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Different from other fungal species that can be largely cultivated in ‘axenic conditions’ using plant material (e.g., species of Lentinula and Pleurotus in ‘sterile’ straw-based substrate), the commercial Agaricus bisporus cultivation system relies heavily on ecological relationships with a broad range of microorganisms present in the system (compost and casing). Since the A. bisporus cultivation system consists of a microbial manipulation process, it is important to know the microbial community dynamics during the entire cultivation cycle to design further studies and/or crop management strategies to optimize this system. To capture the bacterial community ‘flow’ from compost raw materials to the casing to the formation and maturation of mushroom caps, community snapshots were generated by direct DNA recovery (amplicon sequencing). The ‘bacterial community flow’ revealed that compost, casing and mushrooms represent different niches for bacteria present in the cultivation system, but at the same time, a bacterial exchange between microenvironments can occur for a portion of the community. Within each microenvironment, compost showed intense bacterial populational dynamics, probably due to the environmental changes imposed by composting conditions. In casing, the colonization of A. bisporus appeared, to reshape the native bacterial community which later, with some other members present in compost, becomes the core community in mushroom caps. The current bacterial survey along with previous results provides more cues of specific bacteria groups that can be in association with A. bisporus development and health.

1. Plant tolerance to herbivory has been accepted as a mechanism of defense that can be expressed jointly with resistance. Recent advances have partially validated previous theoretical predictions and improved our understanding of tolerance. Here, I highlight the necessity of integrating tolerance into ecological and co-evolutionary theory to better understand the biology of this defensive mechanism. 2. Existing work has been biased toward understanding the adaptive nature and constraints acting on tolerance rather than its ecological implications. Increasing consensus that tolerance may alter the classical antagonistic dynamic between plants and herbivores suggests possible avenues to explore its population and community consequences. 3. In this review, I summarize previous advances in the ecology and evolution of tolerance to herbivory. I also discuss recent evidence that improves our understanding of unresolved issues such as the specificity of tolerance in response to herbivory, its role as an agent of selection on herbivores, and its ecological and evolutionary consequences which include a role of tolerance during biological invasions. 4. Although there is good support for an adaptive role of tolerance in response to herbivory damage, tolerance can itself impose selection on herbivores. Furthermore, tolerance can influence herbivore population dynamics and coexistence, as recent studies show that tolerance responses increase diversity of the associated herbivore communities on individual host plants. 5. Future studies that take into account the role of herbivores on the expression of tolerance will provide novel insight that will help disentangle the mechanisms of tolerance and its ecological and evolutionary implications.

Aim: Spatial extent is inherently related to the potential roles of the main mechanisms structuring metacommunities. We examined the effects of varying spatial extent (ecological province, region and subregion) on the environmental and spatial components of variation in lake macrophyte communities. We also studied these effects separately for three macrophyte functional groups. Location: The US state of Minnesota. Methods: We examined average and heterogeneity differences in macrophyte community composition and environmental variation among the subregions of Minnesota using canonical analysis of principal coordinates (CAP) and homogeneity of multivariate dispersion (PERMDISP), respectively. We further used partial redundancy analysis (pRDA) to decompose variation in macrophyte community composition between environmental variables and spatial location at each spatial extent and geographical region. Spatial variables were derived using principal coordinates of neighbour matrices (PCNM) analysis. Results: CAP and PERMDISP analyses showed that the subregions differed both in average community composition and in the heterogeneity of community composition for all macrophyte taxa, for emergent and submerged macrophytes, but not for non-rooted macrophytes. We did not, however, find significant differences in overall environmental heterogeneity among the subregions. Variation partitioning using pRDAs showed that species sorting is more important than spatial processes for macrophytes, although these patterns were relatively weak. There was, however, much regional specificity, with the environmental and spatial fractions of community composition varying widely at different spatial extents, among different geographical regions and among functional groups. Contrary to our initial expectations, we did not find increasing spatial structuring and decreasing environmental control with increasing spatial extent. Main conclusions: Our findings indicate that, in macrophyte metacommunities, the relative contribution of spatial processes and environmental control varies rather unpredictably with spatial extent and geographical region. Our findings are thus of importance in advancing metacommunity ecology by showing that drawing wide-ranging conclusions based on a single spatial extent or a single geographical region may be unwise.

Much of life's diversity has arisen through ecological opportunity and adaptive radiations, but the mechanistic underpinning of such diversification is not fully understood. Competition and predation can affect adaptive radiations, but contrasting theoretical and empirical results show that they can both promote and interrupt diversification. A mechanistic understanding of the link between microevolutionary processes and macroevolutionary patterns is thus needed, especially in trophic communities. Here, we use a trait-based eco-evolutionary model to investigate the mechanisms linking competition, predation and adaptive radiations. By combining available micro-evolutionary theory and simulations of adaptive radiations we show that intraspecific competition is crucial for diversification as it induces disruptive selection, in particular in early phases of radiation. The diversification rate is however decreased in later phases owing to interspecific competition as niche availability, and population sizes are decreased. We provide new insight into how predation tends to have a negative effect on prey diversification through decreased population sizes, decreased disruptive selection and through the exclusion of prey from parts of niche space. The seemingly disparate effects of competition and predation on adaptive radiations, listed in the literature, may thus be acting and interacting in the same adaptive radiation at different relative strength as the radiation progresses.

The extraordinary diversity in long-lived lakes is largely driven by distinct eco-evolutionary processes. With their unique biota and numerous endemic taxa, these lakes are key settings for fundamental studies related to ecology, diversity, and evolution. Here, we test how the environment shapes diatom diversity and community patterns over space in ancient Lake Ohrid. By applying Bray–Curtis similarity analyses of diatom community data, including widespread and endemic taxa, we identified two major zones: littoral and sublittoral. The latter one is being characterized with higher endemic diversity. The α and β diatom diversity and community distribution in the northern and eastern part of the lake are influenced by the presence of vertical (bathymetrical) and horizontal barriers. The zonation of the diatom communities appears driven by two large-scale factors: (i) water depth, and (ii) water chemistry, primarily, the concentration of total phosphorus, nitrogen ammonia, and conductivity. Both drivers appear to equally influence diatom diversity and community patterns. We present initial data on diatom–environment relations, where the results support earlier ecological studies emphasizing the relevance of ongoing human-induced eutrophication in the northern lake area. This study provides background information on the role of the environment in structuring contemporary diatom diversity. However, future research needs to focus on the biotic component including species competition in order to reveal the mechanisms driving spatial community dynamics in Lake Ohrid.

Understanding how wetland plant communities are organized in different ecosystems and spatial scales is essential to support conservation. Studies that have addressed this primary need, however, are exceptionally scarce. Here, we compared the diversity (alpha, beta and gamma) and composition of herbaceous and woody communities (treated separately and jointly) in ponds, streambanks and riverbanks in the upper Uruguay River Basin, southern Brazil. Results showed that each wetland ecosystem exhibited unique community patterns, depending on the plant group, data property (e.g., presence-absence or abundance), and community parameter. All ecosystem types had exclusive species, beta diversity explained by high rates of species turnover and balanced variation in abundance components, and particular floristic composition, revealing that each wetland type and site contributes fundamentally to the overall wetland plant diversity. These findings indicate that safeguarding wetland plant diversity depends on the adoption of holistic conservation measures.

While considering important juvenile fish habitats individually, both seagrass and saltmarsh are often highly connected with other subtidal and intertidal habitats. As a result, juvenile fishes and crustaceans may utilize multiple habitats across tidal, diel, or seasonal cycles in a manner that makes interhabitat proximity an important driver of fish distribution and community composition. In this context, we examined the importance of seagrass (Zostera marina and Halodule wrightii) and saltmarsh (Spartina alterniflora) habitat characteristics in driving fish and crustacean catch rates and community composition in a temperate, polyhalineeuhaline, estuary. We found that habitats with highly connected seagrass and saltmarsh vegetation exhibited higher average catch rates of many recreationally and commercially valuable fish and crustacean species, as well as overall nekton catch rates and Shannon diversity (H), than habitats composed of either seagrass or saltmarsh habitat alone. Nekton-habitat associations varied temporally, showing strong seasonal trends which were potentially indicative of temporal shifts in relative habitat value. Catch rates of numerous recreationally and commercially targeted species were correlated with patchscale variables, particularly seagrass canopy height, water temperature, and depth; however, regression analysis indicated that habitat type was more powerful in predicting overall nekton catch rates and Shannon diversity (H). We conclude that emergent properties (i.e., those operating at 10-100s m) are important drivers of nekton distributions among and within habitats. Considering the spatial and temporal scales at which humans are encroaching on estuarine ecosystems, our findings highlight the need for investigating organism-habitat associations at expanded spatial scales, as well as the need to adopt fishery and coastal management plans that consider habitat characteristics at multiple spatial scales to account for interhabitat connectivity.

Newly created academic programs at Brazilian universities have provided the impetus for new archaeological projects in southeastern South America during the last two decades. The new data are changing our views on emergent social complexity, natural and human-induced transformation of the landscape, and transcontinental expansions and cultural interactions across the Rio de la Plata basin during the Middle and Late Holocene. We concentrate on six major archaeological traditions/regions: the Sambaquis, the Pantanal, the Constructores de Cerritos, the Tupiguarani, the Southern Proto-Jê, and the middle and lower Paraná River. Diverse and autonomous complex developments exhibit distinct built landscapes in a region previously thought of as marginal compared with cultural developments in the Andes or Mesoamerica. The trajectories toward increased sociopolitical complexity flourished in very different and changing environmental conditions. While some groups were pushed to wetland areas during a drier mid-Holocene, others took advantage of the more humid Late Holocene climate to intensively manage Araucaria forests. The start of the second millennium AD was a critical period marked by an increased number of archaeological sites, the construction of ceremonial architecture, and the intensification of landscape transformation; it also was marked by the rapid expansion of influences from outside the La Plata basin. The Amazonian Tupiguarani and Arawak newcomers brought with them significant changes in technologies and social and political structures, as well as novel landscape management practices.

Taxonomic sufficiency (TS) has been proposed for assessing community composition and environmental impacts as a way to balance the need to indicate the biology of the organisms present with time and effort needed for species identification. TS has been applied most often to marine and freshwater macroinvertebrates, but tests of its usefulness are lacking for other freshwater groups. We analyzed the effects of taxonomic resolution, functional groupings, and data transformation on multivariate community patterns in periphyton, macrophytes, macroinvertebrates, and fishes, and on the quantification of biodiversity and environmental gradients. The applicability of TS differed strongly among taxonomic groups, depending on the average taxonomic breadth of the species sets. Numerical data resolution had more pronounced effects on community patterns than taxonomic resolution. Richness was strongly affected by data aggregation, but diversity indices were statistically reliable up to order level. Taxonomic aggregation had no significant influence on ability to detect environmental gradients. Functional surrogates based on biological traits, such as feeding type, reproductive strategy, and trophic state, were strongly correlated (ρ  =  0.64–0.85) with taxonomic community composition. However, environmental correlations were generally lower with data aggregated to functional traits rather than to species. TS was universally applicable within taxonomic groups for different habitats in one biogeographic region. Aggregation to family or order was suitable for quantifying biodiversity and environmental gradients, but multivariate community analyses required finer resolution in fishes and macrophytes than in periphyton and macroinvertebrates. Sampling effort in environmental-impact studies and monitoring programs would be better invested in quantitative data and number of spatial and temporal replicates than in taxonomic detail.

This study is kindly supported by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation (FZT 118). The Article processing charges were funded by the Open Science Office of the Leipzig University Library.