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Accompanying the climate crisis is the more enigmatic biodiversity crisis. Rapid reorganization of biodiversity due to global environmental change has defied prediction and tested the basic tenets of conservation and restoration. Conceptual and practical innovation is needed to support decision making in the face of these unprecedented shifts. Critical questions include: How can we generalize biodiversity change at the community level? When are systems able to reorganize and maintain integrity, and when does abiotic change result in collapse or restructuring? How does this understanding provide a template to guide when and how to intervene in conservation and restoration? To this end, we frame changes in community organization as the modulation of external abiotic drivers on the internal topology of species interactions, using plant-plant interactions in terrestrial communities as a starting point. We then explore how this framing can help translate available data on species abundance and trait distributions to corresponding decisions in management. Given the expectation that community response and reorganization are highly complex, the external-driver internal-topology (EDIT) framework offers a way to capture general patterns of biodiversity that can help guide resilience and adaptation in changing environments.

Bacterial and fungal root endophytes can impact the fitness of their host plants, but the relative importance of drivers for root endophyte communities is not well known. Host plant species, the composition and density of the surrounding plants, space, and abiotic drivers could significantly affect bacterial and fungal root endophyte communities. We investigated their influence in endophyte communities of alpine plants across a harsh high mountain landscape using high-throughput sequencing. There was less compositional overlap between fungal than bacterial root endophyte communities, with four 'cosmopolitan' bacterial OTUs found in every root sampled, but no fungal OTUs found across all samples. We found that host plant species, which included nine species from three families, explained the greatest variation in root endophyte composition for both bacterial and fungal communities. We detected similar levels of variation explained by plant neighborhood, space, and abiotic drivers on both communities, but the plant neighborhood explained less variation in fungal endophytes than expected. Overall, these findings suggest a more cosmopolitan distribution of bacterial OTUs compared to fungal OTUs, a structuring role of the plant host species for both communities, and largely similar effects of the plant neighborhood, abiotic drivers, and space on both communities.

While it is well established that microbial composition and diversity shift along environmental gradients, how interactions among microbes change is poorly understood. Here, we tested how community structure and species interactions among diverse groups of soil microbes (bacteria, fungi, non-fungal eukaryotes) change across a fundamental ecological gradient, succession. Our study system is a high-elevation alpine ecosystem that exhibits variability in successional stage due to topography and harsh environmental conditions. We used hierarchical Bayesian joint distribution modeling to remove the influence of environmental covariates on species distributions and generated interaction networks using the residual species-to-species variance-covariance matrix. We hypothesized that as ecological succession proceeds, diversity will increase, species composition will change, and soil microbial networks will become more complex. As expected, we found that diversity of most taxonomic groups increased over succession, and species composition changed considerably. Interestingly, and contrary to our hypothesis, interaction networks became less complex over succession (fewer interactions per taxon). Interactions between photosynthetic microbes and any other organism became less frequent over the gradient, whereas interactions between plants or soil microfauna and any other organism were more abundant in late succession. Results demonstrate that patterns in diversity and composition do not necessarily relate to patterns in network complexity and suggest that network analyses provide new insight into the ecology of highly diverse, microscopic communities.

Arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) are two fungal groups that colonize plant roots and can benefit plant growth, but little is known about their landscape distributions. We performed sequencing and microscopy on a variety of plants across a high-elevation landscape featuring plant density, snowpack, and nutrient gradients. Percent colonization by both AMF and DSE varied significantly among plant species, and DSE colonized forbs and grasses more than sedges. AMF were more abundant in roots at lower elevation areas with lower snowpack and lower phosphorus and nitrogen content, suggesting increased hyphal recruitment by plants to aid in nutrient uptake. DSE colonization was highest in areas with less snowpack and higher inorganic nitrogen levels, suggesting an important role for these fungi in mineralizing organic nitrogen. Both of these groups of fungi are likely to be important for plant fitness and establishment in areas limited by phosphorus and nitrogen.

Despite decades of interest, few studies have provided evidence supporting theoretical expectations for coupled relationships between aboveground and belowground diversity and ecosystem functioning in non-manipulated natural ecosystems. We characterized plant species richness and density, soil bacterial, fungal and eukaryotic species richness and phylogenetic diversity (using 16S, ITS, and 18S gene sequencing), and ecosystem function (levels of soil C and N, and rates of microbial enzyme activities) along a natural gradient in plant richness and density in high-elevation, C-deficient soils to examine the coupling between above- and belowground systems. Overall, we observed a strong positive relationship between aboveground (plant richness and density) and belowground (bacteria, fungi, and non-fungal eukaryotes) richness. In addition to the correlations between plants and soil communities, C and N pools, and rates of enzyme activities increased as plant and soil communities became richer and more diverse. Our results suggest that the theoretically expected positive correlation between above- and belowground communities does exist in natural systems, but may be undetectable in late successional ecosystems due to the buildup of legacy organic matter that results in extremely complex belowground communities. In contrast, microbial communities in early successional systems, such as the system described here, are more directly dependent on contemporary inputs from plants and therefore are strongly correlated with plant diversity and density.

Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past disturbances can alter microbial community structure and their response to subsequent disturbance events, but it remains unclear if the same recovery patterns persist after long‐term exposure to stress. Here, we compare bacterial community composition in a community that experienced 2 years of monthly salinity addition disturbances with a community that has not experienced salinity additions. We then track the response and recovery to an additional salinity addition based on past disturbance exposure. We tested the following hypotheses: first, communities with a repeated disturbance history will have a different community composition than communities without a disturbance history; second, communities exposed to repeated disturbances will undergo a different recovery trajectory than communities experiencing a novel disturbance. We find that repeated disturbances alter community composition and affect community response and recovery to a subsequent disturbance after 2 years, primarily through increased resistance. This work enhances our understanding of microbial temporal dynamics and suggests that novel disturbances may pose a threat to microbial community structure and function. [ABSTRACT FROM AUTHOR]

Background: High-elevation mountain systems may be particularly responsive to climate change. Aims: Here we investigate how changes along elevation gradients in mountain systems can aid in predicting vegetation distributional changes in time, focusing on how changing climatic controls affect meso-scale transitions at the lower and upper boundaries of alpine vegetation (with forest and subnival zones, respectively) as well as micro-scale transitions among plant communities within the alpine belt. We focus on climate-related drivers, particularly in relation to climate change, but also consider how species interactions, dispersal and responses to disturbance may influence plant responses to these abiotic drivers. Results: Empirical observations and experimental studies indicate that changing climatic controls influence both meso-scale transitions at the upper and lower boundaries of alpine vegetation and micro-scale transitions among plant communities within tundra. Micro-scale heterogeneity appears to buffer response in many cases, while interactions between climate and other changes may often accelerate change. Conclusions: Interactions with microtopography and larger edaphic gradients have the capacity to both facilitate rapid changes and reinforce stability, and that these interactions will affect the responsiveness of vegetation to climate change at different spatial scales.

Summary: Environmental change can affect species directly by altering their physical environment and indirectly by altering the abundance of interacting species. A key challenge at the interface of community ecology and conservation biology is to predict how direct and indirect effects combine to influence response in a changing environment. In particular, little is known about how direct and indirect effects on biodiversity develop over time or their potential to influence ecosystem function. We studied how nitrogen (N), winter precipitation (snow) and warming influenced diversity and ecosystem function over 6 years in alpine tundra. We used path analyses to partition direct effects of environmental manipulations from indirect effects due to changes in the abundance of two dominant plants. We hypothesize that (i) indirect effects will develop more slowly but will become stronger than direct effects over time and (ii) after 6 years, indirect effects will more strongly influence diversity while direct effects will influence ecosystem function. Indirect effects of N on diversity were consistently stronger than direct effects and actually developed quickly, prior to direct effects. Direct effects of snow on diversity were detected in year 2 but then subsequently were reversed, while indirect effects were detected in year 4 and grew stronger over time. Overall in year 6, indirect effects were much stronger than direct effects on diversity. Direct effects predominated for three of four ecosystem functions we measured (productivity, N mineralization, winter N availability). The only indirect effects we found were that N and snow indirectly affected microbial biomass N by influencing Geum abundance. Across all four ecosystem measures, indirect effects were infrequent and weaker than direct effects. Synthesis. Increasing indirect effects on diversity over time indicate that short-term experiments or monitoring of natural systems may underestimate the full magnitude of global change effects on plant communities. Moreover, explicitly accounting for changes in dominant plant abundance may be necessary for forecasting plant community response to environmental change. Conversely, weak indirect effects for ecosystem processes suggest that predicting ecosystem function without knowledge of plant responses to global change may be possible. Increasing indirect effects on diversity over time indicate that short-term experiments or monitoring of natural systems may underestimate the full magnitude of global change effects on plant communities. Explicitly accounting for changes in dominant plant abundance may be necessary for forecasting plant community response to environmental change. Conversely, weak indirect effects for ecosystem processes suggest that predicting ecosystem function without knowledge of plant responses to global change may be possible.

Understanding how biotic mechanisms confer stability in variable environments is a fundamental quest in ecology, and one that is becoming increasingly urgent with global change. Several mechanisms, notably a portfolio effect associated with species richness, compensatory dynamics generated by negative species covariance and selection for stable dominant species populations can increase the stability of the overall community. While the importance of these mechanisms is debated, few studies have contrasted their importance in an environmental context. We analyzed nine long-term data sets of grassland species composition to investigate how two key environmental factors, precipitation amount and variability, may directly influence community stability and how they may indirectly influence stability via biotic mechanisms. We found that the importance of stability mechanisms varied along the environmental gradient: strong negative species covariance occurred in sites characterized by high precipitation variability, whereas portfolio effects increased in sites with high mean annual precipitation. Instead of questioning whether compensatory dynamics are important in nature, our findings suggest that debate should widen to include several stability mechanisms and how these mechanisms vary in importance across environmental gradients.

Strawberry guava (waiawī, Psidium cattleyanum Sabine, Myrtaceae) is a small tree invasive on oceanic islands where it may alter forest ecosystem processes and community structure. To better understand the dynamics of its invasion in Hawaiian rainforests in anticipation of the release of a biocontrol agent, we measured growth and abundance of vertical stems ≥0.5 cm DBH for 16 years (2005–2020) in Metrosideros‐Cibotium rainforest on windward Hawai'i Island. Specifically, we compared the growth and abundance of both shoots (originating from seed or from the root mat) and sprouts (originating above ground from established stems) in four replicate study sites. Mean stem density increased from 9562 stems/ha in 2005 to 26,595 stems/ha in 2020, the majority of which were stems <2 cm DBH. Early in the invasion, both density and per capita recruitment of shoots was greater than that of sprouts, but as overall stem density increased, sprout abundance and recruitment came to surpass that of shoots. Relative growth rates among small stems <2 cm DBH declined over time for both shoots and sprouts, but relative growth rates of sprouts were consistently greater than that of shoots after the first 3 years. The capacity of strawberry guava to recruit from both shoots and sprouts facilitates its invasion of rainforest, its persistence in the forest understory, and its response to canopy opening. Strawberry guava thus poses a considerable risk of stand replacement for Hawaiian rainforests. Stand management will require perpetual efforts to control both seed production and sprouting. [ABSTRACT FROM AUTHOR]

Climate gradients shape spatial variation in the richness and composition of plant communities. Given future predicted changes in climate means and variability, and likely regional variation in the magnitudes of these changes, it is important to determine how temporal variation in climate influences temporal variation in plant community structure. Here, we evaluated how species richness, turnover, and composition of grassland plant communities responded to interannual variation in precipitation by synthesizing long-term data from grasslands across the United States. We found that mean annual precipitation,(MAP) was a positive predictor of species richness across sites, but a positive temporal relationship between annual precipitation and richness was only evident within two sites with low MAP. We also found higher average rates of species turnover in dry sites that in turn had a high proportion of annual species, although interannual rates of species turnover were surprisingly high across all locations. Annual species were less abundant than perennial species at nearly all sites, and our analysis showed that the probability of a species being lost or gained from one year to the next increased with decreasing species abundance. Bray-Curtis dissimilarity from one year to the next, a measure of species composition change that is influenced mainly by abundant species, was insensitive to precipitation at all sites. These results suggest that the richness and turnover patterns we observed were driven primarily by rare species, which comprise the majority of the local species pools at these grassland sites. These findings are consistent with the idea that short-lived and less abundant species are more sensitive to interannual climate variability than longer-lived and more abundant species. We conclude that, among grassland ecosystems, xeric grasslands are likely to exhibit the greatest responsiveness of community composition (richness and turnover) to predicted future increases in interannual precipitation variability. Over the long-term, species composition may shift to reflect spatial patterns of mean precipitation; however, perennial-dominated systems will be buffered against rising interannual variation, while systems that have a large number of rare, annual species will show the greatest temporal variability in species composition in response to rising interannual variability in precipitation.

Abstract Background Approximately 25% of hospitalized patients have a urinary catheter, and catheter associated urinary tract infection is the most common nosocomial infection in the US, causing >1 million cases/year. However, the natural history of the biofilms that rapidly form on urinary catheters and lead to infection is not well described. Findings We characterized the dynamics of catheter colonization among catheters collected from 3 women and 5 men in a trauma burn unit with different indwelling times using TRFLP and culture. All patients received antibiotic therapy. Results: Colony-forming units increased along the extraluminal catheter surface from the catheter balloon to the urethra, but no trend was apparent for the intraluminal surface. This suggests extraluminal bacteria come from periurethral communities while intraluminal bacteria are introduced via the catheter or already inhabit the urine/bladder. Richness of operational taxonomic units (OTUs) increased over time on the intraluminal surface, but was constant extraluminally. Conclusions OTU community composition was explained best by time rather than axial location or surface. Our results suggest that catheter colonization can be very dynamic, and possibly have a predictable succession.

Premise: The soil microbiome plays a role in plant trait expression and fitness, and plants may be locally adapted or maladapted to their soil microbiota. However, few studies of local adaptation in plants have incorporated a microbial treatment separate from manipulations of the abiotic environment, so our understanding of microbes in plant adaptation is limited. Methods: Here we tested microbial effects on local adaptation in four paired populations of an abundant alpine plant from two community types, dry and moist meadow. In a 5‐month greenhouse experiment, we manipulated source population, soil moisture, and soil microbiome and measured plant survival and biomass to assess treatment effects. Results: Dry meadow populations had higher biomass than moist meadow populations at low moisture, demonstrating evidence of local adaptation to soil moisture in the absence of microbes. In the presence of microbes, dry meadow populations had greater survival than moist meadow populations when grown with dry meadow microbes regardless of moisture. Moist meadow populations showed no signs of adaptation or maladaptation. Conclusions: Our research highlights the importance of microbial mutualists in local adaptation, particularly in dry environments with higher abiotic stress. Plant populations from environments with greater abiotic stress exhibit different patterns of adaptation when grown with soil microbes versus without, while plant populations from less abiotically stressful environments do not. Improving our understanding of the role microbes play in plant adaptation will require further studies incorporating microbial manipulations. [ABSTRACT FROM AUTHOR]