Microbial ecology of the salmon necrobiome: evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes

Carrion ecology in inland aquatic ecosystems: a systematic review

Carrion ecology, i.e. the decomposition and recycling of dead animals, has traditionally been neglected as a key process in ecosystem functioning. Similarly, despite the large threats that inland aquatic ecosystems (hereafter, aquatic ecosystems) face, the scientific literature is still largely biased towards terrestrial ecosystems. However, there has been an increasing number of studies on carrion ecology in aquatic ecosystems in the last two decades, highlighting their key role in nutrient recirculation and disease control. Thus, a global assessment of the ecological role of scavengers and carrion in aquatic ecosystems is timely. Here, we systematically reviewed scientific articles on carrion ecology in aquatic ecosystems to describe current knowledge, identify research gaps, and promote future studies that will deepen our understanding in this field. We found 206 relevant studies, which were highly biased towards North America, especially in lotic ecosystems, covering short time periods, and overlooking seasonality, a crucial factor in scavenging dynamics. Despite the low number of studies on scavenger assemblages, we recorded 55 orders of invertebrates from 179 families, with Diptera and Coleoptera being the most frequent orders. For vertebrates, we recorded 114 species from 40 families, with birds and mammals being the most common. Our results emphasise the significance of scavengers in stabilising food webs and facilitating nutrient cycling within aquatic ecosystems. Studies were strongly biased towards the assessment of the ecosystem effects of carrion, particularly of salmon carcasses in North America. The second most common research topic was the foraging ecology of vertebrates, which was mostly evaluated through sporadic observations of carrion in the diet. Articles assessing scavenger assemblages were scarce, and only a limited number of these studies evaluated carrion consumption patterns, which serve as a proxy for the role of scavengers in the ecosystem. The ecological functions performed by carrion and scavengers in aquatic ecosystems were diverse. The main ecological functions were carrion as food source and the role of scavengers in nutrient cycling, which appeared in 52.4% (N = 108) and 46.1% (N = 95) of publications, respectively. Ecosystem threats associated with carrion ecology were also identified, the most common being water eutrophication and carrion as source of pathogens (2.4%; N = 5 each). Regarding the effects of carrion on ecosystems, we found studies spanning all ecosystem components (N = 85), from soil or the water column to terrestrial vertebrates, with a particular focus on aquatic invertebrates and fish. Most of these articles found positive effects of carrion on ecosystems (e.g. higher species richness, abundance or fitness; 84.7%; N = 72), while a minority found negative effects, changes in community composition, or even no effects. Enhancing our understanding of scavengers and carrion in aquatic ecosystems is crucial to assessing their current and future roles amidst global change, mainly for water-land nutrient transport, due to changes in the amount and speed of nutrient movement, and for disease control and impact mitigation, due to the predicted increase in occurrence and magnitude of mortality events in aquatic ecosystems.

Aquatic conditions & bacterial communities as drivers of the decomposition of submerged remains

Aquatic decomposition, as a forensic discipline, has been largely under-investigated as a consequence of the highly complex and influential variability of the water environment. The limitation to the adaptability of scenario specific results justifies the necessity for experimental research to increase our understanding of the aquatic environment and the development of post-mortem submersion interval (PMSI) methods of estimation. This preliminary research aims to address this contextual gap by assessing the variation in the bacterial composition of aquatic biofilms as explained by water parameter measurements over time, associated with clothed and bare decomposing remains. As part of three field investigations, a total of 9 still-born piglets (n = 3, per trial) were used as human analogues and were submerged bare or clothed in either natural cotton or synthetic nylon. Changes in the bacterial community composition of the water surrounding the submerged remains were assessed at 4 discrete time points post submersion (7, 14, 21 and 28 days) by 16 S rRNA gene Next Generation Sequencing analysis and compared to coinciding water parameter measurements (i.e. conductivity, total dissolved solids (TDS), salinity, pH, and dissolved oxygen (DO)). Bacterial diversity was found to change over time and relative to clothing type, where significant variation was observed between synthetic nylon samples and bare/cotton samples. Seasonality was a major driver of bacterial diversity, where substantial variation was found between samples collected in early winter to those collected in mid - late winter. Water parameter measures of pH, salinity and DO were identified to best explain the global bacterial community composition and their corresponding dynamic trajectory patterns overtime. Further investigation into bacterial community dynamics in accordance with varying environmental conditions could potentially lead to the determination of influential extrinsic factors that may drive bacterial activity in aquatic decomposition. Together with the identification of potential bacterial markers that complement the different stages of decomposition, this may provide a future approach to PMSI estimations.

A review of multi-disciplinary decomposition research and key drivers of variation in decay

The decomposition of animal remains is a multifaceted process, involving ecological, biological, and chemical interactions. While the complexity is acknowledged through concepts like the necrobiome, it's unclear if this complexity is reflected in research. Appreciation of the complexity of decomposition is crucial for identifying sources of variation in estimations of time since death in medico-legal science, as well as building broader ecological knowledge of the decomposition process. To gain insights into the extent of multidisciplinary research in the field of decomposition science, we conducted an examination of peer-reviewed literature on four key drivers of variation: volatile organic compounds, microbes, drugs/toxins, and insects. Among 650 articles, we identified their scientific discipline, driver/s of variation investigated, and year of publication. We found that 19% explored relationships between two drivers, while only 4% investigated interactions between three. None considered all four drivers. Over the past three decades, there has been a steady increase in decomposition research publications, signifying its growing importance. Most research (79%) was linked to forensic science, highlighting opportunities for interdisciplinary collaboration in decomposition science. Overall, our review underscores the need to incorporate multidisciplinary approaches and theory into contemporary decomposition research.

Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome

Larval net-spinning caddisflies (Hydropsychidae) function as ecosystem engineers in streams where they construct protective retreats composed of organic and inorganic material affixed with silk filtration nets that alter streambed hydrology. We hypothesized that hydropsychid bio-structures (retreats, nets) are microhabitats for microbes with oxygen-sensitive metabolisms, and therefore increase the metabolic heterogeneity of streambed microbial assemblages. Metagenomic and 16 S rRNA gene amplicon analysis of samples from a montane stream (Cherry Creek, Montana, USA) revealed that microbiomes of caddisfly bio-structures are taxonomically and functionally distinct from those of the immediately adjacent rock biofilm (~2 cm distant) and enriched in microbial taxa with established roles in denitrification, nitrification, and methane production. Genes for denitrification, high oxygen affinity terminal oxidases, hydrogenases, oxidative dissimilatory sulfite reductases, and complete ammonia oxidation are significantly enriched in caddisfly bio-structures. The results suggest a novel ecosystem engineering effect of caddisflies through the creation of low-oxygen, denitrifier-enriched niches in the stream microbiome. Facilitation of metabolic diversity in streambeds may be a largely unrecognized mechanism by which caddisflies alter whole-stream biogeochemistry.

Dissecting the microbial community structure of internal organs during the early postmortem period in a murine corpse model

BACKGROUND

Microorganisms distribute and proliferate both inside and outside the body, which are the main mediators of decomposition after death. However, limited information is available on the postmortem microbiota changes of extraintestinal body sites in the early decomposition stage of mammalian corpses.

RESULTS

This study investigated microbial composition variations among different organs and the relationship between microbial communities and time since death over 1 day of decomposition in male C57BL/6 J mice by 16S rRNA sequencing. During 1 day of decomposition, Agrobacterium, Prevotella, Bacillus, and Turicibacter were regarded as time-relevant genera in internal organs at different timepoints. Pathways associated with lipid, amino acid, carbohydrate and terpenoid and polyketide metabolism were significantly enriched at 8 h than that at 0.5 or 4 h. The microbiome compositions and postmortem metabolic pathways differed by time since death, and more importantly, these alterations were organ specific.

CONCLUSION

The dominant microbes differed by organ, while they tended toward similarity as decomposition progressed. The observed thanatomicrobiome variation by body site provides new knowledge into decomposition ecology and forensic microbiology. Additionally, the microbes detected at 0.5 h in internal organs may inform a new direction for organ transplantation.

The ephemeral resource patch concept

Ephemeral resource patches (ERPs) - short lived resources including dung, carrion, temporary pools, rotting vegetation, decaying wood, and fungi - are found throughout every ecosystem. Their short-lived dynamics greatly enhance ecosystem heterogeneity and have shaped the evolutionary trajectories of a wide range of organisms - from bacteria to insects and amphibians. Despite this, there has been no attempt to distinguish ERPs clearly from other resource types, to identify their shared spatiotemporal characteristics, or to articulate their broad ecological and evolutionary influences on biotic communities. Here, we define ERPs as any distinct consumable resources which (i) are homogeneous (genetically, chemically, or structurally) relative to the surrounding matrix, (ii) host a discrete multitrophic community consisting of species that cannot replicate solely in any of the surrounding matrix, and (iii) cannot maintain a balance between depletion and renewal, which in turn, prevents multiple generations of consumers/users or reaching a community equilibrium. We outline the wide range of ERPs that fit these criteria, propose 12 spatiotemporal characteristics along which ERPs can vary, and synthesise a large body of literature that relates ERP dynamics to ecological and evolutionary theory. We draw this knowledge together and present a new unifying conceptual framework that incorporates how ERPs have shaped the adaptive trajectories of organisms, the structure of ecosystems, and how they can be integrated into biodiversity management and conservation. Future research should focus on how inter- and intra-resource variation occurs in nature - with a particular focus on resource × environment × genotype interactions. This will likely reveal novel adaptive strategies, aid the development of new eco-evolutionary theory, and greatly improve our understanding of the form and function of organisms and ecosystems.

Corpse decomposition of freshwater economic fish leads to similar resistomes and the enrichment of high-risk antibiotic resistance genes in different water types

Animal carcass decay produces many poisonous metabolites and chemical pollutants, which pose potential ecological risks to the aquatic environment and human health. However, the effects of animal cadaver decomposition on high-risk antibiotic resistance genes (ARGs) and potential pathogens in different water types are still unknown. In this study, fifteen freshwater economic fish (Carassius auratus) corpses were put into three types of water (i.e., pond water, tap water, and domestic sewage) for a 100-day decomposition. Next generation sequencing and HT-qPCR were used to illustrate how corpse decomposition affected microbial communities and ARG profiles. Our results revealed that fish corpse degradation caused similar resistomes and microbiome in different water types. MLSB (Macrolide-Lincosamide-Streptogramin B), β-lactamase, sulfonamide, tetracycline resistance genes and transposase genes in the experimental groups were increased. Among them, tetracycline resistance genes were enriched by 224 to 136,218-fold during the process of corpse degradation. Furthermore, high-risk ARGs (ermB, floR and dfrA1), which resist to MLSB, multidrug and sulfonamide respectively, were significantly enriched in the cadaver groups and had co-occurrence patterns with opportunistic pathogens, such as Bacteroidetes, which was more than 37 times in carcass groups than that in control groups. The study is able to draw a general conclusion that cadaver decomposition of freshwater economic fish deteriorates the aquatic environment by affecting high-risk ARGs and pathogenic microorganisms regardless of water types, which poses potential threats to human health. Therefore, timely management and treatment of animal carcasses is of great significance to the protection of water environment.

Microbial community succession of submerged bones in an aquatic habitat

After death, microbes (including bacteria and fungi) colonize carrion from a variety of sources during the decomposition process. The predictable succession of microbes could be useful for forensics, such as postmortem submersion interval estimation (PMSI) for aquatic deaths. However, gaps exist in our understanding of microbial succession on submerged bone, particularly regarding longer-term decomposition (>1 year), fungal composition, and differences between internal and external microbial communities. To further explore this potential forensic tool, we described the postmortem microbial communities (bacteria and fungi) on and within submerged bones using targeted amplicon sequencing. We hypothesized predictable successional patterns of microbial colonization would be detected on the surface and within submerged bones, which would eventually converge to a similar microbial community. To best replicate forensic contexts, we sampled bones from replicate swine (Sus scrofa domesticus) carcasses submerged in a freshwater pond, every three months for nearly two years. Microbial bone (internal vs. external) community structure (taxa abundance and diversity) of bones differed for both bacteria and fungi, but internal and external communities did not converge to a similar structure. PMSI estimation models built with random forest regression of postmortem microbiomes were highly accurate (>80% variation explained in PMSI) and showed promise for forensic purposes. Overall, we provide further evidence that internal and external bone microbial communities submerged in an aquatic habitat are distinct and each community undergoes predictable succession, demonstrating potential utility in forensics for modeling PMSI in unattended deaths and/or cold cases.

Successions of rare and abundant microbial subcommunities during fish carcass decomposition in a microcosm under the influence of variable factors

Animal carcasses are hotspots of ecological activity. The study of the role of microbes in carcass decomposition has been exclusively focused on microbes with higher abundance. The comparative study of abundant and rare subcommunities associated with decomposition needs in-depth exploration. The current experiment has been conducted on the decomposition of a fish carcass in a microcosm. We conducted 16S rRNA gene sequencing of the microbial communities. The correlation of the physicochemical properties of tap and Yellow river water with the microbial communities was evaluated. Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were found to be the dominant phyla in both abundant and rare subcommunities. Among bacteria, the Acidobacteria, Planctomycetes, and Cyanobacteria were found only in the rare subcommunity. In both subcommunities, the abundance of Proteobacteria was found to increase over time, and that of Firmicutes to decrease. The rare subcommunity shows higher alpha diversity than the abundant one. The variation in the abundant subcommunity was influenced by time and water type, and that in the rare subcommunity was influenced by pH and water type. These results have implications for future research on the ecological role of rare and abundant subcommunities in the decomposition of carcasses in the aquatic ecosystem.

Is Resource Change a Useful Predictor of Carrion Insect Succession on Pigs and Humans?

Carrion is a dynamic and nutrient-rich resource that attracts numerous insect species that undergo succession due to the rapid change in the carrion resource. Despite this process being well-understood, few studies have examined resource change as a driver of carrion insect succession, and instead have focused on the effects of time per se, or on coarse, qualitative measures such as decay stage. Here we report on three field succession experiments using pig carcasses and human cadavers encompassing two winters and one summer. We quantified the effects of resource change (measured as total body score, TBS), carrion type, initial carrion mass, ambient temperature, and season on insect species richness and community composition. We found that all variables had an effect on different taxonomic or trophic components of the insect community composition, with the exception of initial carrion mass which had no effect. We found significant positive effects of TBS on beetle species richness and composition, while fly species richness was not significantly affected by TBS, but was by ambient temperature. TBS had a significant positive effect on all trophic groups, while ambient temperature also had a significant positive effect on the necrophages and predator/parasitoids. Our study indicates that resource change, as indicated by TBS, is an important driver of carrion insect species turnover and succession on carrion, and that TBS can provide information about insect ecological patterns on carrion that other temporal measures of change cannot.

Exploring microbial communities, assessment methodologies and applications of animal's carcass decomposition: a review

Animals are an essential part of the ecosystem, and their carcasses are the nutrient patches or hotspots where nutrients accumulate for a long time. After death, the physical and chemical properties undergo alterations inside the carcass. The animal carcass is decomposed by many decomposers such as bacteria, fungi, microeukaryotes and insects. The role of microbial symbionts in living organisms is well explored and studied, but there is a scarcity of knowledge and research related to their role in decomposing animal carcasses. Microbes play an important role in carcass decomposition. The origins of microbial communities associated with a carcass, including the internal and external microbiome, are discussed in this review. The succession and methods used for the detection and exploration of decomposition-associated microbial communities have been briefly described. Also, the applications of carcass-associated microbial taxa have been outlined. This review is intended to understand the dynamics of microbial communities associated with the carcass and pave the way to estimate postmortem interval and its role in recycling nutrients.

Chironomus ramosus Larval Microbiome Composition Provides Evidence for the Presence of Detoxifying Enzymes

Chironomids (Diptera; Chironomidae) are aquatic insects that are abundant in freshwater. We aimed to study the endogenous microbiota composition of Chironomus ramosus larvae that were sampled from the Mutha River and a laboratory culture in India. Furthermore, we performed a metagenomic analysis of the larval microbiome, sampled from the Mutha River. Significant differences were found between the bacterial community composition of C. ramosus larvae that were sampled from the Mutha River and the laboratory culture. A total of 54.7% of the amplicon sequence variants (ASVs) that were identified in the larvae from the Mutha River were unique, compared to only 12.9% of unique ASVs that were identified from the laboratory-reared larvae. The four most abundant phyla across all samples were: Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes, while the nine most abundant genera were: Aeromonas, Alkanindiges, Breznakia, Cetobacterium, Chryseobacterium, Desulfovibrio, Dysgonomonas, Thiothrix, and Vibrio. Moreover, in the metagenomic analysis, we detected bacterial genes and bacterial pathways that demonstrated the ability to degrade different toxic compounds, detoxify metal, and confer resistance to antibiotics and UV radiation, amongst other functions. The results illuminate the fact that there are detoxifying enzymes in the C. ramosus larval microbiome that possibly play a role in protecting the insect in polluted environments.

Postmortem submersion interval (PMSI) estimation from the microbiome of sus scrofa bone in a freshwater lake

While many studies have developed microbial succession-based models for the prediction of postmortem interval (PMI) in terrestrial systems, similar well-replicated long-term decomposition studies are lacking for aquatic systems. Therefore, this study sought to identify temporal changes in bacterial community structure associated with porcine skeletal remains (n = 198) for an extended period in a fresh water lake. Every ca. 250 ADD, one cage, containing 5 ribs and 5 scapulae, was removed from the lake for a total of nineteen collections. Water was also sampled at each interval. Variable region 4 (V4) of 16S rDNA was amplified and sequenced for all collected samples using Illumina MiSeq FGx Sequencing platform; resulting data were analyzed with the mothur (v1.39.5) and R (v3.6.0). Bacterial communities associated with ribs differed significantly from those associated with scapulae. This difference was mainly attributed to Clostridia, Holophagae, and Spirochaete relative abundances. For each bone type, α-diversity increased with ADD; similarly, β-diversity bacterial community structure changed significantly with ADD and were explained using environmental parameters and inferred functional pathways. Models developed using 24 rib and 34 scapula family-level taxa allowed the prediction of PMSI with root mean square error of 522.97 ADD (~57 days) and 333.8 ADD (~37 days), respectively.

Carcass decomposition influences the metabolic profiles and enriches noxious metabolites in different water types by widely targeted metabolomics

Carcass decomposition could be considered as a common phenomenon in nature. However, during degradation processes, animal carcasses produce many toxic and harmful metabolites, posing potential ecological risks to water safety, thereby threatening human health. However, the metabolites produced by decomposition of animal corpses are not well understood. In this study, building on our previous baseline study of microbial community between the experimental groups (with animal carcasses) and control groups (without carcasses), the samples at the ultimate stage (19th day) of carcass decomposition were chosen to investigate the metabolic profiles and uncover the relationships between water quality, microbes and noxious metabolites in two types of water (Yellow River water and tap water) using fish as animal model by widely targeted metabolomics. Our results showed amino acid metabolomics, indole and its derivatives, and pyridine and pyridine derivatives mainly occurred in the corpse groups, suggesting that these metabolites are markers of carcass decomposition. And some noxious metabolites (e.g., polyamine, amines, and benzene and substituted derivatives) highly associated with carcass decomposition, which revealed new insights into how to investigate the hazard materials in water. And these noxious metabolites in the corpse groups were even increased 214543-fold in average compared with the control groups. Meanwhile, treatment was the most important factor affecting the water metabolites while microbiome contributed a small proportion to the metabolic profiles. Several opportunistic pathogenic genera Comamonas, Bacteriodes and Alcaligenes co-occurred most frequently with several kinds of polyamines and amines while some dominant genera Rhodoferax, Delftia and Brevundimonas had significant positive relationships with specific benzene and substituted derivatives. This work demonstrates that carcass decomposition causes water quality deterioration by producing various toxic metabolites, thus providing new insights into noxious metabolites when exposed to animal carcasses in aquatic environment.

Temporal succession of water microbiomes and resistomes during carcass decomposition in a fish model

Carcass decomposition in water may cause serious environmental pollution, which poses a great threat to water quality and public health. However, water microbial community succession and antibiotic resistance genes (ARGs) during carcass decomposition process are less explored. Using high-throughput sequencing and high-throughput quantitative PCR techniques, the temporal succession of water bacterial communities and ARGs profiles in experimental groups (fish carcasses) and control groups (no carcasses) containing two different types of water (the Yellow River water and tap water) in different successional stages were studied. Our results showed that NH₃-N concentration in the corpse groups has greatly risen and exceeded more than 28 times on average over the safety thresholds of water quality. Some potential pathogenic genera Comamonas, Bacteroides and Pseudomonas significantly increased during carcass decomposition process. The bacterial communities of the Yellow River water and tap water in the experimental groups exhibited similar succession patterns, and community dissimilarities between the two groups decreased and smaller over time, indicating that bacterial community convergence. NH₃-N, NO₃-N and time were three most important factors in determining bacteria community structures. The influence of water type on corpse bacterial community structures was significant but weak. The gene copy number of seven detected ARGs (cmlA1-01, floR, sul1, sul2, tetG-01, tetM-01 and tetQ) in the experimental groups was more abundant than that in the control groups. The ARGs concentrations in the corpse groups were even enriched 19-fold (minimum) to 148-fold (maximum) compared to the gene tetQ of the Yellow River water in the control groups on the initial stage. Redundancy analysis (RDA) indicated that Bacteroidetes and Firmicutes were significantly correlated with all detected ARGs. This study emphasizes that cadaver degradation leads to the deterioration of nitrogen pollution, the abundance increase of potential pathogens, and the transfer of ARGs from dead animals to water environment, thereby uncovering the harmful effects of related water pollution for human health.

Identification of novel bacterial biomarkers to detect bird scavenging by invasive rats

Rapid advances in genomic tools for use in ecological contexts and non-model systems allow unprecedented insight into interactions that occur beyond direct observation. We developed an approach that couples microbial forensics with molecular dietary analysis to identify species interactions and scavenging by invasive rats on native and introduced birds in Hawaii. First, we characterized bacterial signatures of bird carcass decay by conducting 16S rRNA high-throughput sequencing on chicken (Gallus gallus domesticus) tissues collected over an 11-day decomposition study in natural Hawaiian habitats. Second, we determined if field-collected invasive black rats (Rattus rattus; n = 51, stomach and fecal samples) had consumed birds using molecular diet analysis with two independent PCR assays (mitochondrial Cytochrome Oxidase I and Cytochrome b genes) and Sanger sequencing. Third, we characterized the gut microbiome of the same rats using 16S rRNA high-throughput sequencing and identified 15 bacterial taxa that were (a) detected only in rats that consumed birds (n = 20/51) and (b) were indicative of decaying tissue in the chicken decomposition experiment. We found that 18% of rats (n = 9/51) likely consumed birds as carrion by the presence of bacterial biomarkers of decayed tissue in their gut microbiome. One species of native bird (Myadestes obscurus) and three introduced bird species (Lophura leucomelanos, Meleagris gallopavo, Zosterops japonicus) were detected in the rats' diets, with individuals from these species (except L. nycthemera) likely consumed through scavenging. Bacterial biomarkers of bird carcass decay can persist through rat digestion and may serve as biomarkers of scavenging. Our approach can be used to reveal trophic interactions that are challenging to measure through direct observation.

Bacterial association observations in Lucilia sericata and Lucilia cuprina organs through 16S rRNA gene sequencing

Blowfly (Diptera: Calliphoridae) species Lucilia sericata (Meigen) and related species Lucilia cuprina (Wiedmann) are important agricultural pests, assist in forensic fields and also have a therapeutic role in medicine. Both species (though predominantly L. sericata) are utilised in a clinical setting for maggot debridement therapy (MDT) where the larvae ingest necrotic tissue and bacteria from non-healing wounds. Conversely, larvae of L. cuprina feed invasively, as major initiators of sheep myiasis in Australia, New Zealand, and the UK, among other regions. Both species exhibit larval and adult interactions with bacterially rich environments, but the significance of this in the composition of their microbiome has yet to be considered. This study utilised dissected samples of digestive and reproductive organs from both disinfected and non-disinfected adults and larvae of both species for bacterial DNA extraction, followed by 16S rRNA gene sequencing. Sequencing data indicated unsurprisingly that digestive tracts of both genders and female salivary glands from all non-disinfected samples carry the most concentrated amounts of bacteria. Genera Pseudomonas and Corynebacterium were also highly represented within all organs and species analysed. Comparison of bait lures to sample sequence read output of insect specimens showed no correlation with genera such as Pseudomonas present in insects, while absent from wild bait, and in reduced amounts from fleece bait profiles. With this information, future work can focus on key organs such as the spermathecae and salivary glands, while also providing the potential to identify the role these bacteria may play in the blowfly life cycle. KEY POINTS: Genera Pseudomonas appears consistently in the microbiome of Lucilia species. Female spermathecae and salivary glands show the highest microbial diversity. Bacterial profiles of L. sericata and L. cuprina have similar composition.

Community Ecology and Conservation of Bear-Salmon Ecosystems

Apex predators play keystone roles in ecosystems through top-down control, but the effects of apex omnivores on ecosystems could be more varied because changes in the resource base alter their densities and reverberate through ecosystems in complex ways. In coastal temperate ecosystems throughout much of the Northern Hemisphere, anadromous salmon once supported abundant bear populations, but both taxa have declined or been extirpated from large parts of their former ranges with limited research on the consequences of diminished or absent interactions among species. Here we review the biogeography of bear-salmon interactions and the role of salmon-subsidized bears in (1) resource provisioning to plants and scavengers through the distribution of salmon carcasses, (2) competition among bears and other large carnivores, (3) predation of ungulate neonates, (4) seed dispersal, and (5) resource subsidies to rodents with seed-filled scats. In addition to our review of the literature, we present original data to demonstrate two community-level patterns that are currently unexplained. First, deer densities appear to be consistently higher on islands with abundant brown bears than adjacent islands with black bears and wolves, and moose calf survival is higher at low bear densities (<∼25 bears per 100 km2) but is constant across the vast majority of bear densities found in the wild (i.e., ∼>25 bears per 100 km2). Our review and empirical data highlight key knowledge gaps and research opportunities to understand the complex ecosystem effects related to bear-salmon interactions.

The effects of taxonomy, diet, and ecology on the microbiota of riverine macroinvertebrates

Freshwater macroinvertebrates play key ecological roles in riverine food webs, such as the transfer of nutrients to consumers and decomposition of organic matter. Although local habitat quality drives macroinvertebrate diversity and abundance, little is known about their microbiota. In most animals, the microbiota provides benefits, such as increasing the rate at which nutrients are metabolized, facilitating immune system development, and defending against pathogenic attack. Our objectives were to identify the bacteria within aquatic invertebrates and determine whether their composition varied with taxonomy, habitat, diet, and time of sample collection. In 2016 and 2017, we collected 264 aquatic invertebrates from the mainstem Saint John (Wolastoq) River in New Brunswick, Canada, representing 15 orders. We then amplified the V3-V4 hypervariable region of the 16S rRNA gene within each individual, which revealed nearly 20,000 bacterial operational taxonomic units (OTUs). The microbiota across all aquatic invertebrates were dominated by Proteobacteria (69.25% of the total sequence reads), but they differed significantly in beta diversity, both among host invertebrate taxa (genus-, family-, and order-levels) and temporally. In contrast to previous work, we observed no microbiota differences among functional feeding groups or traditional feeding habits, and neither water velocity nor microhabitat type structured microbiota variability. Our findings suggest that host invertebrate taxonomy was the most important factor in modulating the composition of the microbiota, likely through a combination of vertical and horizontal bacterial transmission, and evolutionary processes. This is one of the most comprehensive studies of freshwater invertebrate microbiota to date, and it underscores the need for future studies of invertebrate microbiota evolution and linkages to environmental bacteria and physico-chemical conditions.

Postmortem submersion interval (PMSI) estimation from the microbiome of Sus scrofa bone in a freshwater river

Due to inherent differences between terrestrial and aquatic systems, methods for estimating the postmortem interval (PMI) are not directly applicable to remains recovered from water. Recent studies have explored the use of microbial succession for estimating the postmortem submersion interval (PMSI); however, a non-disturbed, highly replicated and long-term aquatic decomposition study in a freshwater river has not been performed. In this study, porcine skeletal remains (N = 200) were submerged in a freshwater river from November 2017-2018 (6322 accumulated degree days (ADD)/353 days) to identify changes and successional patterns in bacterial communities. One cage (e.g., 5 ribs and 5 scapulae) was collected approximately every 250 ADD for twenty-four collections; baseline samples never exposed to water acted as controls. Variable region 4 (V4) of 16S rDNA, was amplified and sequenced via the Illumina MiSeq FGx sequencing platform. Resulting sequences were analyzed using mothur (v1.39.5) and R (v3.6.0). The abundances of bacterial communities differed significantly between sample types. These differences in relative abundance were attributed to Clostridia, Holophagae and Gammaproteobacteria. Phylogenetic diversity increased with ADD for each bone type; comparably, β-diversity bacterial community structure ordinated chronologically, which was explained with environmental parameters and inferred functional pathways. Models fit using rib samples provided a tighter prediction interval than scapulae, with a prediction of PMSI with root mean square error of within 472.31 (∼27 days) and 498.47 (∼29 days), respectively.

A Preliminary Forensic Entomological Study of Beetles (Coleoptera) in Interior Alaska, USA

Forensic entomology uses knowledge of arthropod ecology to help solve crimes. There has been no published forensic entomological research in Alaska. We used one piglet carcass split in half to create two carcass plots in Fairbanks (~64.8°N, subarctic) that were sampled over a period of 59 days in 2019. Four pitfall traps were placed around each carcass, and four similarly arranged pitfall traps were placed 40 m distant as controls. Traps were emptied approximately weekly covering the first four stages of decomposition. We focused on adults of the larger-bodied (>9 mm) families and subfamilies of Coleoptera: Staphylinidae (subfamily Staphylininae), Carabidae, and Silphidae. A total of 621 specimens were collected and processed: 29 staphylinines, 210 carabids, and 382 silphids. A one-way ANOVA showed no significant difference between the mean numbers of staphylinines or carabids caught in carcass versus control traps. Silphids showed significantly greater mean number of beetles caught in carcass traps relative to control traps. Four species of Silphidae were documented, but contrary to similar studies, the vast majority of specimens belonged to two species of Nicrophorus (N. vespilloides Herbst and N. investigator Zetterstedt). Each of the three target taxa showed a peak in the number of specimens collected during the bloat stage of decomposition despite the carabid peak being driven by a phytophagous species.

Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens

The microbial decomposition of animal tissues is an important ecological process that impacts nutrient cycling in natural environments. We studied the microbial decomposition of a common North American fish (rainbow darters) over four time points, combining 16S rRNA gene and shotgun metagenomic sequence data to obtain both taxonomic and functional perspectives. Our data revealed a strong community succession that was reproduced across different fish and environments. Decomposition time point was the main driver of community composition and functional potential; fish environmental origin (upstream or downstream of a wastewater treatment plant) had a secondary effect. We also identified strains related to the putative pathogen Aeromonas veronii as dominant members of the decomposition community. These bacteria peaked early in decomposition and coincided with the metagenomic abundance of hemolytic toxin genes. Our work reveals a strong decomposer succession in wild-caught fish, providing functional and taxonomic insights into the vertebrate necrobiome.

Despite progress understanding microbial communities involved in terrestrial vertebrate decomposition, little is known about the microbial decomposition of aquatic vertebrates from a functional and environmental context. Here, we analyzed temporal changes in the “necrobiome” of rainbow darters, which are common North American fish that are sensitive indicators of water quality. By combining 16S rRNA gene and shotgun metagenomic sequence data from four time points, we studied the progression of decomposers from both taxonomic and functional perspectives. The 16S rRNA gene profiles revealed strong community succession, with early decomposition stages associated with Aeromonas and Clostridium taxa and later stages dominated by members of the Rikenellaceae (i.e., Alistipes/Acetobacteroides genera). These results were reproducible and independent of environmental perturbation, given that exposure to wastewater treatment plant effluent did not substantially influence the necrobiome composition of fish or the associated water sample microbiota. Metagenomic analysis revealed significant changes throughout decomposition in degradation pathways for amino acids, carbohydrates/glycans, and other compounds, in addition to putrefaction pathways for production of putrescine, cadaverine, and indole. Binning of contigs confirmed a predominance of Aeromonas genome assemblies, including those from novel strains related to the pathogen Aeromonas veronii. These bins of Aeromonas genes also encoded known hemolysin toxins (e.g., aerolysin) that were particularly abundant early in the process, potentially contributing to host cell lysis during decomposition. Overall, our results demonstrate that wild-caught fish have a reproducible decomposer succession and that the fish necrobiome serves as a potential source of putative pathogens and toxigenic bacteria.

IMPORTANCE The microbial decomposition of animal tissues is an important ecological process that impacts nutrient cycling in natural environments. We studied the microbial decomposition of a common North American fish (rainbow darters) over four time points, combining 16S rRNA gene and shotgun metagenomic sequence data to obtain both taxonomic and functional perspectives. Our data revealed a strong community succession that was reproduced across different fish and environments. Decomposition time point was the main driver of community composition and functional potential; fish environmental origin (upstream or downstream of a wastewater treatment plant) had a secondary effect. We also identified strains related to the putative pathogen Aeromonas veronii as dominant members of the decomposition community. These bacteria peaked early in decomposition and coincided with the metagenomic abundance of hemolytic toxin genes. Our work reveals a strong decomposer succession in wild-caught fish, providing functional and taxonomic insights into the vertebrate necrobiome.

New Insights Into Culturable and Unculturable Bacteria Across the Life History of Medicinal Maggots Lucilia sericata (Meigen) (Diptera: Calliphoridae)

Because of the nutritional ecology of dung- and carrion-feeding, bacteria are the integral part of Lucilia sericata life cycle. Nevertheless, the disinfected larvae of the blowfly are applied to treat human chronic wounds in a biosurgery named maggot debridement therapy (MDT). To realize the effects of location/diet on the gut bacteria, to infer the role of bacteria in the blowfly ecology plus in the MDT process, and to disclose bacteria circulating horizontally in and vertically between generations, bacterial communities associated with L. sericata specimens from various sources were investigated using culture-based and culture-independent methods. In total, 265 bacteria, including 20 families, 28 genera, and 40 species, were identified in many sources of the L. sericata. Culture-dependent method identified a number of 144 bacterial isolates, including 21 species, in flies reared in an insectary; specimens were collected from the field, and third-instar larvae retrieved from chronic wounds of patients. Metagenetic approach exposed the occurrences of 121 operational taxonomic units comprising of 32 bacterial species from immature and adult stages of L. sericata. Gammaproteobacteria was distinguished as the dominant class of bacteria by both methods. Bacteria came into the life cycle of L. sericata over the foods and transovarially infected eggs. Enterococcus faecalis, Myroides phaeus, Proteus species, Providencia vermicola, and Serratia marcescens were exchanged among individuals via transstadial transmission. Factors, including diets, feeding status, identification tool, gut compartment, and life stage, governed the bacteria species. Herein, we reemphasized that L. sericata is thoroughly connected to the bacteria both in numerous gut compartments and in different life stages. Among all, transstadially transmitted bacteria are underlined, indicating the lack of antagonistic effect of the larval excretions/secretions on these resident bacteria. While the culture-dependent method generated useful data on the viable aerobic gut bacteria, metagenomic method enabled us to identify bacteria directly from the tissues without any need for cultivation and to facilitate the identification of anaerobic and unculturable bacteria. These findings are planned to pave the way for further research to determine the role of each bacterial species/strain in the insect ecology, as well as in antimicrobial, antibiofilm, anti-inflammatory, and wound healing activities.

Cold Case Experiment Demonstrates the Potential Utility of Aquatic Microbial Community Assembly in Estimating a Postmortem Submersion Interval

Microbial community assembly (MCA) of both human and nonhuman animal carcasses provides indicators useful for estimating the postmortem interval (PMI) in terrestrial settings. However, there are fewer studies estimating postmortem submersion intervals (PMSIs) in aquatic habitats. No aquatic studies to date assessed MCA in the context of a death investigation, with all previous studies focusing on important basic ecological questions. Within the context of a cold case investigation, we performed an experiment using replicate adult swine carcasses to describe postmortem MCA variability within a nonflowing aquatic habitat. Using high-throughput sequencing of carcass postmortem microbiomes, we described MCA variability and identified key taxa associated with decomposition in an aquatic habitat similar to the cold case body recovery site. We also modeled key taxa for estimating PMSIs, modeling within ±3 days (mean square error) postmortem using random forest regression. Our findings show significant changes in microbial communities as decomposition progressed, and several taxa were identified as important indicator taxa which may be useful for future estimates of PMSI. While descriptive, this study provides initial findings quantifying MCA variability within a nonflowing aquatic habitat. Within the context of the cold case investigation, we discuss how postmortem microbial samples collected at the time of body recovery could have been an important piece of evidence for understanding the PMSI of recovered remains. Additional experimental studies are needed to explicitly test and identify mechanisms associated with postmortem MCA variability in other habitats and under different temperature (e.g., seasons) conditions.

A survey of bacteria associated with various life stages of primary colonizers: Lucilia sericata and Phormia regina

Blow flies are common primary colonizers of carrion, play an important role in the transfer of microbes between environments, and serve as a vector for many human pathogens. While some investigation has begun regarding the bacteria associated with different life stages of blow flies, a well replicated study is currently not available for the majority of blow flies. This study investigated bacteria associated with successive life stages of blow fly species Lucilia sericata and Phormia regina. A total of 38 samples were collected from four true replicates of L. sericata and P. regina. Variable region four (V4) of 16S ribosomal DNA (16S rDNA) was amplified and sequenced on MiSeq FGx sequencing platform using universal 16S rDNA primers and dual-index sequencing strategy. Bacterial communities associated with different life stages of L. sericata and P. regina didn't differ significantly from each other. In both blow fly species, Bacilli (e.g., Lactococcus) and Gammaproteobacteria (e.g., Providencia) constituted >95% of all bacterial classes across all life stages. At the genus level, Vagococcus and Leuconostoc were present at relatively high abundances in L. sericata whereas Yersinia and Proteus were present at comparatively high abundances in P. regina. Overall, information on bacterial structures associated with various life stages of blow flies can help scientists in better understanding or management of vector-borne pathogen dispersal and in increasing the accuracy of microbial evidence based postmortem interval (PMI) prediction models.

The effect of a multi-strain probiotic on growth performance, non-specific immune response, and intestinal health of juvenile turbot, Scophthalmus maximus L

Probiotic is well known because of its health benefit on the host, including improve growth, treat disease, and enhance immunity. Currently, probiotic has been widely used in aquaculture. However, there is little information about the effect of probiotic on turbot. Therefore, an effort was made to explore the effect of a multi-strain probiotic on growth performance, non-specific immune response, and intestinal health of juvenile turbot, Scophthalmus maximus L. One hundred eighty juvenile turbot (20.04 ± 0.23 g) were randomly divided into three groups (T0, T1, T2), and fed diet were formulated to contain 0%, 1%, and 5% multi-strain probiotic, respectively. Sixty days after the feeding experiment, the growth performance, body composition, enzyme activities, and intestinal microorganism of turbot were analyzed. T2 and T1 showed better growth performance and significant higher (P < 0.05) enzyme activities than T0 (except lysozyme). Moreover, the IV (intestinal villus), IW (intestinal wall), and GC (goblet cell) were well modulated in probiotic treatments. Furthermore, Lactobacillus was found colonized in the intestine of the group fed with 5% multi-strain probiotic. These results suggested adding dietary multi-strain probiotic could positively affect for turbot aquaculture.

Experimental evaluation on the applicability of necrobiome analysis in forensic veterinary science

Despite the wide usage of animals as models in forensic studies, the investigations of fundamental legal questions involving domesticated and nondomesticated animals were always given marginal attention compared to “human forensic,” and only recently the interest in the discipline is increasing. Our research focuses on the effect of the fur coat on the activity and development of microbial decomposers. In order to test this variable never assessed before, rabbit carcasses were used and results show that: (i) distinct and significant temporal changes in terms of metabolic activity and taxa distribution can be tracked over the decomposition process; (ii) the richness and the diversity of the bacterial communities does not significantly vary over time, but it does not mean that the species Operational Taxonomic Units (OTUs) do not change; (iii) the presence/absence of the fur on the carcasses does not significantly affect either the bacterial communities’ functional activity or the diversity intra‐ and intercommunity, neither at phylum nor at family resolution; (iv) the functional activity and the ecological diversity of the bacterial communities are significantly affected by the body region, while the relative abundance is not. Obtained data confirm previous observations and provide new insight in the Forensic Veterinary field in terms of equally using them in order to derive a statistical model for the PMI estimation. As a future perspective, a contribution to the Forensic Entomology approach will be given in legal investigations when domestic or wild animals are involved, regardless of the presence of a hair layer.

Changes in Larval Mosquito Microbiota Reveal Non-target Effects of Insecticide Treatments in Hurricane-Created Habitats

Ephemeral aquatic habitats and their associated microbial communities (microbiomes) play important roles in the growth and development of numerous aquatic insects, including mosquitoes (Diptera). Biological control agents, such as Bacillus thuringiensis israelensis (Bti) or insect growth regulators (e.g., methoprene), are commonly used to control mosquitoes in these habitats. However, it is unknown how commonly used control compounds affect the mosquito internal microbiome and potentially alter their life history traits. The objectives of this study were threefold: characterize the internal microbiota of Aedes larvae (Culicidae) in ephemeral forested mosquito habitat using high-throughput amplicon based sequencing, assess how mosquito control treatments affect the internal microbial communities of larval mosquitoes, and determine if changes to the microbiome resulted from direct or indirect treatment effects. The larval microbiome varied in community composition and diversity with development stage and treatment, suggesting potential effects of control compounds on insect microbial ecology. While microbial community differences due to Bti treatment were a result of indirect effects on larval development, methoprene had significant impacts on bacterial and algal taxa that could not be explained by indirect treatment effects. These results provide new information on the interactions between pesticide treatments and insect microbial communities.

Temporal dynamics of microbiota before and after host death

The habitats that animals, humans and plants provide for microbial communities are inevitably transient, changing drastically when these hosts die. Because microbes associated with living hosts are ensured prime access to the deceased host’s organic matter, it is feasible that opportunistic, adaptable lifestyles are widespread among host-associated microbes. Here we investigate the temporal dynamics of microbiota by starving to death a host—the planktonic Crustacean Daphnia magna—and tracking the changes in its microbial community as it approaches death, dies and decomposes. Along with obligate host-associated microbes that vanished after the host’s death and decomposers that appeared after the host’s death, we also detected microbes with opportunistic lifestyles, seemingly capable of exploiting the host even before its death. We suggest that the period around host death plays an important role for host–microbiota ecology and for the evolution of hosts and their microbes.

Cascading effects on bacterial communities: cattle grazing causes a shift in the microbiome of a herbivorous caterpillar

Large mammalian herbivores greatly influence the functioning of grassland ecosystems. Through plant consumption, excreta, and trampling, they modify biodiversity, nutrient cycling, and soil properties. Grazing mammals can also alter soil and rhizosphere bacterial communities, but their effect on the microbiome of other animals in the habitat (i.e., insects) is unknown. Using an experimental field approach and Illumina MiSeq 16S rRNA gene sequencing, we analyzed the influence of cattle grazing on the microbial community of spring webworm caterpillars, Ocnogyna loewii. Our experimental setup included replicated grazed and non-grazed paddocks from which caterpillars were collected twice (first-second and fourth-fifth instar). The caterpillars' microbiome is composed mostly of Proteobacteria and Firmicutes, and contains a potential symbiont from the genus Carnobacterium (55% of reads). We found that grazing significantly altered the microbiome composition of late instar caterpillars, probably through changes in diet (plant) composition and availability. Furthermore, the microbiome composition of early instar caterpillars significantly differed from late instar caterpillars in 221 OTUs (58 genera). Pseudomonas and Acinetobacter were dominant in early instars, while Carnobacterium and Acinetobacter were dominant in late instars. This study provides new ecological perspectives on the cascading effects mammalian herbivores may have on the microbiome of other animals in their shared habitat.

A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition

The microbiome plays many roles in human health, often through the exclusive lens of clinical interest. The inevitable end point for all living hosts, death, has its own altered microbiome configurations. However, little is understood about the ecology and changes of microbial communities after death, or their potential utility for understanding the health condition of the recently living. Here we reveal distinct postmortem microbiomes of human hosts from a large-scale survey of death cases representing a predominantly urban population, and demonstrated these microbiomes reflected antemortem health conditions within 24–48 hours of death. Our results characterized microbial community structure and predicted function from 188 cases representing a cross-section of an industrial-urban population. We found strong niche differentiation of anatomic habitat and microbial community turnover based on topographical distribution. Microbial community stability was documented up to two days after death. Additionally, we observed a positive relationship between cell motility and time since host death. Interestingly, we discovered evidence that microbial biodiversity is a predictor of antemortem host health condition (e.g., heart disease). These findings improve the understanding of postmortem host microbiota dynamics, and provide a robust dataset to test the postmortem microbiome as a tool for assessing health conditions in living populations.

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3-732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences.

Necrophilous Insect Dynamics at Small Vertebrate Carrion in a Temperate Eucalypt Woodland

Insects associated with carrion are critical to the decomposition process and nutrient cycling in ecosystems. Yet the communities of insects associated with carrion vary between locations, and detailed case studies are necessary for identifying differences and similarities among contrasting habitats. In this study, we examined temporal changes in the crawling insect community collected from rabbit carcasses placed in contrasting grassland and tree habitats in southeastern Australia. We collected 18,400 adult insects, including 22 species of fly, 57 species of beetle, and 37 species of ant. We found significant effects of habitat type and time, but not their interaction, on the composition of the entire insect community. Several ant species showed early and rapid colonization and highest abundances during early stages of decay, including Iridomyrmex purpureus (Smith, 1858) under trees, and Iridomyrmex rufoniger (Lowne, 1865) and Rhytidoponera metallica (Smith, 1858) in grassland. We found that most fly species showed highest abundance during active decay, but Chrysomya varipes (Macquart 1851) was more abundant under trees than in grassland during this time. Beetles peaked during active or advanced decay stages, with Saprinus and Omorgus the most abundant genera. Our study demonstrates that strong replication of contrasting environmental treatments can reveal new information on habitat preferences of important carrion insect species. The numerical dominance of ants early in decomposition has implications for insect community structure via potential competitive interactions with flies, and should be more rigorously examined in future carrion studies.