Altered Community Composition Research Articles

Pathogenic fungus causes density‐ and trait‐mediated trophic cascades in an aquatic community

AbstractPathogens can alter species composition and ecosystem function by causing direct and indirect effects on communities. Zoospores of the chytrid fungus Batrachochytrium dendrobatidis (hereafter, Bd), a pathogen implicated in worldwide amphibian declines, can be consumed by filter‐feeding zooplankton and can damage mouthparts of infected amphibian larvae. Consequently, we hypothesized that this pathogen would affect the abundance of zooplankton and survival and feeding abilities of larval amphibian hosts. In turn, this could affect the algal food resources of zooplankton and tadpoles, which can include phytoplankton and periphyton. We tested these hypotheses by manipulating the presence of western toad (Anaxyrus boreas) larvae and Bd in outdoor mesocosms and quantifying the densities of amphibians, zooplankton, phytoplankton, and periphyton. Bd infections reduced amphibian larval densities, but this only weakly benefitted periphyton (a density‐mediated indirect effect). After controlling for larval densities, mesocosms with Bd‐exposed larvae had significantly more periphyton biomass than mesocosms with larvae but no Bd, consistent with infection‐induced mouthpart damage reducing larval feeding rates on attached algae (a trait‐mediated indirect effect). In fact, the estimated trait‐mediated effect of Bd on periphyton biomass was larger than the density‐mediated effect. However, we did not find evidence that Bd exposure triggered a switch to filter‐feeding phytoplankton. The presence of Bd was associated with increased copepod abundance, consistent with zooplankton consuming chytrid zoospores. These results suggest that Bd has the potential to cause both trait‐ and density‐mediated indirect effects that can alter community composition and perhaps the primary productivity of freshwater ecosystems.

Toxic effect of triphenyl phosphate (TPHP) on Cyprinus carpio and the intestinal microbial community response

Triphenyl phosphate (TPHP) is a kind of organophosphorus flame retardants, and its use is increasing annually. However, the toxic effect associated with exposure to it has not been adequately investigated. Therefore, in this study, we determined the toxic dose of TPHP in the economic fish species, Cyprinus carpio. Acute and subacute toxicity tests were conducted, and the enrichment of TPHP in the gills, brain, intestines, and liver were determined by Liquid Chromatography-Mass Spectrometry, and the response of carp gut microbial community to TPHP stress was determined using 16 S rRNA gene high-throughput sequencing. Results showed that the 96-h LC50 of TPHP in carp was 7 mg/L. At the 7 d, the order of TPHP absorption was as follows (from highest to lowest): gills > intestine > liver > brain, but at the 28 d and the purification period, the order of TPHP absorption was brain > gills > intestine > liver. TPHP exposure at 3.5 mg/L decreased α-diversity of the intestinal microbial community (p < 0.05), and altered community composition, in particular the relative abundance of dominant microbial populations. Functional profiles of the microbial communities predicted based on 16 S rRNA gene data showed upregulation in the degradation of exogenous substances and energy metabolism of the TPHP-treated groups (p < 0.05), suggesting that intestinal microbial taxa play a role in reducing TPHP toxicity. The results provide insights that could facilitate risk assessments of TPHP pollutants in aquatic environments and the management of associated water pollution.

Temporal effects of fine sediment deposition on benthic macroinvertebrate community structure, function and biodiversity likely reflects landscape setting

Globally, excessive fine sediment (particles <2 mm) deposition is acknowledged to have deleterious effects on aquatic biodiversity. However, the impacts are often equivocal possibly reflecting landscape context, although this is rarely considered. To address this, we examined the temporal response of macroinvertebrate taxonomic and functional diversity to experimental fine sediment clogging in a prealpine (Italy) and lowland setting (UK). Colonisation devices were installed insitu with either clean or clogged substrates and examined for short (7–14 days), medium (21–28 days) and long (56–63 days) timescales. Clogging resulted in altered taxonomic community composition in both the lowland and prealpine rivers and modified functional community composition in the prealpine river. Nestedness was consistently found to be the dominant process driving differences in taxonomic composition between the clean and clogged substrates in the prealpine environment, with clogged substrates forming a nested community. No dominant component structured lowland taxonomic communities. Functional community composition was driven by nestedness in both environments but was heavily dominant in the case of the prealpine river, possibly reflecting low functional redundancy. Widely employed community richness metrics (EPT, taxa and functional richness) only displayed a response to fine sediment loading in the prealpine environment but taxa characterized as sensitive to fine sediment as well as some functional feeding groups did exhibit differences in both settings. In the prealpine environment, the effects of fine sediment intensified over time for several community metrics. Although further research is required to corroborate our findings and extend our observations across more rivers and typologies, excessive fine sediment is a pervasive stressor affecting macroinvertebrate communities in prealpine and lowland environments. However, the biodiversity facets that responded to clogging differed between the two landscape settings probably reflecting wider environmental filtering. Monitoring and managing fine sediment loading likely requires context specific approaches to maximise ecological benefits.

Deep incorporation of corn straw benefits soil organic carbon and microbial community composition in a black soil of Northeast China

Abstract‘Deep incorporation of corn straw’ (CSDI) is to concentrate the burial of corn straw into the subsurface soil layer (20–40 cm) and to break the plough pan, thereby creating a loosened plough layer (0–20 cm) and a fertile subsurface soil layer. However, its impacts on soil organic carbon (SOC) and the microbial community remain poorly understood. A field experiment was conducted to investigate the effects of 1‐year CSDI (CD1), 3‐year CSDI (CD3) and 5‐year CSDI (CD5) on soil aggregates and aggregate‐associated SOC, as well as bacterial and fungal community characteristics (examined by the high‐throughput gene sequencing method). The results demonstrated that SOC and soil fungal diversity were decreased by CD1, but increased by CD3 and CD5. Compared with the control, CD5 promoted 2–0.25 mm soil macroaggregation, significantly increased SOC by 8.94% and aggregate‐associated SOC by 5.96%–8.84%, consequently improving the physical protection of SOC by soil aggregates. CD3 and CD5 enhanced the richness and diversity of soil bacteria and fungi, and altered community composition. For soil bacteria, the relative abundance of Acidobacteria and Chloroflexi was increased, while that of Firmicutes, Gemmatimonadetes, Sphingomonas and Bacillus was decreased. For soil fungi, the relative abundance of Ascomycota, Zygomycota, Mortierella and Fusarium was greatly improved, but that of Basidiomycota was reduced. These obvious variations in microbial community structure were beneficial to straw degradation and SOC accumulation. Overall, the optimization of microbial community with CSDI plays a positive role in promoting soil organic matter, nutrient cycling and carbon sequestration, and thus improving soil fertility.

Seawater browning alters community composition and reduces nutritional quality of plankton in a subarctic marine ecosystem

Inflows of coloured terrestrial organic matter cause seawater browning and reduced phytoplankton production in subarctic coastal ecosystems, potentially deteriorating the nutritional quality of marine food webs. We analyzed the fatty-acid (FA) compositions of seston and the zooplankton taxa Eurytemora affinis and cladocerans at three locations of the northern Baltic Sea. At the coastal and northerly locations, salinity and phosphorus concentrations were low, while concentrations of humic substances (i.e., terrestrial organic matter) were high. The southerly location showed the opposite trend. The ratio between alga-specific ω3 polyunsaturated FA and terrigenous monounsaturated FA (MUFA) in Eurytemora decreased from south to north, as did the ratio between the alga-specific docosahexaenoic acid (DHA) and terrigenous MUFA in cladocerans. With increasing humic substances, the biomass of DHA-rich phytoplankton decreased and the zooplankton MUFA content increased. Our results indicate that coloured terrestrial organic matter alters the phytoplankton composition, consequently affecting the zooplankton nutritional quality.

Climatic drivers and ecological impacts of a rapid range expansion by non-native smallmouth bass

Smallmouth bass (Micropterus dolomieu) are a globally introduced fish species that have experienced widespread range expansions in recent decades and which can have deleterious effects on native fish communities. Rapidly assessing their expansions will aid conservation and management actions geared towards controlling their spread and mitigating their impacts. Smallmouth bass have recently experienced a rapid upstream expansion in a Great Plains river (Laramie River, Wyoming, USA), which provided an opportunity to evaluate the drivers and impacts of this expansion by using a modified before-after, control-impact (BACI) design. Our objectives were to test whether climatic drivers (temperature, precipitation, flow) were related to this range expansion and subsequent effects of the expansion on native fish communities. Smallmouth bass population size in Grayrocks Reservoir increased following a climatically extreme wet year, with statistically extreme amounts of spring-time and June precipitation creating high discharge events that coincided with the upstream expansion. Unlike previous studies highlighting the invasive nature of smallmouth bass, the modified BACI analysis revealed no declines in species richness induced by the expansion. However, there was evidence that native small-bodied minnow species (family Leuciscidae) declined in relative abundance and that community-level and species-level trophic niches were compressed for invaded sites. Our findings provide important insight into how climatic extremes can prompt biological invasions that can alter community composition and food web structure even if local extirpations do not occur.

Permafrost thaw with warming reduces microbial metabolic capacities in subsurface soils.

Microorganisms are major constituents of the total biomass in permafrost regions, whose underlain soils are frozen for at least two consecutive years. To understand potential microbial responses to climate change, here we examined microbial community compositions and functional capacities across four soil depths in an Alaska tundra site. We showed that a 5-year warming treatment increased soil thaw depth by 25.7% (p = .011) within the deep organic layer (15-25cm). Concurrently, warming reduced 37% of bacterial abundance and 64% of fungal abundances in the deep organic layer, while it did not affect microbial abundance in other soil layers (i.e., 0-5, 5-15, and 45-55cm). Warming treatment altered fungal community composition and microbial functional structure (p < .050), but not bacterial community composition. Using a functional gene array, we found that the relative abundances of a variety of carbon (C)-decomposing, iron-reducing, and sulphate-reducing genes in the deep organic layer were decreased, which was not observed by the shotgun sequencing-based metagenomics analysis of those samples. To explain the reduced metabolic capacities, we found that warming treatment elicited higher deterministic environmental filtering, which could be linked to water-saturated time, soil moisture, and soil thaw duration. In contrast, plant factors showed little influence on microbial communities in subsurface soils below 15cm, despite a 25.2% higher (p < .05) aboveground plant biomass by warming treatment. Collectively, we demonstrate that microbial metabolic capacities in subsurface soils are reduced, probably arising from enhanced thaw by warming.

House fly larval grazing alters dairy cattle manure microbial communities

BackgroundHouse fly larvae (Musca domestica L.) require a live microbial community to successfully develop. Cattle manure is rich in organic matter and microorganisms, comprising a suitable substrate for larvae who feed on both the decomposing manure and the prokaryotic and eukaryotic microbes therein. Microbial communities change as manure ages, and when fly larvae are present changes attributable to larval grazing also occur. Here, we used high throughput sequencing of 16S and 18S rRNA genes to characterize microbial communities in dairy cattle manure and evaluated the changes in those communities over time by comparing the communities in fresh manure to aged manure with or without house fly larvae.ResultsBacteria, archaea and protist community compositions significantly differed across manure types (e.g. fresh, aged, larval-grazed). Irrespective of manure type, microbial communities were dominated by the following phyla: Euryarchaeota (Archaea); Proteobacteria, Firmicutes and Bacteroidetes (Bacteria); Ciliophora, Metamonanda, Ochrophyta, Apicomplexa, Discoba, Lobosa and Cercozoa (Protists). Larval grazing significantly reduced the abundances of Bacteroidetes, Ciliophora, Cercozoa and increased the abundances of Apicomplexa and Discoba. Manure aging alone significantly altered the abundance bacteria (Acinetobacter, Clostridium, Petrimonas, Succinovibro), protists (Buxtonella, Enteromonas) and archaea (Methanosphaera and Methanomassiliicoccus). Larval grazing also altered the abundance of several bacterial genera (Pseudomonas, Bacteroides, Flavobacterium, Taibaiella, Sphingopyxis, Sphingobacterium), protists (Oxytricha, Cercomonas, Colpodella, Parabodo) and archaea (Methanobrevibacter and Methanocorpusculum). Overall, larval grazing significantly reduced bacterial and archaeal diversities but increased protist diversity. Moreover, total carbon (TC) and nitrogen (TN) decreased in larval grazed manure, and both TC and TN were highly correlated with several of bacterial, archaeal and protist communities.ConclusionsHouse fly larval grazing altered the abundance and diversity of bacterial, archaeal and protist communities differently than manure aging alone. Fly larvae likely alter community composition by directly feeding on and eliminating microbes and by competing with predatory microbes for available nutrients and microbial prey. Our results lend insight into the role house fly larvae play in shaping manure microbial communities and help identify microbes that house fly larvae utilize as food sources in manure. Information extrapolated from this study can be used to develop manure management strategies to interfere with house fly development and reduce house fly populations.

Species‐specific responses to warming alter community composition

Abstract Species are responding to global climate change in varied and nuanced ways. However, how species‐specific responses to climate change= affect interactions among species remains poorly understood. It is important to understand species interactions under potential climate change scenarios because those interactions can in turn alter community dynamics. In this study, we conducted two complementary experiments to examine how simulated warming might alter larval intraguild predation (IGP) rates and resulting adult assemblage composition in three species of North American dragonflies: Pachydiplax longipennis, Plathemis lydia and Libellula luctuosa. First, using both P. longipennis and L. luctuosa, we isolated interspecific and intraspecific pairs of larval dragonflies of different size differentials to determine how the size and species identity might influence IGP rates. In tandem, we conducted a year‐long mesocosm experiment with all three species to assess how simulated warming and heat waves influenced the resulting adult dragonfly assemblages. IGP trials revealed that P. longipennis individuals were much more likely to engage in IGP than L. luctuosa, regardless of size differential. In the mesocosm experiment, emerging adult assemblages were dominated by P. longipennis individuals, a pattern that was most pronounced in the control treatment. Our results indicate that while P. longipennis may be the competitively dominant species under current ambient conditions, warming may alter this dynamic and lessen the dominance of this species on the resulting assemblage composition.

Does Climate Warming Favour Early Season Species?

Plant species that start early in spring are generally more responsive to rising temperatures, raising concerns that climate warming may favour early season species and result in altered interspecific interactions and community structure and composition. This hypothesis is based on changes in spring phenology and therefore active growing season length, which would not be indicative of possible changes in growth as would changes in cumulative forcing temperatures (growing degree days/hours) in the Northern Hemisphere. In this study we analysed the effects of a moderate climate warming (2°C warmer than the 1981–2010 baseline) on the leaf-out of hypothetical species without chilling restriction and actual plant species with different chilling and forcing requirements in different parts of the globe. In both cases, early season species had larger phenological shifts due to low leaf-out temperatures, but accumulated fewer forcing gains (changes in cumulative forcing temperatures by warming) from those shifts because of their early spring phenology. Leaf-out time was closely associated with leaf-out temperatures and therefore plant phenological responses to climate warming. All plant species would be equally affected by climate warming in terms of total forcing gains added from higher temperatures when forcing gains occurring between early and late season species are included. Our findings will improve the understanding of possible mechanisms and consequences of differential responses in plant phenology to climate warming.

An examination of the use of antibiotics as a method to experimentally perturb the microbiota of suspension‐feeding bivalves

AbstractSuspension‐feeding bivalves are critical members of aquatic ecosystems worldwide, which is why research into their host‐associated microbiota is growing. Experiments that artificially diminish the native microbial communities of bivalves in vivo will be increasingly necessary to evaluate the functional role of microbes within their hosts. Previous methods to manipulate the microbiome of bivalves lack standardization and, often, verification of successful disturbance. The goal of this study was to evaluate antibiotic administration as a method for perturbing the gut microbiome of bivalves in two separate, but related, experiments. In the first, a mixture of antibiotics was delivered to eastern oysters for 4 days to probe effects on gut microbial carbon usage, diversity, and taxonomic composition. In the second, the same antibiotic mixture was administered to blue mussels for 21 days to probe effects on microbial abundance, diversity, and taxonomic composition. In both experiments, animals were administered antibiotics in isolation, and stringent sterilization methods were employed, which included sterilized seawater and microalgal food. The results of the oyster experiment revealed that antibiotics substantially reduced microbial carbon usage and perturbed community composition. In the mussel experiment, antibiotics lowered microbial abundance and species richness and significantly altered community composition. Taken together, results from the two experiments demonstrate that antibiotics can be used to effectively alter the function and composition of the gut microbial community of bivalves. Future research that aims to perturb the microbiomes of suspension‐feeding animals should incorporate aspects similar to the protocols described herein. Additionally, future studies must include verification, ideally high‐throughput DNA sequencing coupled with microbial quantification, that the antibiotic perturbation was successful.

Pre-flooding soil used in monocropping increased strawberry biomass and altered bacterial community composition

ABSTRACT SummaryContinuous monocropping degrades soil physicochemical properties, leads to the accumulation of toxic compounds and changes soil microbial community composition. Pre-flooding the soil is a promising strategy to improve its productivity; however, little is known about the underlying mechanisms. Here, strawberry (Fragaria × ananassa) pot experiments were conducted with soil that had been used for continuous monocropping. The treatments were pre-flooding alone, with rice straw added and with rice straw plus a biofertilizer (mainly contained Bacillus velezensis) amendment, and the impacts of the treatments on soil physicochemical properties, bacterial diversity and composition and the integrated plant–soil–microbe responses were tracked. The strawberry biomass significantly increased after pre-flooding treatments. Pre-flooding increased the soil pH and the available P and K concentrations, while it decreased soil electrical conductivity. The bacterial diversity and abundance significantly increased after pre-flooding treatments. A Mantel test showed that soil pH and salinity were the two most important factors in shaping bacterial composition, but they exerted opposite effects. The increased strawberry biomass after pre-flooding was significantly correlated with bacterial composition and soil salinity in long-term continuous strawberry monocropping systems.

Simulated ocean acidification altered community composition and growth of a coastal phytoplankton assemblage (South West coast of India, eastern Arabian Sea).

Marine phytoplankton can be highly sensitive to ocean acidification; however, their responses are diverse and therefore, phytoplankton response study on the regional scale is of high research priority. The present study documented the community shift and growth responses of a natural phytoplankton assemblage from the South West coastal water of India (South Eastern Arabian Sea) under ambient CO2 (A-CO2 ≈ 400 µatm) and high CO2 (H-CO2 ≈ 830 µatm) levels in microcosms during the winter monsoon. A doubling of pCO2 resulted in increased cell density, particulate organic carbon and nitrogen (POC, PON) contents, and C:N ratios. The depleted values of δ13CPOC in the H-CO2-incubated cells indicated a higher diffusive CO2 influx. HPLC marker pigment analysis revealed that the community was microphytoplankton dominated (mostly diatoms); nanoplanktonic prymnesiophytic algae and picoplanktonic cyanobacteria showed insignificant response to the simulated ocean acidification. A high CO2-induced increased growth rate was noticed in 6 diatoms (Leptocylindrus danicus; Rhizosolenia setigera; Navicula sp., Asterionella glacialis, Dactyliosolen fragilissimus, and Thalassiosira sp.). The cell volumes of Thalassionema frauenfeldii, Asterionella glacialis, and Cylindrotheca closterium increased significantly, whereas Rhizosolenia setigera and Thalassiosira sp. showed decreased cell volume at the elevated CO2 levels. These changes in growth rate, cell volume, and elemental stoichiometry could be related to CO2 acquisition and the nutritional status of the cells. Some phytoplankton genera from this region are probably acclimatized to pCO2 fluctuations and are likely to benefit from the future increase in CO2 levels. Higher POC production and increased C:N ratio along with variable cell volume may impact the trophic transfer and cycling of organic carbon in this coastal water. However, a multi-stressor approach in a longer experimental exposure should be considered in future research.

16S rRNA metabarcoding unearths responses of rare gut microbiome of fathead minnows exposed to benzo[a]pyrene

Activities of gut microbiomes are often overlooked in assessments of ecotoxicological effects of environmental contaminants. Effects of the polycyclic aromatic hydrocarbon, benzo[a]pyrene (BaP) on active gut microbiomes of juvenile fathead minnows (Pimephales promelas) were investigated. Fish were exposed for two weeks, to concentrations of 0, 1, 10, 100, or 1000 μg BaP g−1 in the diet. The active gut microbiome was characterized using 16S rRNA metabarcoding to determine its response to dietary exposure of BaP. BaP reduced alpha-diversity at the greatest exposure concentrations. Additionally, exposure to BaP altered community composition of active microbiome and resulted in differential proportion of taxa associated with hydrocarbon degradation and fish health. Neighborhood selection networks of active microbiomes were not reduced with greater concentrations of BaP, which suggests ecological resistance and/or resilience of gut microbiota. The active gut microbiome had a similar overall biodiversity as that of the genomic gut microbiota, but had a distinct composition from that of the 16S rDNA profile. Responses of alpha- and beta-diversities of the active microbiome to BaP exposure were consistent with that of genomic microbiomes. Normalized activity of microbiome via the ratio of rRNA to rDNA abundance revealed rare taxa that became active or dormant due to exposure to BaP. These differences highlight the need to assess both 16S rDNA and rRNA metabarcoding to fully derive bacterial compositional changes resulting from exposure to contaminants.

Molecular mechanism of oil induced growth inhibition in diatoms using Thalassiosira pseudonana as the model species

The 2010 Deepwater Horizon oil-spill exposed the microbes of Gulf of Mexico to unprecedented amount of oil. Conclusive evidence of the underlying molecular mechanism(s) on the negative effects of oil exposure on certain phytoplankton species such as Thalassiosira pseudonana is still lacking, curtailing our understanding of how oil spills alter community composition. We performed experiments on model diatom T. pseudonana to understand the mechanisms underpinning observed reduced growth and photosynthesis rates during oil exposure. Results show severe impairment to processes upstream of photosynthesis, such as light absorption, with proteins associated with the light harvesting complex damaged while the pigments were unaffected. Proteins associated with photosynthetic electron transport were also damaged, severely affecting photosynthetic apparatus and depriving cells of energy and carbon for growth. Negative growth effects were alleviated when an organic carbon source was provided. Further investigation through proteomics combined with pathway enrichment analysis confirmed the above findings, while highlighting other negatively affected processes such as those associated with ferroxidase complex, high-affinity iron-permease complex, and multiple transmembrane transport. We also show that oxidative stress is not the primary route of negative effects, rather secondary. Overall, this study provides a mechanistic understanding of the cellular damage that occurs during oil exposure to T. pseudonana.

Concurrent and rapid recovery of bacteria and protist communities in Canadian boreal forest ecosystems following wildfire

Wildfire plays an important role in restructuring bacterial and protist taxonomic and functional communities in forest ecosystems. Yet, the recovery of bacterial and protist communities following wildfire has not been rigorously investigated across long-term wildfire chronosequences. We compared changes in bacterial and protist alpha diversity, community composition, co-occurrence networks and determinant edaphic factors between burnt and unburnt (reference) soils at 11 different sites representing a 76-year wildfire chronosequence in Canadian boreal forests. The fire increased bacterial and protist alpha diversity and altered community composition (beta diversity) as compared to the site-specific controls during the early recovery stage (<5 years since fire), but had no effect on bacterial and protist communities in the middle (8–20 years) and late (>30 years) recovery stages. Bacterial and protist communities showed similar patterns of change across the wildfire chronosequence. The post-fire recovery of bacterial communities was associated with changes in soil chemical properties (e.g., nutrient status and pH) and vegetation succession. The protist community assembly was co-influenced by changes in bacterial communities and vegetation succession/soil properties. The concurrent recovery of bacterial and protist communities, and their influencing factors of vegetation and soil properties, imply the above- and belowground living communities are strongly linked in wildfire-perturbed forest ecosystems.

Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts

BackgroundAntibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and methods to mitigate associated negative effects remain poorly understood, particularly outside of human-clinical and model-rodent studies that focus on outcome over process. To improve conceptual understanding of host-microbe symbiosis in more naturalistic contexts, we applied an ecological framework to a non-traditional, strepsirrhine primate model via long-term, multi-faceted study of microbial community structure before, during, and following two experimental manipulations. Specifically, we administered a broad-spectrum antibiotic, either alone or with subsequent fecal transfaunation, to healthy, male ring-tailed lemurs (Lemur catta), then used 16S rRNA and shotgun metagenomic sequencing to longitudinally track the diversity, composition, associations, and resistomes of their gut microbiota both within and across baseline, treatment, and recovery phases.ResultsAntibiotic treatment resulted in a drastic decline in microbial diversity and a dramatic alteration in community composition. Whereas microbial diversity recovered rapidly regardless of experimental group, patterns of microbial community composition reflected long-term instability following treatment with antibiotics alone, a pattern that was attenuated by fecal transfaunation. Covariation analysis revealed that certain taxa dominated bacterial associations, representing potential keystone species in lemur gut microbiota. Antibiotic resistance genes, which were universally present, including in lemurs that had never been administered antibiotics, varied across individuals and treatment groups.ConclusionsLong-term, integrated study post antibiotic-induced microbial imbalance revealed differential, metric-dependent evidence of recovery, with beneficial effects of fecal transfaunation on recovering community composition, and potentially negative consequences to lemur resistomes. Beyond providing new perspectives on the dynamics that govern host-associated communities, particularly in the Anthropocene era, our holistic study in an endangered species is a first step in addressing the recent, interdisciplinary calls for greater integration of microbiome science into animal care and conservation.

The dynamic influence of methane seepage on macrofauna inhabiting authigenic carbonates

AbstractMethane seeps are highly productive deep‐sea ecosystems reliant on chemosynthetic primary production. They are increasingly affected by direct human activities that threaten key ecosystem services. Methane seepage often generates precipitation of authigenic carbonate rocks, which host diverse microbes, and a dynamic invertebrate community. By providing hard substrate, even after seepage ceases, these rocks may promote a long‐lasting ecological interaction between seep and background communities. We analyzed community composition, density, and trophic structure of invertebrates on authigenic carbonates at Mound 12, a seep on the Pacific margin of Costa Rica, using one mensurative and two manipulative experiments. We asked whether carbonate macrofaunal communities are able to survive, adapt, and recover from changes in environmental factors (i.e., seepage activity, chemosynthetic production, and food availability), and we hypothesized a key role for seepage activity in defining these communities and responses. Communities on in situ carbonates under different seepage activities showed declining density with increasing distance from the seep and a shift in composition from gastropod dominance in areas of active seepage to more annelids and peracarid crustaceans that are less dependent on chemosynthetic production under lesser seepage. Response to changing environmental context was evident from altered community composition following (1) a natural decline in seepage over successive years, (2) transplanting of carbonates to different seepage conditions for 17 months, and (3) defaunated carbonate deployments under different seepage regimes over 7.4 yr. Seep faunas on transplants to lesser seepage emerge and recover faster than transition fauna (characterized by native seep and background faunas, respectively) and are able to persist by adapting their diets or by retaining their symbiotic bacteria. The macrofaunal community colonizing defaunated carbonates deployed for 7.4 yr developed communities with a similar successional stage as in situ rocks, although trophic structure was not fully recovered. Thus, macrofaunal successional dynamics are affected by habitat complexity and the availability of microbial chemosynthetic productivity. This multi‐experiment study highlights the interaction between biotic and abiotic factors at methane seeps at different time scales along a spatial gradient connecting seep and surrounding deep‐sea communities and offers insight on the resilience of deep‐sea macrofaunal communities.

Multispecies modelling reveals potential for habitat restoration to re‐establish boreal vertebrate community dynamics

Abstract The restoration of habitats degraded by industrial disturbance is essential for achieving conservation objectives in disturbed landscapes. In boreal ecosystems, disturbances from seismic exploration lines and other linear features have adversely affected biodiversity, most notably leading to declines in threatened woodland caribou. Large‐scale restoration of disturbed habitats is needed, yet empirical assessments of restoration effectiveness on wildlife communities remain rare. We used 73 camera trap deployments from 2015 to 2019 and joint species distribution models to investigate how habitat use by the larger vertebrate community (&gt;0.2 kg) responded to variation in key seismic line characteristics (line‐of‐sight, width, density and mounding) following restoration treatments in a landscape disturbed by oil and gas development in northeastern Alberta. The proportion of variation explained by line characteristics was low in comparison to habitat type and season, suggesting short‐term responses to restoration treatments were relatively weak. However, we found that lines with characteristics consistent with restored conditions were predicted to support an altered community composition, with reduced use by wolf and coyote, thereby indicating that line restoration will result in reduced contact rates between caribou and these key predators. Synthesis and applications. Our analysis provides a framework to assess and predict wildlife community responses to emerging restoration efforts. With the growing importance of habitat restoration for caribou and other vertebrate species, we recommend longer‐term monitoring combined with landscape‐scale comparisons of different restoration approaches to more fully understand and direct these critical conservation investments. Only by combining rigorous multispecies monitoring with large‐scale restoration, will we effectively conserve biodiversity within rapidly changing environments.

Termites in restoration: the forgotten insect?

Few restoration studies consider soil invertebrates such as termites although these are present throughout many ecosystems worldwide and provide a range of ecosystem services as soil engineers. The few studies that do consider the recovery of termites after human‐induced disturbance are geographically concentrated in Africa and South America and tropical seasonal savannah ecosystems. These studies suggest that termites can in some cases recover to pre‐disturbance levels after a few years, or take up to 30 years, although with altered community composition. While termites could potentially have negative impacts on restoration efforts by damaging vegetation, their recovery was shown to have benefits on ecosystems which warrants further research into their recovery across a wider range of continents and biomes.