Intraspecific Gene Flow and Vector Competence among Periplaneta americana Cockroaches (Blattodea: Blattidae) in Central Texas

One of the most overlooked areas in forensic entomology is urban, which applies to insects and their arthropod relatives that have interactions with humans, their associated structures, and companion animals. American cockroaches, Periplaneta americana (L.), are common pests of urban environments. Analyzing spatial distribution of P. americana populations in an artificial, outdoor environment provided insight of gene flow among populations collected in central Texas. This information provides for a better understanding of how and if populations were segregated, or if there was a single unified population. Populations can be genetically differentiated through determining variation of specific gene regions within populations. This study revealed a ubiquitous distribution of cockroach populations, and their ability to indiscriminately inhabit areas within an urban environment. Overall, cockroaches were identified from a large interbreeding population with no discernable relationship between genetic variation of P. americana and spatial distribution. Identifying cockroach populations is relative to understanding the ability of surrogate species indirectly affecting man by their ability to transfer disease-causing organisms including bacteria. This may have potentially deleterious health consequences on animal and/or human populations. There are several pathogens associated with cockroaches which are overlooked during diagnosis of sudden ailments with symptoms being similar to food-borne illnesses, including abdominal cramping, diarrhea, nausea, and fever. Analyzing spatial distributions of Escherichia coli and Campylobacter spp. in relationship to collected cockroaches allowed for prevalence of bacteria species to be identified among populations. The prevalence of bacteria isolated from total populations collected indicated a high prevalence (92.3%) of bacteria carried by the exoskeleton of P. americana. Gram-negative bacteria acquisition and dissemination of organisms such as E. coli was prevalent on campus. Screening for E. coli 1057:H7 and Campylobacter spp. resulted in no positive colony growth. The lack of Campylobacter spp. growth from cuticular surfaces may have resulted from undesirable conditions required to sustain colony growth. Data from this study corroborates the potential ability of cockroaches to mechanically transmit pathogens

The Importance of Microbial and Primary Colonizer Interactions on an Ephemeral Resource

Carrion decomposition is an essential ecosystem function as it is an important component of nutrient cycling. Carrion decomposition has primarily been attributed to insect consumption, with little attention given to microbial communities or their potential interactions with insects. The first objective was to use passive insect-trapping methods to assess primary colonizer communities on swine carcasses between two treatments: 1) carrion with access to insects and 2) carrion excluded from insect access for five days using exclusion cages. Despite similarities between succession patterns within each treatment, carcasses initially exposed to insects had significantly fewer insect taxa. Therefore, collections of adult insect communities associated with carrion are promising as an indication of whether or not there has been a delay in insect colonization of a resource. There has yet to be a study documenting bacterial communities during carrion decomposition. The second objective was to describe bacterial community succession and composition during decomposition in the presence and absence of naturally occurring insects. Total genomic DNA was used to identify bacterial community composition via a modified bacterial tagged encoded FLX amplicon pyrosequencing. I obtained 378,904 sequences and documented distinct bacterial community successional trajectories associated with insect access and exclusion carcasses. By the fifth day of decomposition, Proteus was the dominant (72%) bacterial genus on exclusion carcasses while Psychrobacillus (58%) and Ignatzschineria (18%) were dominant bacterial genera on insect carcasses. These data are the first to document bacterial community composition and succession on carrion. My final objective was to assess microbial community function in response to carrion insect colonization using metabolic profiling. I characterized microbial community metabolic function in the presence and absence of the primary necrophagous insects. I documented significant microbial community metabolic profile changes during active decomposition of carcasses. Mean carcass microbial community metabolic function with insect access continuously decreased over decomposition during both field seasons. Thus demonstrating microbial metabolic activity may have discriminatory power to differentiate early and late stages of decomposition. Overall, my data contributes to an understudied area of microbial research important to organic matter decomposition, forensic entomology, and microbial-insect ecological interactions

Towards quantifying carrion biomass in ecosystems

The decomposition of animal biomass (carrion) contributes to the recycling of energy and nutrients through ecosystems. Whereas the role of plant decomposition in ecosystems is broadly recognised, the significance of carrion to ecosystem functioning remains poorly understood. Quantitative data on carrion biomass are lacking and there is no clear pathway towards improved knowledge in this area. Here, we present a framework to show how quantities derived from individual carcasses can be scaled up using population metrics, allowing for comparisons among ecosystems and other forms of biomass. Our framework facilitates the generation of new data that is critical to building a quantitative understanding of the contribution of carrion to trophic processes and ecosystem stocks and flows. © 2019 Elsevier Ltd. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Philip Barton” is provided in this record*

Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals

Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as a method to determine the postmortem submersion interval (PMSI) of remains because there are no standard methods for estimating the PMSI and biofilms are ubiquitous in aquatic habitats. We sought to compare the development of epinecrotic (biofilms on Sus scrofa domesticus carcasses) and epilithic (biofilms on unglazed ceramic tiles) communities in two small streams using bacterial automated ribosomal intergenic spacer analysis. Epinecrotic communities were significantly different from epilithic communities even though environmental factors associated with each stream location also had a significant influence on biofilm structure. All communities at both locations exhibited significant succession suggesting that changing communities throughout time is a general characteristic of stream biofilm communities. The implications resulting from this work are that epinecrotic communities have distinctive shifts at the first and second weeks, and therefore the potential to be used in forensic applications by associating successional changes with submersion time to estimate a PMSI. The influence of environmental factors, however, indicates the lack of a successional pattern with the same organisms and a focus on functional diversity may be more applicable in a forensic context

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 theunderlying soil, which can impact associated biological community structure andfunction. 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

Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis*,†,‡

Microbial communities have potential evidential utility for forensic applications. However, bioinformatic analysis of high‐throughput sequencing data varies widely among laboratories. These differences can potentially affect microbial community composition and downstream analyses. To illustrate the importance of standardizing methodology, we compared analyses of postmortem microbiome samples using several bioinformatic pipelines, varying minimum library size or minimum number of sequences per sample, and sample size. Using the same input sequence data, we found that three open‐source bioinformatic pipelines, MG‐RAST, mothur, and QIIME2, had significant differences in relative abundance, alpha‐diversity, and beta‐diversity, despite the same input data. Increasing minimum library size and sample size increased the number of low‐abundant and infrequent taxa detected. Our results show that bioinformatic pipeline and parameter choice affect results in important ways. Given the growing potential application of forensic microbiology to the criminal justice system, continued research on standardizing computational methodology will be important for downstream applications.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154468/1/jfo14213_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154468/2/jfo14213.pd

Total RNA Analysis of Bacterial Community Structural and Functional Shifts Throughout Vertebrate Decomposition

Multiple methods have been proposed to provide accurate time since death estimations, and recently, the discovery of bacterial community turnover during decomposition has shown itself to have predictable patterns that may prove useful. In this study, we demonstrate the use of metatranscriptomics from the postmortem microbiome to simultaneously obtain community structure and functional data across postmortem intervals (PMIs). We found that bacterial succession patterns reveal similar trends as detected through DNA analysis, such as increasing Clostridiaceae as decomposition occurs, strengthening the reliability of total RNA community analyses. We also provide one of the first analyses of RNA transcripts to characterize bacterial metabolic pathways during decomposition. We found distinct pathways, such as amino acid metabolism, to be strongly up‐regulated with increasing PMIs. Elucidating the metabolic activity of postmortem microbial communities provides the first steps to discovering postmortem functional biomarkers since functional redundancy across bacteria may reduce host individual microbiome variability.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152033/1/jfo14083_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/152033/2/jfo14083.pd

NECROBIOME FRAMEWORK FOR BRIDGING DECOMPOSITION ECOLOGY OF AUTOTROPHICALLY AND HETEROTROPHICALLY DERIVED ORGANIC MATTER

Life arises from death through species that decompose dead biomass or necromass. This paper provides a synthesis of the species responsible for dead plant and animal decomposition and describes a conceptual perspective—the “necrobiome”— that defines the diverse and complex communities that interact to recycle necromass. The concept brings unification to the previously disparate fields of plant and animal decomposition by discussing the universal processes occurring across all forms of necromass. It highlights the factors that make each form of dead biomass different in a way that defines how unique necrobiomes drive decomposition and ultimately shape ecosystem structure and function

Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter

Decomposition contributes to global ecosystem function by contributing to nutrient recycling, energy flow, and limiting biomass accumulation. The decomposer organisms influencing this process form diverse, complex, and highly dynamic communities that often specialize on different plant or animal resources. Despite performing the same net role, there is a need to conceptually synthesize information on the structure and function of decomposer communities across the spectrum of dead plant and animal resources. A lack of synthesis has limited cross-disciplinary learning and research in important areas of ecosystem and community ecology. Here we expound on the “necrobiome” concept and develop a framework describing the decomposer communities and their interactions associated with plant and animal resource types within multiple ecosystems.We outline the biotic structure and ecological functions of the necrobiome, along with how the necrobiome fits into a broader landscape and ecosystem context. The expanded necrobiome model provides a set of perspectives on decomposer communities across resource types, and conceptually unifies plant and animal decomposer communities into the same framework, while acknowledging key differences in processes and mechanisms. This framework is intended to raise awareness among researchers, and advance the construction of explicit, mechanistic hypotheses that further our understanding of decomposer community contributions to biodiversity, the structure and function of ecosystems, global nutrient recycling and energy flow

Microbial Community Functional Change during Vertebrate Carrion Decomposition

Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects). Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition