Abiotic and Biotic Factors Regulating Inter-Kingdom Engagement between Insects and Microbe Activity on Vertebrate Remains

Preservation of agri-food byproducts by acidification and fermentation in black soldier fly larvae bioconversion

Maintaining a consistent supply of feedstock for efficient bioconversion of black soldier fly larvae (BSFL) presents challenges due to the fluctuating availability of biowastes and agri-food products. To address the challenge of consistent feedstock supply for BSFL, this study investigated the influence of three preservation methods: wild fermentation, inoculated fermentation, and acidification on agri-food by-products applied over three storage durations (1, 7, and 14 days), evaluating their impact on BSFL bioconversion, and feedstock nutrient and microbiota composition. The preserved feedstocks were characterized for gross nutrient, sugar, fermentation metabolite, and bacterial community analyses. All feedstock preservation methods and storage durations had a high bioconversion rate (21-25 % dry mass) and wet larval mass (170-196 mg). Notably, 7-and-14-day acidified feedstock had a significantly higher bioconversion rate compared to fermented feedstock. Acidification preserved feedstock nutrients best with only a 10 % difference compared to initial nutrient values. Fermentation produced typical lactic acid fermentation metabolites with reducing sugar contents; however, adding a lactic acid bacterial inoculum (7 log10 CFU kg feedstock-1) had no benefit, presumably due to the high nutrient content and existing richness in lactic acid bacteria. Preservations had little influence on Enterobacteriaceae (6.2-7.5 log10 CFU g-1) in freshly harvested larvae. Future research should assess the acidification and fermentation of different BSFL feedstocks and investigate the roles of feedstock pH, organic acids, and fermentation metabolites in more detail. Therefore, this study advances toward reliable and efficient insect-based nutrient recovery from agri-food by-products within the food system.

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.

Assessment of Fungal Succession in Decomposing Swine Carcasses (Sus scrofa L.) Using DNA Metabarcoding

The decomposition of animal bodies is a process defined by specific stages, described by the state of the body and participation of certain guilds of invertebrates and microorganisms. While the participation of invertebrates in decomposing is well-studied and actively used in crime scene investigations, information on bacteria and fungi from the scene is rarely collected or used in the identification of important factors such as estimated time of death. Modern molecular techniques such as DNA metabarcoding allow the identification and quantification of the composition of microbial communities. In this study, we used DNA metabarcoding to monitor fungal succession during the decomposition of juvenile pigs in grasslands of New Jersey, USA. Our findings show that decomposition stages differ in a diversity of fungal communities. In particular, we noted increased fungal species richness in the more advanced stages of decomposition (e.g., bloat and decay stages), with unique fungal taxa becoming active with the progression of decay. Overall, our findings improve knowledge of how fungi contribute to forensically relevant decomposition and could help with the assessment of crime scenes.

Exploring postmortem succession of rat intestinal microbiome for PMI based on machine learning algorithms and potential use for humans

The microbial communities may undergo a meaningful successional change during the progress of decay and decomposition that could aid in determining the post-mortem interval (PMI). However, there are still challenges to applying microbiome-based evidence in law enforcement practice. In this study, we attempted to investigate the principles governing microbial community succession during decomposition of rat and human corpse, and explore their potential use for PMI of human cadavers. A controlled experiment was conducted to characterize temporal changes in microbial communities associated with rat corpses as they decomposed for 30 days. Obvious differences of microbial community structures were observed among different stages of decomposition, especially between decomposition of 0-7d and 9-30d. Thus, a two-layer model for PMI prediction was developed based on the succession of bacteria by combining classification and regression models using machine learning algorithms. Our results achieved 90.48% accuracy for discriminating groups of PMI 0-7d and 9-30d, and yielded a mean absolute error of 0.580d within 7d decomposition and 3.165d within 9-30d decomposition. Furthermore, samples from human cadavers were collected to gain the common succession of microbial community between rats and humans. Based on the 44 shared genera of rats and humans, a two-layer model of PMI was rebuilt to be applied for PMI prediction of human cadavers. Accurate estimates indicated a reproducible succession of gut microbes across rats and humans. Together these results suggest that microbial succession was predictable and can be developed into a forensic tool for estimating PMI.

Toward Oral Thanatomicrobiology-An Overview of the Forensic Implications of Oral Microflora

Introduction

The oral cavity is home to numerous microorganisms including bacteria, fungi, and viruses which together form the oral microflora. It is the second most diverse microbial site in the human body after the gastrointestinal tract. Microbial degradation is a common phenomenon that occurs after death, with the early and advanced stages of decomposition being closely associated with oral microbial activity.

Methods

This article reviews the current state of knowledge on the role of the oral microflora in postmortem events, and highlights the growing importance of terms such as forensic microbiology and thanatomicrobiome. This article also discusses next-generation sequencing, metagenomic sequencing studies, and RNA sequencing to study the oral thanatomicrobiome and epinecrotic communities in forensic oral genetics.

Results

The indigenous microorganisms in the oral cavity are among the first to respond to the process of decomposition. DNA/RNA sequencing is a relatively simple, precise, and cost-effective method to estimate biological diversity during various stages of postmortem decomposition. The field of thanatomicrobiology is rapidly evolving into a key area in forensic research.

Conclusion

This article briefly narrates oral microflora and its implications in forensic odontology. The role of microbial activity in postmortem events is gaining importance in forensic research, and further studies are needed to fully understand the potential applications of advanced technology in the study of the oral thanatomicrobiome.

Linking bacteria, volatiles and insects on carrion: the role of temporal and spatial factors regulating inter-kingdom communication via volatiles

Multi-kingdom community complexity and the chemically mediated dynamics between bacteria and insects have recently received increased attention in carrion research. However, the strength of these inter-kingdom interactions and the factors that regulate them are poorly studied. We used 75 piglet cadavers across three forest regions to survey the relationship between three actors (epinecrotic bacteria, volatile organic compounds (VOCs) and flies) during the first 4 days of decomposition and the factors that regulate this interdependence. The results showed a dynamic bacterial change during decomposition (temperature-time index) and across the forest management gradient, but not between regions. Similarly, VOC emission was dynamic across a temperature-time index and the forest management gradient but did not differ between regions. However, fly occurrence was dynamic across both space and time. The strong interdependence between the three actors was mainly regulated by the temperature-time index and the study regions, thereby revealing regulation at temporal and spatial scales. Additionally, the actor interdependence was stable across a gradient of forest management intensity. By combining different actors of decomposition, we have expanded our knowledge of the holistic mechanisms regulating carrion community dynamics and inter-kingdom interactions, an important precondition for better describing food web dynamics and entire ecosystem functions.

[Estimation of time since death with the postmortem microbiome: a modern view and approaches to solving the problem]

The aim of the review is to summarize and update the data of modern studies devoted to determining the post-mortem interval (PMI) with the use of microorganisms, as well as disclosing prospects for further study in the presented direction. Estimating the time elapsed since death based on the postmortem microbiome has great potential for accurate determination of PMI, but all methods currently used have their limitations. The dynamics of changes in microbial communities due to the influence of many external and internal factors significantly complicates the process of interpreting the results. The change of microbial communities in the human corpse has shown promising results for the assessment of PMI, but to date there is no evidence of the repeatability of such a continuity in various geographic and ecological conditions. The question of conducting new, large-scale studies, taking in all the factors that could affect the posthumous microbiome, is becoming urgent.

Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems

Microorganisms are ubiquitous on Earth and can inhabit almost every environment. In a complex heterogeneous environment or in face of ecological disturbance, the microbes adjust to fluctuating environmental conditions through a cascade of cellular and molecular systems. Their habitats differ from cold microcosms of Antarctica to the geothermal volcanic areas, terrestrial to marine, highly alkaline zones to the extremely acidic areas and freshwater to brackish water sources. The diverse ecological microbial niches are attributed to the versatile, adaptable nature under fluctuating temperature, nutrient availability and pH of the microorganisms. These organisms have developed a series of mechanisms to face the environmental changes and thereby keep their role in mediate important ecosystem functions. The underlying mechanisms of adaptable microbial nature are thoroughly investigated at the cellular, genetic and molecular levels. The adaptation is mediated by a spectrum of processes like natural selection, genetic recombination, horizontal gene transfer, DNA damage repair and pleiotropy-like events. This review paper provides the fundamentals insight into the microbial adaptability besides highlighting the molecular network of microbial adaptation under different environmental conditions.

Microbiome pattern of Lucilia sericata (Meigen) (Diptera: Calliphoridae) and feeding substrate in the presence of the foodborne pathogen Salmonella enterica

The microbial diversity and quantitative dynamics during the insect’s development stages constitute recently developed putative tools in forensic and medical studies. Meanwhile, little is known on the role of insects in spreading foodborne pathogenic bacteria and on the impact of these pathogens on the overall insects and feeding substrate microbiome composition. Here, we provide the first characterization of the bacterial communities harbored in adult and immature stages of Lucilia sericata, one of the first colonizers of decomposed human remains, in the presence of the foodborne pathogen Salmonella enterica using 16S rRNA Illumina sequencing and qPCR. The pathogen transmission from the wild adults to the second generation was observed, with a 10^1.25× quantitative increase. The microbial patterns from both insect and liver samples were not influenced by the artificial introduction of this pathogenic foodborne bacteria, being dominated by Firmicutes and Proteobacteria. Overall, our results provided a first detailed overview of the insect and decomposed substrate microbiome in the presence of a human pathogen, advancing the knowledge on the role of microbes as postmortem interval estimators and the transmission of pathogenic bacteria.

Convergence of Social Strategies in Carrion Breeding Insects

Carrion is a highly ephemeral and nutrient rich resource, characterized by extreme biotic and abiotic stressors. We hypothesized that specific constraints of the carrion ecosystem, and especially its nutrient richness, ephemerality, and competition with microbes, have promoted the evolution of social behaviors in necrophagous insects. We show that group living is prevalent among early succession carrion breeding insects, suggesting that this trait has emerged as an adaptation to facilitate survival in the highly competitive environment of fresh carrion. We then highlight how developmental niche construction allows larvae to compete with microbes, efficiently feed on fresh cadavers, and rapidly reach maturity. We observed that larval societies and parental care are two different strategies responding to similar competitive and environmental constraints. We conclude that intra and interspecific competition on carrion are mitigated by social behavior.

Microbiome in Death and Beyond: Current Vistas and Future Trends

Forensic medicine has, for a long time, been relying on biochemical, anthropologic, and histopathologic evidences in solving various investigations. However, depending on the method used, lengthy sample processing time, scanty sample, and less sensitivity and accuracy pervade these procedures. Accordingly, newer arenas such as the thanatomicrobiome have come forward to aid in its quandaries; furthermore, the parallel advances in genomic and proteomic techniques have complemented and are still emerging to be used in forensic experiments and investigations. Postmortem interval (PMI) is one of the most important aspects of medico-legal investigations. The current trend in PMI estimation is toward genomic analyses of autopsy samples. Similarly, determination of cause of death, although a domain of medical sciences, is being targeted as the next level of forensic casework. With the current trend in laboratory sciences moving to the discovery of newer disease-specific markers for diagnostic and prognostic purposes, the same is being explored for the determination of the cause of death by using techniques such as Real-Time PCR, DNA micro-array, to Next-Gen Sequencing. Establishing an individual’s biological profile has been done using medicolegal methods and anthropology as well as bar-bodies/Davidson bodies (gender determination); and in cases where the determination of age/gender is a challenge using morphological characteristics; the recent advances in the field of genomics and proteomics have played a significant role, e.g., use of mitochondrial DNA in age estimation and in maternity disputes. The major hurdle forensic medical research faces is the fact that most of the studies are conducted in animal models, which are often difficult to mimic in human and real-time scenarios. Additionally, the high accuracy required in criminal investigations to be used in a court of law as evidence has prevented these results to come out of the labs and be used to the optimum. The current review aims at giving a comprehensive and critical account of the various molecular biology techniques including “thanatogenomics,” currently being utilized in the veritable fields of forensic medicine.

Volatile organic compounds in variably aged carrion impacted by the presence of the primary colonizer, Cochliomyia macellaria (Diptera: Calliphoridae)

The attraction and colonization of vertebrate remains by carrion-associated arthropods are processes largely governed by olfaction. As remains decompose, they emit a bouquet of volatile organic compounds (VOCs), which in part originate from endogenous and exogenous microbes surrounding the carcass or from the carcass itself. The composition and concentration of VOCs are influenced by the presence and abundance of microbial species and arthropods. Blowfly species, such as Cochliomyia macellaria, play a critical role in nutrient recycling and the decomposition process of carrion. Gas chromatography-mass spectroscopy analysis was used to identify and classify volatile emissions from insect-colonized (with C. macellaria) and uncolonized rat carcasses, as well as a standard Gainesville diet, over a 10-day period. There were significant differences in composition and abundance of compounds present in each treatment, with significant effects of time, and different compound composition between treatments. Notable indicator compounds included, but were not limited to, indole, dimethyl disulfide, and dimethyl trisulfide. A high compound richness, and a low compound diversity, was detected over the 10-day period. The indicator compounds detected across all treatments were found to be of microbial origin, highlighting the importance of microbes in decomposition processes and arthropod attraction to carrion. This study also discusses the significant impact of necrophagous arthropods to the VOC profile of carrion. The results of this study provide insight into the changes in decomposition VOCs over time, with an explanation of compounds in high concentration known to be attractive to carrion-colonizing arthropods.

Thanatomicrobiome and epinecrotic community signatures for estimation of post-mortem time interval in human cadaver

Estimation of post-mortem time interval (PMI) is a key parameter in the forensic investigation which poses a huge challenge to the medico-legal experts. The succession of microbes within different parts of the human body after death has shown huge potential in the determination of PMI. Human body harbors trillions of microorganisms as commensals. With the death of an individual when biological functions are stopped, these microorganisms behave contrarily along with the invasion of degrading microbes from the environment. Human cadaver becomes a rich source of nutrients due to autolysis of cells, which attracts various invading microorganisms as well as macroorganisms. At different stages of degradation, the succession of microorganisms differs significantly which can be explored for accurate PMI estimation. With the advent of microbial genomics technique and reduction in the cost of DNA sequencing, thanatomicrobiome and epinecrotic community analysis have gained huge attention in PMI estimation. The article summarizes different sources of microorganisms in a human cadaver, their succession pattern, and analytical techniques for application in the field of microbial forensics. KEY POINTS: • Thanatomicrobiome and epinecrotic microbiome develop in postmortem human body. • Lack of metabolic, immune, neuroendocrine systems facilitate microbial succession. • Analysis of postmortem microbial communities predicts accurate PMI.

Cuticular hydrocarbons as a tool for determining the age of Chrysomya rufifacies (Diptera: Calliphoridae) larvae

Calliphoridae are one of the most important insect groups encountered as evidence collected from a crime scene. Age determination of the immature stages of these necrophagous flies is an important step toward estimating the time of colonization and inferring a minimum postmortem interval (PMI_min ) in most instances. To determine if the cuticular hydrocarbons could be used to establish whether the development stages yield characteristics profiles, allowing for age estimation, hydrocarbons were extracted from 1st and 2nd, as well as feeding and post-feeding 3rd instar Chrysomya rufifacies, the hairy maggot blow fly. Extracted hydrocarbons were analyzed using gas chromatography coupled to mass spectrometry with the aim to investigate the changes in chemical profiles of each larval stage. A total of 23 compounds were identified with most of them being alkanes (65%) with carbon chain lengths of 9-33 carbons, alkenes (18%), and methyl-branched alkanes (17%). All the hydrocarbons except pentadecane (C15), hexadecane (C16), and nonacosane (C29) showed significant differences in their expression throughout larval development. For 1st instars, nonane was the most abundant (17% of the total hydrocarbons content) compound. Accounting for 11% and 10% of the cuticular hydrocarbons, tricosane and pentacosane, respectively, were the notable hydrocarbons in 2nd instars. For post-feeding 3rd instars, hentriacontane and tritriacontane were present with relative abundances 18% and 15%, respectively. On average, there was a shift from low to high molecular weight hydrocarbons as the larvae aged. These results indicate the change in hydrocarbons makeup as larvae age and could potentially be used to determine the age of immature C. rufifacies and hence aid in PMI_min estimations. However, future research is needed to validate these results under natural conditions in the field.

Cold Responses of the Mediterranean Fruit Fly Ceratitis capitata Wiedemann (Diptera: Tephritidae) in Blueberry

In this study, the effects of cold treatment at 1.0 ± 0.2 °C were investigated on the eggs of the 1st, 2nd, and 3rd instar larvae of Ceratitis capitata in two Australian blueberry cultivars C99-42 and C00-09. Pupariation, emerged adults, and sex ratios were examined on C. capitata after the treatment. The results showed that exposure time at low temperatures was a key factor to affect pupariation and adult emergence. Eleven days of exposure to cold treatment at 1.0 ± 0.2 °C were enough to eradicate all four immature stages in both cultivars. Cold tolerance of the four C. capitata stages was not affected when reared on two different blueberry cultivars. The third instar larva is the most tolerant stage for cold treatment in two blueberry cultivars. There were no significant differences in sex ratios from surviving C. capitata among different stages after treatment. This study improves understanding of C. capitata responses to cold treatment in blueberries, which may contribute to phytosanitary required quarantine treatment of this destructive horticulture pest species.

Identification of cadaveric liver tissues using thanatotranscriptome biomarkers

Thanatotranscriptome studies involve the examination of mRNA transcript abundance and gene expression patterns in the internal organs of deceased humans. Postmortem gene expression is indicative of the cellular status of a corpse at the time of death, a portion of which may represent a cascade of molecular events occasioned by death. Specific gene biomarkers identify perceptible transcriptional changes induced by stochastic responses to the cessation of biological functions. Transcriptome analyses of postmortem mRNA from a tissue fragment may determine unique molecular identifiers for specific organs and demonstrate unique patterns of gene expression that can provide essential contextual anatomical information. We evaluated the impact of targeted transcriptome analysis using RNA sequencing to reveal global changes in postmortem gene expression in liver tissues from 27 Italian and United States corpses: 3.5-hour-old to 37-day-old. We found that our single blind study using eight liver tissue-specific gene biomarkers (e.g. AMBP and AHSG) is highly specific, with autopsy-derived organ samples correctly identified as tissues originating from postmortem livers. The results demonstrate that 98–100% of sequencing reads were mapped to these liver biomarkers. Our findings indicate that gene expression signatures of mRNA exposed up to 37 days of autolysis, can be used to validate the putative identity of tissue fragments.

Bacterial Semiochemicals and Transkingdom Interactions with Insects and Plants

A peculiar feature of all living beings is their capability to communicate. With the discovery of the quorum sensing phenomenon in bioluminescent bacteria in the late 1960s, it became clear that intraspecies and interspecies communications and social behaviors also occur in simple microorganisms such as bacteria. However, at that time, it was difficult to imagine how such small organisms-invisible to the naked eye-could influence the behavior and wellbeing of the larger, more complex and visible organisms they colonize. Now that we know this information, the challenge is to identify the myriad of bacterial chemical signals and communication networks that regulate the life of what can be defined, in a whole, as a meta-organism. In this review, we described the transkingdom crosstalk between bacteria, insects, and plants from an ecological perspective, providing some paradigmatic examples. Second, we reviewed what is known about the genetic and biochemical bases of the bacterial chemical communication with other organisms and how explore the semiochemical potential of a bacterium can be explored. Finally, we illustrated how bacterial semiochemicals managing the transkingdom communication may be exploited from a biotechnological point of view.

Plant Aquaporins: Diversity, Evolution and Biotechnological Applications

The plasma membrane forms a permeable barrier that separates the cytoplasm from the external environment, defining the physical and chemical limits in each cell in all organisms. The movement of molecules and ions into and out of cells is controlled by the plasma membrane as a critical process for cell stability and survival, maintaining essential differences between the composition of the extracellular fluid and the cytosol. In this process aquaporins (AQPs) figure as important actors, comprising highly conserved membrane proteins that carry water, glycerol and other hydrophilic molecules through biomembranes, including the cell wall and membranes of cytoplasmic organelles. While mammals have 15 types of AQPs described so far (displaying 18 paralogs), a single plant species can present more than 120 isoforms, providing transport of different types of solutes. Such aquaporins may be present in the whole plant or can be associated with different tissues or situations, including biotic and especially abiotic stresses, such as drought, salinity or tolerance to soils rich in heavy metals, for instance. The present review addresses several aspects of plant aquaporins, from their structure, classification, and function, to in silico methodologies for their analysis and identification in transcriptomes and genomes. Aspects of evolution and diversification of AQPs (with a focus on plants) are approached for the first time with the aid of the LCA (Last Common Ancestor) analysis. Finally, the main practical applications involving the use of AQPs are discussed, including patents and future perspectives involving this important protein family.

Potential for insecticide-mediated shift in ecological dominance between two competing aphid species

Competition is a key structuring component of biological communities, which is affected by both biotic and abiotic environmental stressors. Among the latter, anthropic stressors and particularly pesticides are noteworthy due to their intrinsic toxicity and large use in agroecosystems. However this issue has been scarcely documented so far. In this context, we carried out experiments under laboratory conditions to evaluate stress imposed by the neonicotinoid insecticide imidacloprid on intra and interspecific competition among two major wheat pest aphids. The bird cherry-oat aphid Rhopalosiphum padi L. and the English grain aphid Sitobion avenae F. were subjected to competition on wheat seedlings under varying density combinations of both species and subjected or not to imidacloprid exposure. Intraspecific competition does take place without insecticide exposure, but so does interspecific competition between both aphid species with R. padi prevailing over S. avenae. Imidacloprid interfered with both intra and interspecific competition suppressing the former and even the latter for up to 14 days, but not afterwards when a shift in dominance takes place favoring S. avenae over R. padi, in contrast with the interspecific competition without imidacloprid exposure. These findings hinted that insecticides are indeed able to mediate species interaction and competition influencing community structure and raising management concerns for favoring potential secondary pest outbreaks.

Facing death together: heterospecific aggregations of blowfly larvae evince mutual benefits

Heterospecific aggregations and foraging associations have been observed between different species, from apes to birds to insects. Such associations are hypothesized to result in a mutually beneficial relationship entailing benefits that are not apparent in conspecific groupings. Therefore, the objectives of the present study were to investigate 1) how 3 blowfly species, namely, Calliphora vicina, Calliphora vomitoria, and Lucilia sericata, aggregate according to species, and 2) if developmental benefits are linked to heterospecific aggregation. For objective (1), larvae of 2 species were placed between 2 conspecific aggregates, each with a different species (i.e., a binary choice test). After 20 h, the positions of all larvae were determined. On average, 98% of the maggots added later settled together on one of the 2 pre-existing aggregations, demonstrating a collective choice. The aggregation spot with C. vicina was preferred against others, indicating different attractiveness of different species. To relate this behavior to its benefits (objective ii), C. vicina and L. sericata larvae were raised from first instar to adult in con- and heterospecific conditions, and their development time, mortality rates, and morphometrics were measured. Thereby, mutual and asymmetric consequences were observed: specifically, there were significant increases in size and survival for L. sericata and faster development for C. vicina in heterospecific groups. These results indicate that the predilection for heterospecific association leads to mutual developmental benefits. This heterospecific aggregation behavior may be a resource-management strategy of blowflies to face carrion-based selection pressure.