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• A host-plant and its associated microbiota depend on one another. However, the assembly process and the functioning of host-associated microbiota are poorly understood. • Herein, rice was used as model plant to investigate the assemblage of bacterial microbiota, including those in the seed, root endosphere and rhizosphere. We also assessed the degree to which endosphere and rhizosphere communities were influenced by vertical transmission through seed and identified the core microbes that potentially associated with plant phenotypic properties. • Plant microhabitat, rather than subspecies type, was the major driver shaping plant-associated bacterial microbiota. Deterministic processes were primarily responsible for community assembly in all microhabitats. The influence of vertical transmission from seed to root-associated bacterial communities appeared to be quite weak (endosphere) or even absent (rhizosphere). A core microbial community composed of 15 generalist species persisted across different microhabitats and represented key connectors in networks. Host-plant functional traits were linked to the relative abundance of these generalist core microbes and could be predicted from them using machine learning algorithms. • Overall, bacterial microbiota is assembled by host-plant interactions in a deterministic-based manner. This study enhances our understanding of the driving mechanisms and associations of microbiota in various plant microhabitats and provides new perspectives to improve plant performance.

Species-specific spatial distribution in relation to environmental characteristics underpins the species diversity of coral reef fishes. This study aimed to elucidate (1) the broad-scale spatial distribution (spatial variation of fish density at intervals of several-kilometers), influenced by topographic features (exposed reef vs. inner reef), substrate characteristics and depth, and (2) the microhabitat associations (habitat association within several centimeter scale) concerning substrate availability for seven angelfish species (family Pomacanthidae) in an Okinawan coral reef. Broad-scale analysis revealed (1) Chaetodontoplus mesoleucus was primarily found in deep inner reefs with greater coverage of branching Acropora and dead coral; (2) Centropyge bicolor and C. tibicen were primarily found at shallow inner reefs with greater coverage of branching Acropora, dead coral, and sand; (3) C. ferrugata and C. vrolikii were primarily found at shallow exposed reefs with greater coverage of rock, and (4) C. heraldi and Pygoplites diacanthus were primarily found at deep exposed reefs with greater coverage of rock. Microhabitat-scale analysis revealed that three species (C. mesoleucus, C. bicolor, and C. heraldi) showed significant positive association with acroporid corals. Centropyge tibicen showed a significant positive association with living corals. The remaining three species (C. ferrugata, C. vrolikii, and P. diacanthus) did not show a positive association with living corals. This suggests that coral loss impacts angelfish population in a species-specific manner. These two spatial scale viewpoints offer valuable insight for comprehensive understandings of angelfish spatial distribution in relation to substrate characteristics.

In tropical forests, vascular epiphyte diversity increases with tree size, which could result from an increase in area, time for colonization or an increase in microhabitat heterogeneity within‐tree crowns if vascular epiphyte species are specialized to particular microhabitats within the crown. The importance of microhabitats in structuring epiphyte communities has been hypothesized for more than 120 years but not yet confirmed. We tested the importance of microhabitats in structuring epiphyte communities by examining microhabitat heterogeneity and epiphyte communities within the crowns of different‐sized Virola koschnyi (Myristicaceae) emergent trees in a Costa Rican tropical wet forest. We tested the degree to which epiphyte species composition was associated with environmental conditions and resources (i.e. microhabitats) using multivariate analyses and a null model that compared the observed epiphyte assemblages amongst different‐sized trees and crown zones with assemblages generated randomly. This study is the first to rigorously examine the degree of microhabitat specialization in epiphyte communities. Microhabitat heterogeneity, epiphyte species richness and abundance increased with tree size. The largest trees had the highest microhabitat and epiphyte diversity and a unique inner crown microhabitat with canopy humus. The few epiphytes found on small trees were mostly bark ferns. Large trees had different epiphyte communities in different parts of the crown; the inner crown contained species not abundant in any other microhabitat (i.e. aroids, cyclanths and humus ferns), and the outer crown contained bark ferns and atmospheric bromeliads. Variation in species composition amongst tree size classes was significantly related to the mean daily maximum vapour pressure deficit and tree diameter, while variation within large tree crowns was significantly related to canopy humus cover. Microhabitat specialization of epiphyte species increased with tree size with 6% of species significantly associated with small trees and 57% significantly associated with large trees. Of the species present in large tree crowns, 23% were specialized to the unique inner crown microhabitat. Synthesis. The increase in microhabitat heterogeneity within tree crowns as trees grow contributes to changes in epiphyte community structure, which supports decades‐old hypotheses of the importance of microhabitat diversity and specialization in structuring tropical epiphyte communities.

The freshwater pearl mussel Margaritifera margaritifera is an endangered bivalve which is usually regarded as sedentary, although individual movement has been observed both vertically and horizontally. Little is known about the causes and rates of mussel movement. The objective of this study was to test the effect of microhabitat characteristics on the horizontal movement distance and rates of freshwater pearl mussels. A total of 120 mussels (length range 40–59 mm) were marked individually with passive integrated transponder tags, placed in stream microhabitats differing in their sediment composition and monitored biweekly over a period of 10 weeks. Mussels situated in sand-dominated habitats had a significantly higher mean movement rate (3.2 ± 4.2 cm/day, mean ± SD) than mussels situated in gravel-dominated (1.9 ± 2.7 cm/day) or stone-dominated habitats (1.8 ± 3.2 cm/day). The direction of the movements appeared random; however, an emigration from sandy habitats was observed, probably to avoid dislodgment from these hydraulically unstable habitats. This study demonstrates that freshwater pearl mussels can actively emigrate from unsuitable microhabitats. Once suitable streams with respect to physical, chemical, and biological quality were identified, it is therefore only necessary to identify suitable mesohabitats (area of 10–30 m2) when reintroducing or relocating mussels.

1. National and international forest biodiversity assessments largely rely on indirect indicators, based on elements of forest structure that are used as surrogates for species diversity. These proxies are reputedly easier and cheaper to assess than biodiversity. Tree microhabitats - tree-borne singularities such as cavities, conks of fungi or bark characteristics - have gained attention as potential forest biodiversity indicators. However, as with most biodiversity indicators, there is a lack of scientific evidence documenting their quantitative link with the biodiversity they are supposed to assess. 2. We explored the link between microhabitat indices and the richness and abundance of three taxonomic groups: bats, birds, and saproxylic beetles. Using a nation-wide multi-taxon sampling design in France, we compared 213 plots located inside and outside strict forest reserves. We hypothesized that the positive effect setting aside forest reserves has on biodiversity conservation is indirectly due to an increase in the proportion of large structural elements (e.g. living trees, standing and lying deadwood). These, in turn, are likely to favour the quantity and diversity of microhabitats. We analysed the relationship between the abundance and species richness of different groups and guilds (e.g. red-listed species, forest specialists, cavity dwellers) and microhabitat density and diversity. We then used confirmatory structural equation models to assess the direct and indirect effects of management abandonment, large structural elements and microhabitats on the biodiversity of the target species. 3. For several groups of birds and bats, the indirect effect of management abandonment and large structural elements on biodiversity was mediated by microhabitats. However, the magnitude of the link between microhabitat indices and biodiversity was moderate. In particular, saproxylic beetles' biodiversity was poorly explained by microhabitats, large structural elements or management abandonment. 4. Synthesis and applications: Tree microhabitats may serve as indicators for bats and birds, but they are not a universal biodiversity indicator. Rather, compared to large structural elements, they most likely have a complementary role to biodiversity. In terms of forest management and conservation, preserving diversity of microhabitats at the local scale benefits several groups of both bats and birds.

Structural complexity provided by the living coral reef framework is the basis of the rich and dynamic biodiversity in coral reefs. In many cases today, the reduction in habitat complexity, from live coral to dead coral and rubble, has altered the abundance and diversity of many reef species with impacts on community structure, food webs and ecosystem functioning. Yet, the complex microhabitat provided by rubble can too support a great density and diversity of reef organisms, often with explicit roles in ecosystem functioning. This literature review synthesises available knowledge on the biology and ecology of coral rubble. We highlight key methodologies used to sample rubble communities, and the biological and ecological consequences of ongoing habitat degradation from coral to rubble reefs under future scenarios. We conclude with a number of key research themes that may enhance our capacity to understand the current contribution of rubble communities to reef functioning and predict their ability to modulate future impacts as net framework erosion amplifies.

Nurse plants promote establishment of other plant species by buffering climate extremes and improving soil properties. Soil biota plays an important role, but an analysis to disentangle the effects of soil microorganisms, soil properties and microclimate on facilitation is lacking. In three microhabitats (gaps, small and large Retama shrubs), we placed six microcosms with sterilized soil, two per soil origin (i.e. from each microhabitat). One in every pair received an alive, and the other a sterile, inoculum from its own soil. Seeds of annual plants were sown into the microcosms. Germination, survival and biomass were monitored. Soil bacterial communities were characterized by pyrosequencing. Germination in living Retama inoculum was nearly double that of germination in sterile inoculum. Germination was greater under Retama canopies than in gaps. Biomass was up to three times higher in nurse than in gap soils. Soil microorganisms, soil properties and microclimate showed a range of positive to negative effects on understory plants depending on species identity and life stage. Nurse soil microorganisms promoted germination, but the effect was smaller than the positive effects of soil properties and microclimate under nurses. Nurse below-ground environment (soil properties and microorganisms) promoted plant growth and survival more than nurse microhabitat.

Considerable research is aimed at developing predictions of ecosystem responses to climate change, focusing on the spatial scale, such as range shifts and contractions, as well as activity restrictions to shaded microhabitats. On the other hand, the ability of species to shift their activity times during the diel cycle, and consequently to alter the environment in which activity occurs, has been largely neglected. Daily activity patterns are perceived as fairly fixed; however, natural changes in activity patterns have been reported in increasing numbers of species. Here, we present a framework that explores how shifts in activity patterns may buffer impacts of climate change. To demonstrate our framework, we simulated costs of activity of diurnal and nocturnal rodents and showed that future summers may decrease the energetic demands of nocturnal mammals while increasing water demands of diurnal mammals. Climate projections suggest that vegetation cover and water availability will decrease under future climate scenarios, especially in areas where water demands are expected to increase the most. These changes are expected to limit the ability of diurnal animals to restrict activity to shaded microhabitats and to keep a positive water balance. Our analysis shows that by shifting to nocturnality, diurnal mammals may mitigate the high water costs of future summers. We suggest that future research should explore the role of the diel time axis as an ecological resource when predicting the impacts of climate change.

During the early benthic phase of intertidal invertebrates, desiccation and elevated temperature are increasingly recognized as the most significant stressors, but it is not known whether all species are equally sensitive during this phase. In this study, involving 6 co-occurring rocky intertidal species (Nucella ostrina, Littorina scutulata, Mytilus trossulus, Chthamalus dalli, Balanus glandula, Petrolisthes cinctipes), we examined interspecific variation in (1) tolerance to desiccation and temperature at the early benthic phase and (2) the magnitude of ontogenetic shifts in tolerance. Ontogenetic shifts in temperature tolerance were significant but modest, whereas desiccation tolerance thresholds changed considerably throughout ontogeny in all species, and shifts were greatest in species that changed microhabitats during ontogeny. Tolerance at the early benthic phase also varied markedly among species; temperature tolerance thresholds ranged from 32.3 to 45.8°C, and juveniles were able to survive exposure to desiccation for durations ranging from 10 min to 29 h. Ontogenetic shifts in desiccation tolerance were largely ex plained by differences in body mass; thus individuals achieve increased tolerance through growth. However, variation among species was unrelated to body mass; rather, interspecific variation in tolerance thresholds of the early benthic phase was related to the upper limit of intertidal distribution of the species and to microhabitat use during this phase. The study revealed desiccation to be a greater threat to early benthic phase individuals than temperature in all species, but also discovered considerable interspecific differences in tolerance thresholds, such that species are likely to respond differently to present and future extremes in desiccation and temperature.

Springs ecosystems are globally abundant, geomorphologically diverse, and bioculturally productive, but are highly imperiled by anthropogenic activities. More than a century of scientific discussion about the wide array of ecohydrological factors influencing springs has been informative, but has yielded little agreement on their classification. This lack of agreement has contributed to the global neglect and degradation of springs ecosystems by the public, scientific, and management communities. Here we review the historical literature on springs classification variables, concluding that site-specific source geomorphology remains the most diagnostic approach. We present a conceptual springs ecosystem model that clarifies the central role of geomorphology in springs ecosystem development, function, and typology. We present an illustrated dichotomous key to terrestrial (non-marine) springs ecosystem types and subtypes, and describe those types. We identify representative reference sites, although data limitations presently preclude selection of continentally or globally representative reference springs of each type. We tested the classification key using data from 244 randomly selected springs of 13 types that were inventoried in western North America. The dichotomous key correctly identified springs type in 87.5% of the cases, with discrepancies primarily due to differentiation of primary vs. secondary typology, and insufficient inventory team training. Using that information, we identified sources of confusion and clarified the key. Among the types that required more detailed explanation were hypocrenes, springs in which groundwater is expressed through phreatophytic vegetation. Overall, springs biodiversity and ecosystem complexity are due, in part, to the co-occurrence of multiple intra-springs microhabitats. We describe microhabitats that are commonly associated with different springs types, reporting at least 13 microhabitats, each of which can support discrete biotic assemblages. Interdisciplinary agreement on basic classification is needed to enhance scientific understanding and stewardship of springs ecosystems, the loss and degradation of which constitute a global conservation crisis.