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In recent decades, the use of molecular techniques in rotifers has revealed the existence of many cryptic species. Although strong competition is expected among cryptic species, these species are often sympatric. Here, we present a review of sympatric cryptic rotifer species, focusing on those cases in which niche differentiation has been investigated. There are at least 42 cryptic rotifer species complexes, and species coexistence is commonly reported. Ecological differentiation among cryptic species has been detected in several complexes. However, the only available information regarding mechanisms that allow cryptic species coexistence is for several species of the Brachionus plicatilis complex: B. plicatilis , B. ibericus , B. rotundiformis and B. manjavacas . According to these studies, when species differ in body size, niche differentiation is related to abiotic and biotic factors (e.g. the differential use of resources and vulnerability to predation). In contrast, if species are almost identical in body size, their biotic niches and competitive abilities are very similar, and niche differentiation is facilitated by the differences in the species responses to fluctuating, physical environment in combination with the divergence in life-history traits related to diapause. Further studies of additional cryptic rotifer species are essential to know the generality of these conclusions.

Background The potential benefits of intercropping are manifold and have been repeatedly demonstrated. Intercropping has the potential to create more productive and resilient agroecosystems, by improving land utilisation, yield and yield stability, soil quality, and pest, disease and weed suppression. Despite these potential benefits, significant gaps remain in the understanding of ecological mechanisms that govern the outcomes when crop species are grown together. A major part of plant-plant interactions takes place belowground and these are often overlooked. Scope This review synthesises current evidence for belowground plant-plant interactions of competition, niche differentiation and facilitation, with the aim of identifying root traits that influence the processes contributing to enhanced performance of intercrops compared with monocultures. We identify a suite of potentially complementary root traits for maximising the benefits of intercropping. These traits underpin improved soil exploration, more efficient resource use, and suppression of soil-borne pathogens and pests in intercrops. Conclusion This review brings together understanding of the mechanisms underpinning interactions between intercropped roots, and how root traits and their plasticity can promote positive outcomes. Root trait ‘ideotypes’ for intercropped partners are identified that could be selected for crop improvement. We highlight the importance of examining belowground interactions and consider both spatial and temporal distribution of roots and rhizosphere mechanisms that aid complementarity through niche differentiation and facilitation. Breeding of crop ideotypes with specific beneficial root traits, combined with considerations for optimal spatio-temporal arrangement and ratios of component crops, are essential next steps to promote the adoption of intercropping as a sustainable farming practice.

Arbuscular mycorrhizal (AM) fungi play important functional roles in ecosystems, including the uptake and transfer of nutrients, modification of the physical soil environment and alteration of plant interactions with other biota. Several studies have demonstrated the potential for variation in AM fungal diversity to also affect ecosystem functioning, mainly via effects on primary productivity. Diversity in these studies is usually characterized in terms of the number of species, unique evolutionary lineages or complementary mycorrhizal traits, as well as the ability of plants to discriminate among AM fungi in space and time. However, the emergent outcomes of these relationships are usually indirect, and thus context dependent, and difficult to predict with certainty. Here, we advocate a fungal-centric view of AM fungal biodiversity–ecosystem function relationships that focuses on the direct and specific links betweenAMfungal fitness and consequences for their roles in ecosystems, especially highlighting functional diversity in hyphal resource economics. We conclude by arguing that an understanding of AM fungal functional diversity is fundamental to determine whether AM fungi have a role in the exploitation of marginal/novel environments (whether past, present or future) and highlight avenues for future research.

Nitrification, the oxidation of ammonia via nitrite to nitrate, has been considered to be a stepwise process mediated by two distinct functional groups of microorganisms. The identification of complete nitrifying Nitrospira challenged not only the paradigm of labor division in nitrification, it also raises fundamental questions regarding the environmental distribution, diversity, and ecological significance of complete nitrifiers compared to canonical nitrifying microorganisms. Recent genomic and physiological surveys identified factors controlling their ecology and niche specialization, which thus potentially regulate abundances and population dynamics of the different nitrifying guilds. This review summarizes the recently obtained insights into metabolic differences of the known nitrifiers and discusses these in light of potential functional adaptation and niche differentiation between canonical and complete nitrifiers.

Demand of all living organisms on the same nutrients forms the basis for interspecific competition between plants and microorganisms in soils. This competition is especially strong in the rhizosphere. To evaluate competitive and mutualistic interactions between plants and microorganisms and to analyse ecological consequences of these interactions, we analysed 424 data pairs from 41 15N-labelling studies that investigated 15N redistribution between roots and microorganisms. Calculated Michaelis–Menten kinetics based on K m (Michaelis constant) and V max (maximum uptake capacity) values from 77 studies on the uptake of nitrate, ammonia, and amino acids by roots and microorganisms clearly showed that, shortly after nitrogen (N) mobilization from soil organic matter and litter, microorganisms take up most N. Lower K m values of microorganisms suggest that they are especially efficient at low N concentrations, but can also acquire more N at higher N concentrations (V max) compared with roots. Because of the unidirectional flow of nutrients from soil to roots, plants are the winners for N acquisition in the long run. Therefore, despite strong competition between roots and microorganisms for N, a temporal niche differentiation reflecting their generation times leads to mutualistic relationships in the rhizosphere. This temporal niche differentiation is highly relevant ecologically because it: protects ecosystems from N losses by leaching during periods of slow or no root uptake; continuously provides roots with available N according to plant demand; and contributes to the evolutionary development of mutualistic interactions between roots and microorganisms.

Niche differentiation among species is a key mechanism by which biodiversity may be linked to ecosystem function. We tested a set of widely invoked hypotheses about the extent of niche differentiation in one of the most diverse communities on Earth, decomposer microorganisms, by measuring their response to changes in three abundant litter resources: lignin, cellulose, and nitrogen (N). To do this, we used the model system Arabidopsis thaliana to manipulate lignin, cellulose, and N availability and then used high-throughput sequencing to measure the response of microbial communities during decay. Resequencing the decomposer communities after incubation of decomposed litter with pure substrates showed that groups of species had unique substrate use profiles, such that species organized into functional \"guilds\" of decomposers that were associated with individual litter chemicals. Low concentrations of lignin, cellulose, or N in the litter caused unique shifts in decomposer community composition after 1 yr of decay. Low cellulose plants had low levels of fungi in all decomposer guilds, low lignin plants had high levels of fungi in all decomposer guilds, and low N plants had low levels of fungi in decomposer guilds associated with sucrose and lignin. The relative abundance of decomposer guilds correlated with the total loss of individual litter chemicals during litter decay in the field. In addition, N fertilization shifted decomposer communities during both the early and later stages of decay to those dominated by decomposers in the cellulose guild. Our results contrast the assumption that major carbon (C) and N degradation mechanisms are uniform across whole decomposer communities and instead suggest that decomposition arises from complementarity among groups of metabolically distinct taxa.

Background and aims Crop diversity has been repeatedly shown to support multiple ecosystem functions, both directly and indirectly, driven by interspecific root-root interactions. Despite continuous advances in this field, some research gaps remain, and we need to pay more attention to the design and management of multi-species and multi-cultivar systems in the future. Scope We review advances in intercropping in enhanced ecosystem functioning in competition-based and facilitation-based intercropping systems via root-root interactions. We also consider recent achievements in yield stability and soil fertility. We address several perspectives to focus on towards more sustainable agriculture via intercropping or cultivar mixtures in the future. Conclusions In competition-based systems, scramble competition via root-root competition and contest competition involving allelochemicals offset yield advantages of target crop species. However, niche differentiation and selection of desirable crop combinations to minimize negative effects through secondary metabolites may also help to gain yield advantages in intercropping and cultivar mixtures. In facilitation-based systems, selecting genotypes of facilitated species with root traits that best match the facilitator may strengthen the facilitative interactions in resource enrichment and disease and pest control. We need more long-term research to explore the effects of belowground processes on soil fertility, ecosystem stability, adaptation, and mitigation of climate change to establish sustainable agroecosystems in the future. It is also urgent to develop new methods to link belowground processes to functioning in multi-species and multi-cultivar agroecosystems.

1. A framework for the description and analysis of multilayer networks is established in statistical physics, and calls are increasing for their adoption by community ecologists. Multilayer networks in community ecology will allow space, time and multiple interaction types to be incorporated into species interaction networks.2. While the multilayer network framework is applicable to ecological questions, it is one thing to be able to describe ecological communities as multilayer networks and another for multilayer networks to actually prove useful for answering ecological questions. Importantly, documenting multilayer network structure requires substantially greater empirical investment than standard ecological networks. In response, we argue that this additional effort is worthwhile and describe a series of research lines where we expect multilayer networks will generate the greatest impact.3. Inter‐layer edges are the key component that differentiate multilayer networks from standard ecological networks. Inter‐layer edges join different networks—termed layers—together and represent ecological processes central to the species interactions studied (e.g., inter‐layer edges representing movement for networks separated in space). Inter‐layer edges may take a variety of forms, be species‐ or network‐specific, and be measured with a large suite of empirical techniques. Additionally, the sheer size of ecological multilayer networks also requires somechanges to empirical data collection around interaction quantification, collaborative efforts and collation in public databases.4. Network ecology has already touched on a wide swath of ecology and evolutionary biology. Because network stability and patterns of species linkage are the most developed areas of network ecology, they are a natural starting place for multilayer investigations. However, multilayer etworks will also provide novel insights to niche partitioning, the connection between traits and species’ interactions, and even the geographic mosaic of co‐evolution.5. Synthesis. Multilayer networks provide a formal way to bring together the study of species interaction networks and the processes that influence them. However, describing inter‐layer edges and the increasing amounts of data required represent challenges. The pay‐off for added investment will be ecological networks that describe the composition and capture the dynamics of ecological communities more completely and, consequently, have greater power for understanding the patterns and processes that underpin diversity in ecological communities.

Ectomycorrhizal (ECM) associations were historically considered rare or absent from tropical ecosystems. Although most tropical forests are dominated by arbuscular mycorrhizal (AM) trees, ECM associations are widespread and found in all tropical regions. Here, we highlight emerging patterns of ECM biogeography, diversity and ecosystem functions, identify knowledge gaps, and offer direction for future research. At the continental and regional scales, tropical ECM systems are highly diverse and vary widely in ECM plant and fungal abundance, diversity, composition and phylogenetic affinities. We found strong regional differences among the dominant host plant families, suggesting that biogeographical factors strongly influence tropical ECMsymbioses. BothECMplants and fungi also exhibit strong turnover along altitudinal and soil fertility gradients, suggesting niche differentiation among taxa. Ectomycorrhizal fungi are often more abundant and diverse in sites with nutrient-poor soils, suggesting that ECM associations can optimize plant nutrition and may contribute to the maintenance of tropical monodominant forests. More research is needed to elucidate the diversity patterns of ECM fungi and plants in the tropics and to clarify the role of this symbiosis in nutrient and carbon cycling.

• Root access to bedrock water storage or groundwater is an important trait allowing plant survival in seasonally dry environments. However, the degree of coordination between water uptake depth, leaf-level water-use efficiency (WUEi) and water potential in drought-prone plant communities is not well understood. • We conducted a 135-d rainfall exclusion experiment in a subtropical karst ecosystem with thin skeletal soils to evaluate the responses of 11 co-occurring woody species of contrasting life forms and leaf habits to a severe drought during the wet growing season. • Marked differences in xylem water isotopic composition during drought revealed distinct ecohydrological niche separation among species. The contrasting behaviour of leaf water potential in coexisting species during drought was largely explained by differences in root access to deeper, temporally stable water sources. Smaller-diameter species with shallower water uptake, more negative water potentials and lower WUEi showed extensive drought-induced canopy defoliation and/or mortality. By contrast, larger-diameter species with deeper water uptake, higher leaf-level WUEi and more isohydric behaviour survived drought with only moderate canopy defoliation. • Severe water limitation imposes strong environmental filtering and/or selective pressures resulting in tight coordination between tree diameter, water uptake depth, iso/anisohydric behaviour, WUEi and drought vulnerability in karst plant communities