Jennifer D. Rocca

Temperature significantly impacts microbial communities’ composition and function, which plays a vital role in the global carbon cycle that determines climate change. Nutrient influxes often accompany rising temperatures due to human activity. While ecological interactions between different microorganisms could shape their response to environmental change, we do not understand how predation may influence these responses in a warmer and increasingly nutrient-rich world. Here, we assess whether predation by a ciliate community of bacterial consumers influences changes in the diversity, biomass, and function of a freshwater prokaryotic community under different temperature and nutrient conditions. We found that predator presence mediates the effects of temperature and nutrients on the total prokaryotic community biomass and composition through various mechanisms, including direct and indirect effects. However, the total community function was resilient. Our study supports previous findings that temperature and nutrients are essential drivers of microbial community composition and function but also demonstrates how predation can mediate these effects, indicating that the biotic context is as important as the abiotic context to understanding microbial responses to novel climates. IMPORTANCE: While the importance of the abiotic environment in microbial communities has long been acknowledged, how prevalent ecological interactions like predation may influence these microbial community responses to shifting abiotic conditions is largely unknown. Our study addresses the complex interplay between temperature, nutrients, predation, and their joint effects on microbial community diversity and function. Our findings suggest that while temperature and nutrients are fundamental drivers of microbial community dynamics, the presence of predators significantly alters these responses. Our study underscores the impact of abiotic factors on microbial communities and the importance of accounting for the biotic context in which these occur to understand, let alone predict, these responses properly.

Temperature significantly impacts microbial communities’ composition and function, which subsequently plays a vital role in the global carbon cycle that ultimately fuels climate change. Interactions between different microorganisms might be critical in shaping how these communities react to both temperature changes. Additionally, rising temperatures are occurring in the context of increasingly nutrient-rich ecosystems due to human activity. Nonetheless, we lack a comprehensive understanding of how predation influences microbial communities in future climate scenarios and an increasingly nutrient-rich world. Here, we assess whether predation by key bacterial consumers—ciliates—influences a microbial community’s freshwater temperature and nutrient response regarding biomass, diversity, structure, and function. In a three-week microcosm experiment, we exposed mostly prokaryotic microbial communities to a community of ciliate predators at two different temperature scenarios (ambient and +3°C, i.e., a conservative projection of climate change by 2050) and nutrient levels (low and elevated). Nutrients, temperature, and ciliate presence influenced microbial biomass and function separately, but their interaction had the largest explanatory power over the observed changes in microbial community biomass, structure, and function. Our study supports previous findings that temperature and nutrients are essential drivers of microbial community structure and function but also demonstrates that the presence of predators can mediate these effects, indicating that the biotic context is as important as the abiotic context to understand microbial responses to novel climates. Importance While the importance of the abiotic environment in microbial communities has long been studied, how prevalent ecological interactions, like predation and the broader abiotic context, may influence these responses is largely unknown. Our study disentangles the complex interplay between temperature, nutrients, and predation and their joint effects on microbial community diversity and function. The findings suggest that while temperature and nutrients are fundamental drivers of microbial community dynamics, the presence of predators significantly mediates these responses. Our study underscores the profound impact of abiotic factors on microbial communities, but how to properly understand, let alone predict, these responses, we need to account for the biotic context in which these are occurring.

Intense lasers can accelerate electrons to very high energy over a short distance. Such compact accelerators have several potential applications including fast ignition, high energy physics, and radiography. Among the various schemes of laser-based electron acceleration, vacuum laser acceleration has the merits of super-high acceleration gradient and great simplicity. Yet its realization has been difficult because injecting free electrons into the fast-oscillating laser field is not trivial. Here we demonstrate free-electron injection and subsequent vacuum laser acceleration of electrons up to 20 MeV using the relativistic transparency effect. The key physics are identified through multi-dimensional particle-in-cell simulations, test-particle simulations, and theoretical analysis. When a high-contrast intense laser drives a thin solid foil, electrons from the dense opaque plasma are first accelerated to near-light speed by the standing laser wave in front of the solid foil and subsequently injected into the transmitted laser field as the opaque plasma becomes relativistically transparent. It is possible to further optimize the electron injection/acceleration by manipulating the laser polarization, incident angle, and temporal pulse shaping. Our result also sheds light on the fundamental relativistic transparency process, crucial for producing secondary particle and light sources.

Temperature strongly influences microbial community structure and function, in turn contributing to global carbon cycling that can fuel further warming. Recent studies suggest that biotic interactions among microbes may play an important role in determining the temperature responses of these communities. However, how predation regulates these microbiomes under future climates is still poorly understood. Here, we assess whether predation by a key global bacterial consumer—protists—influences the temperature response of the community structure and function of a freshwater microbiome. To do so, we exposed microbial communities to two cosmopolitan protist species—Tetrahymena thermophila and Colpidium sp.—at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to community shifts, these responses changed over time and in the presence of protists. Protists influenced microbial biomass and respiration rate through direct and indirect effects on bacterial community structure, and predator presence actually reduced microbial respiration at elevated temperature. Indicator species analyses showed that these predator effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities but also demonstrates that the presence of a large predator can mediate these responses to warming.

Every seed germinating in soils, wastewater treatment, and stream confluence exemplify microbial community coalescence—the blending of previously isolated communities. Here, we present theoretical and experimental knowledge on how separated microbial communities mix, with particular focus on managed ecosystems.

The rivers of Appalachia (USA) are among the most biologically diverse freshwater ecosystems in the temperate zone and are home to numerous endemic aquatic organisms. Throughout the Central Appalachian ecoregion, extensive surface coal mines generate alkaline mine drainage that raises the pH, salinity and trace element concentrations in downstream waters. Previous regional assessments have found significant declines in stream macroinvertebrate and fish communities draining these mined areas. Here, we expand these assessments with a more comprehensive evaluation across a broad range of organisms (bacteria, algae, macro-invertebrates, all eukaryotes, and fish) using high-throughput amplicon sequencing of environmental DNA (eDNA). We collected water samples from 93 streams in Central Appalachia (West Virginia, USA) spanning a gradient of mountaintop coal mining intensity and legacy to assess how this land use alters downstream water chemistry and affects aquatic biodiversity. For each group of organisms, we identified the sensitive and tolerant taxa along the gradient and calculated stream specific conductivity thresholds in which large synchronous declines in diversity were observed. Streams below mining operations had steep declines in diversity (-18 to -41%) and substantial shifts in community composition that were consistent across multiple taxonomic groups. Overall, large synchronous declines in bacterial, algal, and macroinvertebrate communities occurred even at low levels of mining impact at stream specific conductivity thresholds of 150 to 200 µS·cm^-1 that are substantially below the current EPA Aquatic Life Benchmark of 300 µS·cm^-1 for Central Appalachian streams. We show that extensive coal surface mining activities led to the extirpation of 40% of biodiversity from impacted rivers throughout the region and that current water quality criteria are likely not protective for many groups of aquatic organisms.

Temperature strongly influences microbial community structure and function, which in turn contributes to the global carbon cycle that can fuel further warming. Recent studies suggest that biotic interactions amongst microbes may play an important role in determining the temperature responses of these communities. However, how microbial predation regulates these communities under future climates is still poorly understood. Here we assess whether predation by one of the most important bacterial consumers globally – protists – influences the temperature response of a freshwater microbial community structure and function. To do so, we exposed these microbial communities to two cosmopolitan species of protists at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to shifts in microbial community structure, these responses changed over time and in the presence of protist predators. Protists influenced microbial biomass and function through effects on community structure, and predation actually reduced microbial respiration rate at elevated temperature. Indicator species and threshold indicator taxa analyses showed that these predation effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities, but also demonstrates that predation can mediate these responses to warming, with important consequences for the global carbon cycle and future warming.

Mountaintop removal coal mining is the predominant form of surface mining in the Appalachian Region of the United States and leads to elevated levels of chemical constituents in streams draining mined watersheds. This data set contains measurements of water chemistry in the mountaintop mined landscape of Central Appalachia. These data were collected to determine the accumulation and transport of mercury (Hg) and selenium (Se) across environmental compartments in mountaintop mining‐impacted waters as well as the impact of mountaintop mining on the aquatic‐terrestrial subsidy. Samples were collected in summer 2017 and spring/summer 2018. Data predominantly include Se, THg, and methylmercury (MeHg) in the following environmental compartments at sites impacted and unimpacted by mountaintop removal coal mining: water, sediment, biofilm, larval cranefly, adult aquatic insects, and spiders. Additional water parameters that have been found to vary across a gradient of mountaintop mining impact (total organic carbon [TOC], total nitrogen [TN], sulfate [SO₄], nitrate [NO₃], chloride [Cl], pH, sodium [Na], potassium [K], magnesium [Mg], calcium [Ca], manganese [Mn], sulfur [S], specific conductance) were also measured. The majority of sites represented are headwater streams, although some settling ponds below valley fills are included. This data set also includes taxonomic characterization of the adult aquatic insect community as well as measurements of spider density at a subset of sites. There are no copyright restrictions; please cite this data paper when the data are used in publications.

Whole microbial communities regularly merge with one another, often in tandem with their environments, in a process called community coalescence. Such events impose substantial changes: abiotic perturbation from environmental blending and biotic perturbation of community merging. We used an aquatic mixing experiment to unravel the effects of these perturbations on the whole microbiome response and on the success of individual taxa when distinct freshwater and marine communities coalesce. We found that an equal mix of freshwater and marine habitats and blended microbiomes resulted in strong convergence of the community structure toward that of the marine microbiome. The enzymatic potential of these blended microbiomes in mixed media also converged toward that of the marine, with strong correlations between the multivariate response patterns of the enzymes and of community structure. Exposing each endmember inocula to an axenic equal mix of their freshwater and marine source waters led to a 96% loss of taxa from our freshwater microbiomes and a 66% loss from our marine microbiomes. When both inocula were added together to this mixed environment, interactions amongst the communities led to a further loss of 29% and 49% of freshwater and marine taxa, respectively. Under both the axenic and competitive scenarios, the diversity lost was somewhat counterbalanced by increased abundance of microbial taxa that were too rare to detect in the initial inocula. Our study emphasizes the importance of the rare biosphere as a critical component of microbial community responses to community coalescence.

Summary: A majority of environmental studies describe microbiomes at coarse scales of taxonomic resolution (bacterial community, phylum), ignoring key ecological knowledge gained from finer‐scales and microbial indicator taxa. Here, we characterized the distribution of 940 bacterial taxa from 41 streams along an urbanization gradient (0%–83% developed watershed area) in the Raleigh‐Durham area of North Carolina (USA). Using statistical approaches derived from macro‐organismal ecology, we found that more bacterial taxa were classified as intolerant than as tolerant to increasing watershed urbanization (143 vs 48 OTUs), and we identified a threshold of 12.1% developed watershed area beyond which the majority of intolerant taxa were lost from streams. Two bacterial families strongly decreased with urbanization: Acidobacteriaceae (Acidobacteria) and Xanthobacteraceae (Alphaproteobacteria). Tolerant taxa were broadly distributed throughout the bacterial phylogeny, with members of the Comamonadaceae family (Betaproteobacteria) presenting the highest number of tolerant taxa. Shifts in microbial community structure were strongly correlated with a stream biotic index, based on macroinvertebrate composition, suggesting that microbial assemblages could be used to establish biotic criteria for monitoring aquatic ecosystems. In addition, our study shows that classic methods in community ecology can be applied to microbiome datasets to identify reliable microbial indicator taxa and determine the environmental constraints on individual taxa distributions along environmental gradients.