communities (beta diversity) is positively associated with spatial variability of productivity, suggesting that changes in species composition can scale up to affect productivity. Experimentally increased spatial environmental heterogeneity weakens the effect of plant alpha and gamma diversity, and reveals that beta diversity can simultaneously decrease and increase spatial variability of productivity. Our findings unveil the generality of the diversity-stability theory across space, and suggest that reduced local diversity and biotic homogenization can affect the spatial reliability of key ecosystem functions.

Revealing the ecological consequences of bark multifunctionality and its underlying traits has become a relatively new but essential focus in plant ecology. Although the enormous differences between the most crucial bark layers, that is, inner and outer bark, in structure and functions have been widely recognized, the overall bark has been regarded as a homogenous tissue in most bark-related studies. This has led to poor knowledge on the functional independence, specialized contributions and possible linkages of inner and outer bark traits across tree species when further evaluating the crucial ecosystem functions that bark provides, especially in driving variation in bark decomposition. To fill this research gap, we used a ‘common garden experiment’ on deadwood of six gymnosperms in a temperate forest in the Netherlands over 4 years of decomposition. We evaluated the differences and associations between the inner and outer bark in initial functional traits, decomposition rates and afterlife effects of traits in driving in situ bark decomposition across tree species at the earlier decomposition stage. We report four main findings: (1) inner and outer bark traits varied significantly and were not coordinated across tree species; (2) correspondingly, the decomposition of the inner and outer bark were asynchronous and not coordinated across species and inner bark generally decomposed faster than outer bark; (3) the strong predictive traits driving bark decomposability were bark layer-specific, with several inner bark traits controlling inner bark decomposition rates but outer bark decomposability being poorly predicted by outer bark traits and (4) besides being controlled by inner bark traits, inner bark decomposition was also indirectly regulated by several functional traits and the structure-related trait spectrum of outer bark. Synthesis. This is the first study that has linked functional traits, decomposability and afterlife effects of the inner and outer bark within the bark quantitatively. We highlight the significance of separating functional traits and ecological consequences of the inner and outer bark in research in bark ecology and deadwood dynamics, rather than erroneously considering bark as a homogeneous tissue. Such research will help to better evaluate the function-oriented contribution of bark to the turnover of forest carbon and biogeochemical cycles from local to global scale.

Dead wood quantity and quality is important for forest biodiversity, by determining wood-inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer- and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long-term carbon dynamics of dead trees.

Although the destabilizing effects of biodiversity loss on ecosystem functioning at local and larger spatial scales are fairly well understood, the consequences of environmental homogenization have received much less attention. Based on detailed measurements of permanent natural forest plots distributed over a large temperate forest region, we explored the effects of environmental heterogeneity and biodiversity on ecosystem stability at local and larger spatial scales. Our results show that the relationship between environmental heterogeneity and biodiversity, as well as between environmental heterogeneity and stability across scales are mostly nonlinear, and that biodiversity stabilizes ecosystem functioning in these natural forests across scales. The unique contribution of biodiversity to stabilizing ecosystem functioning from local to larger scales is greater than the heterogeneity of climate, soils, topography, vegetation, and land cover. To our knowledge, this study is the first to quantify the effects of environmental heterogeneity on the temporal stability of forest productivity in a large natural forest region. Our results imply that biodiversity contributes to stabilizing forest ecosystems from local to larger spatial scales as much as environmental heterogeneity. Research involving large heterogeneous landscapes is critical to understanding the ecological effects of biodiversity across scales. The results of this study are thus relevant for developing effective conservation and land management strategies.

Causal effects of biodiversity on ecosystem functions can be estimated using experimental or observational designs — designs that pose a tradeoff between drawing credible causal inferences from correlations and drawing generalizable inferences. Here, we develop a design that reduces this tradeoff and revisits the question of how plant species diversity affects productivity. Our design leverages longitudinal data from 43 grasslands in 11 countries and approaches borrowed from fields outside of ecology to draw causal inferences from observational data. Contrary to many prior studies, we estimate that increases in plot-level species richness caused productivity to decline: a 10% increase in richness decreased productivity by 2.4%, 95% CI [−4.1, −0.74]. This contradiction stems from two sources. First, prior observational studies incompletely control for confounding factors. Second, most experiments plant fewer rare and non-native species than exist in nature. Although increases in native, dominant species increased productivity, increases in rare and non-native species decreased productivity, making the average effect negative in our study. By reducing the tradeoff between experimental and observational designs, our study demonstrates how observational studies can complement prior ecological experiments and inform future ones.

Periodic inoculations of soil-beneficial microbes can increase their populations, but they also act as recurring biotic disturbances on the native microbial community. Soil rare and abundant microorganisms disproportionally shape the community diversity and stability. Uncovering their dynamic responses to recurring biotic disturbances and the underlying driving factors helps improve our understanding of the inoculation effects. Here, we imposed temporally recurring biotic disturbances by inoculating soils with phosphate-solubilizing bacteria, nitrogen-fixing bacteria, and the combination of both, with the overall aim of studying the successive responses of bacterial and fungal subcommunities along a rarity index. Our results showed that, in both bacterial and fungal communities, the relatively rare taxa exhibited higher diversity than the abundant taxa, and the relative abundance of rare taxa increased with recurring disturbances. However, the responses of rare and abundant taxa to inoculations were different between bacteria and fungi and were related to time and inoculation frequency. The rarer bacteria and the more abundant fungi explained most of the effects of inoculations on the resident microbial community. About 20 percent of the microbes changed their rarity categories over time, and most of the changes and interactions occurred within the rarer taxa during the first 45 days. Modeling analyses and co-occurrence networks indicated that microbial interactions, soil biochemical factors, and inoculation time drove the shifts of subcommunities. In summary, relatively rare bacteria and relatively abundant fungi play major roles in understanding the impacts of recurring biotic disturbances, while the conditionality of microbial rarity is dependent on both biotic and abiotic factors.

Anthropogenic nitrogen (N) input is known to alter the soil microbiome, but how N enrichment influences the abundance, alpha-diversity and community structure of N-cycling functional microbial communities in grasslands remains poorly understood. Here, we collected soils from plant communities subjected to up to 9 years of annual N-addition (10 g N m −2 per year using urea as a N-source) and from unfertilized plots (control) in 30 grasslands worldwide spanning a large range of climatic and soil conditions. We focused on three key microbial groups responsible for two essential processes of the global N cycle: N 2 fixation (soil diazotrophs) and nitrification (AOA: ammonia-oxidizing archaea and AOB: ammonia-oxidizing bacteria). We targeted soil diazotrophs, AOA and AOB using Illumina MiSeq sequencing and measured the abundance (gene copy numbers) using quantitative PCR. N-addition shifted the structure of the diazotrophic communities, although their alpha-diversity and abundance were not affected. AOA and AOB responded differently to N-addition. The abundance and alpha-diversity of AOB increased, and their community structure shifted with N-addition. In contrast, AOA were not affected by N-addition. AOA abundance outnumbered AOB in control plots under conditions of low N availability, whereas N-addition favoured copiotrophic AOB. Overall, N-addition showed a low impact on soil diazotrophs and AOA while effects for AOB communities were considerable. These results reveal that long-term N-addition has important ecological implications for key microbial groups involved in two critical soil N-cycling processes. Increased AOB abundance and community shifts following N-addition may change soil N-cycling, as larger population sizes may promote higher rates of ammonia oxidation and subsequently increase N loss via gaseous and soil N-leaching. These findings bring us a step closer to predicting the responses and feedbacks of microbial-mediated N-cycling processes to long-term anthropogenic N-addition in grasslands.

Hunting impacts tropical vertebrate populations, causing declines of species that function as seed dispersers and predators, or that browse seedlings and saplings. Whether and how the resulting reductions in seed dispersal, seed predation, and browsing translate to changes in the tree composition is poorly understood. Here, we assess the effect of defaunation on the functional composition of communities of tree recruits in tropical rainforests in French Guiana. We selected eight sites along a gradient of defaunation, caused by differences in hunting pressure, in otherwise intact old-growth forests in French Guiana. We measured shifts in functional composition by comparing leaf and fruit traits and wood density between tree recruits (up to 5 cm diameter at breast height) and adults, and tested whether and how these compositional shifts related to defaunation. We found a positive relationship with defaunation for shifts in specific leaf area, a negative relationship for shifts of leaf toughness and wood density, and a weak relationship for shifts in fruit traits. Our results suggest that the loss of vertebrates affects ecological processes such as seed dispersal and browsing, of which browsing remains understudied. Even though these changes sometimes seem minor, together they result in major shifts in forest composition. These changes have long-term ramifications that may alter forest dynamics for generations.

Introduction Bryophyte diaspore banks are a critical aspect of the life strategy of some species yet remain neglected and poorly understood. This study investigated the longevity in natural habitat of the diaspore bank of Physcomitrium eurystomum Sendtn., a moss species that is threatened with extinction in Europe. Methods Undisturbed soil cores of 40 cm depth were collected from Langmere, Norfolk, UK, and were split into investigated sediment layers of 1 cm depth. Dating of sediment layers was done by an analysis of radionuclides, and diaspore germination trials of each layer were carried out in a growth chamber. DNA barcoding was used to help identify plants that germinated. Key results and conclusions Viable diaspores of Physcomitrium eurystomum frequently occurred in sediment layers that were at least 100 years old and continued to occur in much lower layers that were probably several hundred years old. The long-term survival of bryophytes underground can have important implications for conservation decisions.

Background The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome. Results Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots. Conclusion We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera.

Resources can affect plant productivity and biodiversity simultaneously and thus are key drivers of their relationships in addition to plant–plant interactions. However, most previous studies only focused on a single resource while neglecting the nature of resource multidimensionality. Here we integrated four essential resources for plant growth into a single metric of resource diversity (RD) to investigate its effects on the productivity–biodiversity relationship (PBR) across Chinese grasslands. Results showed that habitats differing in RD have different PBRs—positive in low-resource habitats, but neutral in medium- and high-resource ones—while collectively, a weak positive PBR was observed. However, when excluding direct effects of RD on productivity and biodiversity, the PBR in high-resource habitats became negative, which leads to a unimodal instead of a positive PBR along the RD gradient. By integrating resource effects and changing plant–plant interactions into a unified framework with the RD gradient, our work contributes to uncovering underlying mechanisms for inconsistent PBRs at large scales.

Biodiversity has widely been documented to enhance local community stability but whether such stabilizing effects of biodiversity extend to broader scales remains elusive. Here, we investigated the relationships between biodiversity and community stability in natural plant communities from quadrat (1 m 2) to plot (400 m 2) and regional (5-214 km 2) scales and across broad climatic conditions, using an extensive plant community dataset from the National Ecological Observatory Network. We found that plant diversity provided consistent stabilizing effects on total community abundance across three nested spatial scales and climatic gradients. The strength of the stabilizing effects of biodiversity increased modestly with spatial scale and decreased as precipitation seasonality increased. Our findings illustrate the generality of diversity-stability theory across scales and climatic gradients, which provides a robust framework for understanding ecosystem responses to biodiversity and climate changes.

The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment–plant–rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.

Cover crops are a potential pathway for ecological cultivation in agricultural systems. In tropical no-till agricultural systems, the maintenance of residues on the soil surface and the addition of nitrogen (N) benefit the growth and grain yield of cash crops as well as the chemical and physical properties of the soil. However, the effects of these management practices on the soil microbiota are largely unknown. Here, we evaluated the effects of the timing of N application as a pulse disturbance and the growth of different cover crop species before maize in rotation on soil properties, maize productivity, and soil bacterial and fungal community diversity and composition. N fertilizer was applied either on live cover crops (palisade grass or ruzigrass), on cover crop straw just before maize seeding or in the maize V4 growth stage. Soils previously cultivated with palisade grass established similar microbial communities regardless of N application timing, with increases in total bacteria, total archaea, nutrients, and the C:N ratio. The soil microbial alpha diversity in treatments with palisade grass did not vary with N application timing, whereas the bacterial and fungal diversities in the treatments with ruzigrass decreased when N was applied to live ruzigrass or maize in the V4 growth stage. We conclude that palisade grass is a more suitable cover crop than ruzigrass, as palisade grass enhanced soil microbial diversity and maize productivity regardless of N application timing. Ruzigrass could be used as an alternative to palisade grass when N is applied during the straw phase. However, considering the entire agricultural system (soil–plant–microbe), ruzigrass is not as efficient as palisade grass in tropical no-till cover crop–maize rotation systems. Palisade grass is a suitable cover crop alternative for enhancing maize productivity, soil chemical properties and nutrient cycling, regardless of the timing of N application. Additionally, this study demonstrates that a holistic approach is valuable for evaluating soil diversity and crop productivity in agricultural systems.

Introducing probiotics to soil is a sustainable way to stimulate the production of plant metabolites. However, the soil-resident microbes may compromise the efficiency of probiotics. To date, it remains challenging to integrate the effects of probiotics on plant performance with soil microbiome changes. Using Cyclocarya paliurus (Batal.) Iljinsk as a model medicinal plant and two types of probiotic consortia combined with organic fertilizer at three levels (low: 0.5, medium: 1.0, and high: 1.5 kg·plant−1), we examined the impacts of three fertilization regimes (O: organic fertilizer, OMF: O coupled with Bacillus megaterium and Pseudomonas fluorescens, OCB: O coupled with Azotobacter chroococcum and Azospirillum brasilense) on plant metabolites and nutrient stoichiometry after three-year applications and identified the key soil microbes relating to the accumulation of plant metabolites via generalized joint attribute model (GJAM) analysis. Our results indicated that the concentration of flavonoids reached 36.9 mg·g−1 in OCB treatment at a low level, and 30.0 mg·g−1 in OMF treatment at a medium level, both were significantly higher than that in O treatment (25.8 mg·g−1 on average). Furthermore, the accumulations of metabolites were associated with plant nutrient acquisition and C: N: P stoichiometry. GJAM analysis showed that higher fertilizer levels restricted the influence of probiotic consortia on the variance of plant-soil-microbe system, with fewer differences observed between fertilizer types. Specific soil microbes were predicted as potential indicators that may assist or impede the effects of probiotics on plant metabolite production. The predictions were further tested in a comparative pot experiment, and the effects of common indicators in both pot and field experiments were consistently associated with probiotics’ addition. This study reveals that the effects of probiotics on plant metabolites are associated with fertilization regimes and soil-indigenous microbes. Identifying microbial indicators will help to understand the probiotics' effects and further improve plant productivity.

Wind-induced turbulence can strongly impact ecological processes in shallow lake ecosystems. The creation of shelter against wind can be expected to affect both primary producers and herbivores in aquatic food webs. Shelter may benefit particular primary producers more than others by changing relative resource availabilities for different primary producers. Herbivore community compositions may be affected either directly or indirectly as a consequence of changes in their food quantity and quality that, in turn, may affect the transfer efficiency between primary producers and herbivores. A reduction in trophic transfer efficiency resulting from wind-induced turbulence potentially can lead to declines of higher trophic levels, but is generally understudied. Here, we focus on the impact of wind on aquatic primary producers and trophic transfer efficiency. We hypothesised that reducing wind-induced turbulence will stimulate higher trophic production in shallow lakes. However, the multitude of impacts of wind-induced turbulence on aquatic food webs make it challenging to predict the direction of change when creating sheltered conditions. We tested our hypothesis in the shallow waters of a newly constructed archipelago named Marker Wadden in lake Markermeer in the Netherlands. Lake Markermeer has experienced declining numbers of birds and fish. These declines have been related to wind-induced sediment resuspension that potentially limits primary production and trophic transfer efficiency. Marker Wadden is a large-scale restoration project that aims to add sheltered and heterogeneous habitat to the otherwise mostly homogeneous lake, thus targeting the potential problems associated with wind-induced turbulence. We executed a 2-month manipulative field mesocosm experiment in the shallow waters of Marker Wadden to study the effect of reduced wind-induced turbulence (i.e., shelter) on aquatic food webs. Specifically, we studied the effects on primary producers, trophic transfer efficiency between phytoplankton and zooplankton (using zooplankton biomass divided by phytoplankton Chl a as a proxy), and benthic fauna. The experiment consisted of three treatments: no shelter, shelter without macrophytes and shelter with submerged macrophytes (Myriophyllum spicatum) present at the start of the experiment. Our results clearly showed that under unsheltered conditions phytoplankton was the dominant primary producer, whereas in sheltered conditions submerged macrophytes became dominant. Interestingly, submerged macrophytes appeared rapidly in the sheltered treatment where first no macrophytes were visibly present; hence, at the end of the experiment, there was little difference among the sheltered treatments with and without initial presence of submerged macrophytes. Despite that phytoplankton concentrations were 23-fold higher under the unsheltered conditions, this did not result in higher zooplankton biomass. This can be explained by a five-fold greater trophic transfer efficiency between phytoplankton and zooplankton under the sheltered conditions. Furthermore, under the sheltered conditions the Gastropoda density reached 746 individuals m−2, whereas no Gastropoda were found under the no shelter treatment. These findings indicate that for shallow lakes that are negatively affected by wind-induced turbulence, measures aimed at ameliorating this stressor can be effective in facilitating submerged macrophyte recovery, increasing Gastropoda densities and restoring trophic transfer efficiency between phytoplankton and zooplankton. Ultimately, this may support higher trophic levels such as fish and water birds by increasing their food availability in shallow lake ecosystems.