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Abstract Disturbances can produce a spectrum of short‐ and long‐term ecological consequences that depend on complex interactions of the characteristics of the event, antecedent environmental conditions, and the intrinsic properties of resistance and resilience of the affected biological system.We used Hurricane Harvey's impact on coastal rivers of Texas to examine the roles of storm‐related changes in hydrology and long‐term precipitation regime on the response of stream invertebrate communities to hurricane disturbance.We detected declines in richness, diversity and total abundance following the storm, but responses were strongly tied to direct and indirect effects of long‐term aridity and short‐term changes in stream hydrology. The amount of rainfall a site received drove both flood duration and flood magnitude across sites, but lower annual rainfall amounts (i.e. aridity) increased flood magnitude and decreased flood duration. Across all sites, flood duration was positively related to the time it took for invertebrate communities to return to a long‐term baseline and flood magnitude drove larger invertebrate community responses (i.e. changes in diversity and total abundance). However, invertebrate response per unit flood magnitude was lower in sub‐humid sites, potentially because of differences in refuge availability or ecological‐evolutionary interactions. Interestingly, sub‐humid streams had temporary large peaks in invertebrate total abundance and diversity following recovery period that may be indicative of the larger organic matter pulses expected in these systems because of their comparatively well‐developed riparian vegetation.Our findings show that hydrology and long‐term precipitation regime predictably affected invertebrate community responses and, thus, our work underscores the important influence of local climate to ecosystem sensitivity to disturbances. 

Subsurface environments are among Earth’s largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth’s subsurface and surface environments. 

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyze 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical, and gene neighborhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter. 

Abstract Tropical cyclones play an increasingly important role in shaping ecosystems. Understanding and generalizing their responses is challenging because of meteorological variability among storms and its interaction with ecosystems. We present a research framework designed to compare tropical cyclone effects within and across ecosystems that: a) uses a disaggregating approach that measures the responses of individual ecosystem components, b) links the response of ecosystem components at fine temporal scales to meteorology and antecedent conditions, and c) examines responses of ecosystem using a resistance–resilience perspective by quantifying the magnitude of change and recovery time. We demonstrate the utility of the framework using three examples of ecosystem response: gross primary productivity, stream biogeochemical export, and organismal abundances. Finally, we present the case for a network of sentinel sites with consistent monitoring to measure and compare ecosystem responses to cyclones across the United States, which could help improve coastal ecosystem resilience.