Forensic soil DNA analysis using high-throughput sequencing: A comparison of four molecular markers

Assessing three soil removal methods for environmental DNA analysis of mock forensic geology evidence

Soil is useful in criminal investigations as it is highly variable and readily transferred. Forensic geologists use several different techniques to removal soil from evidence prior to the analysis of inorganic components. There has been recent interest from the forensic science community to analyze environmental deoxyribonucleic acid (eDNA) associated with soil to augment existing forensic analyses. Notably however, limited research has been conducted to compare commonly used soil removal methods for downstream eDNA analysis. In this study, three soil removal methods were assessed: picking/scraping, sonication, and swabbing. Three mock evidence types (t-shirts, boot soles, and trowels) were sampled in triplicate with each removal method (n = 27). Soil samples underwent DNA isolation, quantification, and amplification of four genomic barcode regions: 16S for bacteria, ITS1 for fungi, ITS2 for plants, and COI for arthropods. Amplicons were prepared into libraries for DNA sequencing on an Illumina® MiniSeq. DNA concentrations were highest in picked/scraped samples and were statistically significant compared with swabbed and sonicated samples. Amplicon sequence variants (ASVs) were identified, and removal methods had no impact on the recovery of the total number of target ASVs. Additionally, when assessing each sample in multidimensional space, picked/scraped samples tended to cluster separately from swabbed and sonicated samples. The soil core used a reference in this study also clustered with the picked/scraped samples, indicating that these samples may be more reflective of the communities collected from soil cores. Based on these data, we identified that picking/scraping is an acceptable soil removal method for eDNA analysis.

Tracing recent outdoor geolocation by analyzing microbiota from shoe soles and shoeprints even after indoor walking

The microbial communities on shoe soles and shoeprints could carry microbial information about where someone walked. This is possible evidence to link a suspect in a crime case to a geographic location. A previous study had shown that the microbiota found on shoe soles depend on the microbiota of the soil on which people walk. However, there is a turnover of microbial communities on shoe soles during walking. The impact of microbial community turnover on tracing recent geolocation from shoe soles has not been adequately studied. In addition, it is still unclear whether the microbiota of shoeprints can be used to determine recent geolocation. In this preliminary study, we investigated whether the microbial characteristics of shoe soles and shoeprints can be used to trace geolocation and whether this information can be destroyed by walking on indoor floors. In this study, participants were asked to walk outdoors on exposed soil, then walk indoors on a hard wood floor. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial communities of shoe soles, shoeprints, indoor dust, and outdoor soil. Samples of shoe soles and shoeprints were collected at steps 5, 20, and 50 while walking indoors. The PCoA result showed that the samples were clustered by geographic origin. The shoeprint showed a more rapid turnover of microbial community than the shoe sole during indoor walking. The result of FEAST showed that the microbial communities of shoe sole and shoeprint were mainly (shoe sole, 86.21∼92.34 %; shoeprint, 61.66∼90.41 %) from the soil of the outdoor ground where the individual recently walked, and a small portion (shoe sole, 0.68∼3.33 %; shoeprint, 1.43∼27.14 %) from the indoor dust. Based on the matching of microbial communities between geolocation and shoe sole or shoeprint, we were able to infer the recent geolocation of the individual with relatively high accuracy using the random forest prediction model (shoe sole: 100.00 %, shoeprint: 93.33∼100.00 %). Overall, we are able to accurately infer the geolocation of an individual's most recent outdoor walk based on the microbiota of shoe sole and shoeprint, even though these microbiotas show a turnover when walking indoor floor. The pilot study was expected to provide a potential method for tracing recent geolocation of suspects.

Assessing the lysis of diverse pollen from bulk environmental samples for DNA metabarcoding

Pollen is ubiquitous year-round in bulk environmental samples and can provide useful information on previous and current plant communities. Characterization of pollen has traditionally been completed based on morphology, requiring significant time and expertise. DNA metabarcoding is a promising approach for characterizing pollen from bulk environmental samples, but accuracy hinges on successful lysis of pollen grains to free template DNA. In this study, we assessed the lysis of morphologically and taxonomically diverse pollen from one of the most common bulk environmental sample types for DNA metabarcoding, surface soil. To achieve this, a four species artificial pollen mixture was spiked into surface soils collected from Colorado, North Carolina, and Pennsylvania, and subsequently subjected to DNA extraction using both the PowerSoil and PowerSoil Pro Kits (Qiagen) with a heated incubation (either 65 °C or 90 °C). Amplification and Illumina sequencing of the internal transcribed spacer subunit 2 (ITS2) was completed in duplicate for each sample (total n, 76), and the resulting sequencing reads taxonomically identified using GenBank. The PowerSoil Pro Kit statistically outperformed the PowerSoil Kit for total DNA yield. When using either kit, incubation temperature (65 °C or 90 °C) used had no impact on the recovery of DNA, plant amplicon sequence variants (ASVs), or total plant ITS2 reads. This study highlighted that lysis of pollen in bulk environmental samples is feasible using commercially available kits, and downstream DNA metabarcoding can be used to accurately characterize pollen DNA from such sample types.

Spider webs as eDNA samplers: biodiversity assessment across the tree of life

The concept of environmental DNA (eDNA) utilizes nucleic acids of organisms directly from the environment. Recent breakthrough studies have successfully detected a wide spectrum of prokaryotic and eukaryotic eDNA from a variety of environments, ranging from ancient to modern, and from terrestrial to aquatic. With their diversity and ubiquity in nature, spider webs might act as powerful biofilters and could thus represent a promising new source of eDNA, but their utility under natural field conditions is severely understudied. Here, we bridge this knowledge gap to establish spider webs as a source of eDNA with far reaching implications. First, we conducted a field study to track specific arthropod targets from different spider webs. We then employed high-throughput amplicon sequencing of taxonomic barcodes to investigate the utility of spider web eDNA for biodiversity monitoring of animals, fungi, and bacteria. Our results show that genetic remains on spider webs allow the detection of even the smallest target organisms. We also demonstrate that eDNA from spider webs is useful in research of community compositions across the different domains of life, with potentially highly detailed temporal and spatial information.

Assessment of the link between evidence and crime scene through soil bacterial and fungal microbiome: A mock case in forensic study

In forensic studies, soil traces can be used to find clues to the origin of an unknown sample or the relationship between a crime scene and a suspect and can provide invaluable evidence as they frequently adhere to objects, with high persistence. In this study, it was aimed to investigate the potential of the bacterial and fungal microbiome diversity of the soil to be used as legitimate evidence in the resolution of homicide cases. Within the scope of a mock homicide case scenario, a total of 12 soil samples were collected, including two evidence samples, three crime scene samples and seven non-crime scene related control samples. Both bacterial and fungal microbiome profiles of these samples were analysed using Illumina NovaSeq platform. The resulting sequences were analysed using QIIME 2 microbiome bioinformatics platform. Beta diversity analysis was performed to determine the difference between samples. In bacterial community analyses, it has been observed that it is difficult to distinguish evidence samples and crime scene samples from control samples at phylum and class level, whereas differentiation could be made at genus and species level. Fungal community analyses allowed to distinguish evidence samples and crime scene samples from control samples at both phylum and class and genus and species level. Principal coordinate analysis (PCoA) results showed that distance between evidence samples and crime scene reference samples was closer to each other than non-crime scene related control samples. The results of this study showed that bacterial and especially fungal DNA in soil has the potential to contribute effectively to the resolution of forensic cases. Thus, it has been understood that it is possible to establish a relationship between the case and the crime scene with the help of microbiome analyses on soil samples obtained in homicide cases.

First report of infection by Debaryomyces spp. in Myotis velifer (cave myotis) in Mexico

Interest in the study of mycotic diseases in bats has increased after the identification of bats affected by white-nose syndrome in the northern United States. In a temperate forest of the community of San Pedro Yolox, Ixtlán in the Sierra Madre de Oaxaca, Mexico, we collected bats of various species, including 13 specimens of Myotis velifer that showed lesions in the plagio- and uro-patagium. Clinical exploration, histopathological studies and molecular analysis were carried out to determine the causal agent of the lesions present in these individuals. It was determined that the cause was the pathogenic fungus Debaryomyces spp. The present study represents the first report of fungal infection in bats in southern Mexico.

A walk on the dirt: soil microbial forensics from ecological theory to the crime lab

Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.

Microbiomes in forensic botany: a review

Fragments of botanical material can often be found at crime scenes (on live and dead bodies, or on incriminating objects) and can provide circumstantial evidence on various aspects of forensic investigations such as determining crime scene locations, times of death or possession of illegal species. Morphological and genetic analysis are the most commonly applied methods to analyze plant fragment evidence but are limited by their low capacity to differentiate between potential source locations, especially at local scales. Here, we review the current applications and limitations of current plant fragment analysis for forensic investigations and introduce the potential of microbiome analysis to complement the existing forensic plant fragment analysis toolkit. The potential for plant fragment provenance identification at geographic scales meaningful to forensic investigations warrants further investigation of the phyllosphere microbiome in this context. To that end we identify three key areas of future research: 1) Retrieval of microbial DNA of sufficient quality and quantity from botanical material; 2) Variability of the phyllosphere microbiome at different taxonomic and spatial scales, with explicit reference to assignment capacity; 3) Impacts on assignment capacity of time, seasonality and movement of fragments between locations. The development of robust microbiome analysis tools for forensic purposes in botanical material could increase the evidentiary value of the botanical evidence commonly encountered in casework, aiding in the identification of crime scene locations.

Application of DNA barcoding and metabarcoding for species identification in salmon products

Mislabelling is a significant manifestation of food fraud. Traditional Sanger sequencing technology is the gold standard for seafood species identification. However, this method is not suitable for analysing processed samples that may contain more than one species. This study tested the feasibility of next-generation sequencing in identifying mixed salmon products. Salmon samples containing up to eight species were amplified using 16S rRNA mini-barcode primers, and sequenced on an Illumina HiSeq2500 platform. All species were accurately identified, and mixtures as low as 1% (w/w) could be detected. Furthermore, this study conducted a market survey of 32 products labelled as salmon. For pure and mixed fish products, Sanger and next-generation sequencing techniques were respectively used for species identification, and for NGS results, we also used real-time PCR method to cross-validate the mixed products to further verify the accuracy of the DNA metabarcoding technology established in this study. DNA barcoding and metabarcoding of commercial salmon food products revealed the presence of mislabelling in 16 of 32 (50%) samples. The developed DNA barcoding and metabarcoding methods are useful for the identification of salmon species in food and can be used for quality control of various types of salmon products.

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.

Massively parallel sequencing is unlocking the potential of environmental trace evidence

Massively parallel sequencing (MPS) has revolutionised the field of genomics enabling substantial advances in human DNA profiling. Further, the advent of MPS now allows biological signatures to be obtained from complex DNA mixtures and trace amounts of low biomass samples. Environmental samples serve as ideal forms of contact trace evidence as detection at a scene can establish a link between a suspect, location and victim. Many studies have applied MPS technology to characterise the biodiversity within high biomass environmental samples (such as soil and water) to address questions related to ecology, conservation, climate change and human health. However, translation of these tools to forensic science remains in its infancy, due in part to the merging of traditional forensic ecology practices with unfamiliar DNA technologies and complex datasets. In addition, people and objects also carry low biomass environmental signals which have recently been shown to reflect a specific individual or location. The sensitivity, and reducing cost, of MPS is now unlocking the power of both high and low biomass environmental DNA (eDNA) samples as useful sources of genetic information in forensic science. This paper discusses the potential of eDNA to forensic science by reviewing the most explored applications that are leading the integration of this technology into the field. We introduce novel areas of forensic ecology that could also benefit from these tools with a focus on linking a suspect to a scene or establishing provenance of an unknown sample and discuss the current limitations and validation recommendations to achieve translation of eDNA into casework.

Effects of Phthalate Esters on Ipomoea aquatica Forsk. Seedlings and the Soil Microbial Community Structure under Different Soil Conditions

Phthalate acid esters (PAEs) are the most frequently utilized synthetic chemical compounds worldwide. They are typical emergent contaminants and are currently attracting considerable concern due to their risks to plants, animals, and public health. Determining the vital environmental factors that affect the toxicity of target pollutants in soil is important for vegetable production and the maintenance and control of soil productivity. We investigated the influence of di-n-butyl phthalate (DBP) and bis(2-ethylhexyl) phthalate (DEHP) under different soil conditions on physiological changes in water spinach (Ipomoea aquatic Forsk.) seedlings and the rhizosphere soil microbial community. Supported by our former experiments in which we determined the representative concentrations that caused the most pronounced toxic effects, three experimental concentrations were studied including control soils without PAEs and spiked soils with either 20 mg DBP or DEHP kg⁻¹ soil. The soil at all the three PAE concentrations was then adjusted to test two soil pH values, three levels of soil organic matter (SOM) content, and three levels of soil moisture content; thus, we completed 12 treatments or conditions simulating different soil environment conditions in greenhouses. After 30 days of cultivation, we analyzed the toxicity effects of two target PAEs on plant growth and physiological factors, and on soil microbial community characteristics. The toxicity of soil DBP and DEHP to the physiology of water spinach was found to be most affected by the soil pH value, then by SOM content, and least of all by soil moisture. The results of the 454 high-throughput sequencing analysis of the soil microbial community indicated that the toxicity of target PAEs to soil microorganisms was most affected by SOM content and then by soil moisture, and no clear relationship was found with soil pH. Under different soil conditions, declines in leaf biomass, chlorophyll a content, and carotenoid content—as well as increases in free amino acid (FAA) content, superoxide anion free radical activity, and hydroxyl radical activity—occurred in response to DBP or DEHP. Heavy use of chemical fertilizer, organic fertilizer, and high humidity led to the special environmental conditions of greenhouse soil, constituting the main conditions considered in this study. The results indicate that under the special highly intensive production systems of greenhouses, soil conditions may directly influence the effects of pollutant phytotoxicity and may thus endanger the yield, nutrient content, and food safety of vegetables. The combined studies of the impacts on plants and rhizosphere microorganisms give a more detailed picture of the toxic effects of the pollutants under different soil conditions.

Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?

In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.

Food Tracking Perspective: DNA Metabarcoding to Identify Plant Composition in Complex and Processed Food Products

One of the main goals of the quality control evaluation is to identify contaminants in raw material, or contamination after a food is processed and before it is placed on the market. During the treatment processes, contamination, both accidental and economically motivated, can generate incongruence between declared and real composition. In our study, we evaluated if DNA metabarcoding is a suitable tool for unveiling the composition of processed food, when it contains small trace amounts. We tested this method on different types of commercial plant products by using tnrL marker and we applied amplicon-based high-throughput sequencing techniques to identify plant components in different food products. Our results showed that DNA metabarcoding can be an effective approach for food traceability in different type of processed food. Indeed, the vast majority of our samples, we identified the species composition as the labels reported. Although some critical issues still exist, mostly deriving from the starting composition (i.e., variable complexity in taxa composition) of the sample itself and the different processing level (i.e., high or low DNA degradation), our data confirmed the potential of the DNA metabarcoding approach also in quantitative analyses for food composition quality control.

Effects of aeration on microbes and intestinal bacteria in bioaerosols from the BRT of an indoor wastewater treatment facility

The generation and emission of airborne bacteria from a biochemical reaction tank (BRT) for wastewater treatment was investigated by altering the aeration rate. The levels of bioaerosols increased from 715 ± 69 to 1597 ± 135 CFU/m³ (total airborne bacteria) and from 78 ± 6 to 359 ± 18 CFU/m³ (intestinal bacteria) as the aeration rate increased from 0.3 to 1.2 m³/h. Most airborne bacteria were attached to particles smaller than 4.7 μm at an aeration rate of 0.3 m³/h. They were found attached to larger particles (>4.7 μm) when the aeration rate increased to 1.2 m³/h. A similar phenomenon was observed for intestinal bacteria. The high-throughput sequencing technique was used to assay the microbial populations of the bioaerosols. Both microbial counts and diversity increased as the aeration rate increased. Brevundimonas (63.82%), Chryseobacterium (16.54%), and Micrococcaceae (12.37%) were the dominant intestinal bacteria at an aeration rate of 0.3 m³/h. Pseudochrobactrum (33.10%), Citrobacter (21.28%), and Yersinia (18.21%) were the dominant intestinal bacteria at an aeration rate of 1.2 m³/h. The level, particle size distribution, population structure, and diversity of the bioaerosols were all affected by aeration rate. The source tracker results indicated that water and the surrounding air were the two main bioaerosol sources. The contribution of water is greater at larger levels of aeration. Inhalation was the main pathway of microbial aerosol intake for people in the surrounding area. The exposure hazard quotients for adult males were generally higher than those for adult females. Necessary measures should be taken to ensure worker safety.

Mitochondrial DNA Extraction from Burial Soil Samples at Incremental Distances: A Preliminary Study

Preservation variance of soil DNA is neglected in the literature, and exceptional cases exaggerate amplification capabilities. This study sought to amplify a short mitochondrial fragment (212 bp) specific to Sus scrofa domesticus from the soil surrounding decomposing pig remains from an open-air locale. Samples collected above the body at incremental distances after 145 days of initial placement yielded pig DNA. A secondary sampling was collected in 2017, approximately 768 days after burial. Inhibition tests corroborated that pig DNA was no longer present in the soil resulting in a loss of original DNA between 145 and 768 days. The results provide evidence that genetic material leaches out radially from the source and DNA fragments longer than 200 bp do not persist in soil for a relatively short timeframe in western Montana. The conclusions support the collection of soil in crime scene investigation procedures within the first few months of decomposition.

Microbial forensics: new breakthroughs and future prospects

Recent advances in genetic data generation, through massive parallel sequencing (MPS), storage and analysis have fostered significant progresses in microbial forensics (or forensic microbiology). Initial applications in circumstances of biocrime, bioterrorism and epidemiology are now accompanied by the prospect of using microorganisms (i) as ancillary evidence in criminal cases; (ii) to clarify causes of death (e.g., drownings, toxicology, hospital-acquired infections, sudden infant death and shaken baby syndromes); (iii) to assist human identification (skin, hair and body fluid microbiomes); (iv) for geolocation (soil microbiome); and (v) to estimate postmortem interval (thanatomicrobiome and epinecrotic microbial community). When compared with classical microbiological methods, MPS offers a diverse range of advantages and alternative possibilities. However, prior to its implementation in the forensic context, critical efforts concerning the elaboration of standards and guidelines consolidated by the creation of robust and comprehensive reference databases must be undertaken.

Intestinal bacteria in bioaerosols and factors affecting their survival in two oxidation ditch process municipal wastewater treatment plants located in different regions

Samples from two oxidation ditch process municipal wastewater treatment plants (MWTPs) (HJK and GXQ) in two regions of China were analysed for bacteria, particles, total organic carbon, and water-soluble ions in bioaerosols. Diversity and potential pathogen populations were evaluated by high-throughput sequencing. Bioaerosol sources, factors affecting intestinal bacterial survival, and the relationship between bioaerosols and water were analysed by Source tracker and partial least squares-discriminant, principal component, and canonical correspondence analyses. Culturable bacteria concentrations were 110-846 and 27-579 CFU/m³ at HJK and GXQ, respectively. Intestinal bacteria constituted 6-33% of bacteria. Biochemical reaction tank, sludge dewatering house (SDH), and fine screen samples showed the greatest contribution to bioaerosol contamination. Enterobacter aerogenes was the main intestinal bacteria (> 99.5%) in HJK and detected at each sampling site. Enterobacter aerogenes (98.67% in SDH), Aeromonas sp. (76.3% in biochemical reaction tank), and Acinetobacter baumannii (99.89% in fine screens) were the main intestinal bacteria in GXQ. Total suspended particulate masses in SDH were 229.46 and 141.6 μg/m³ in HJK and GXQ, respectively. Percentages of insoluble compounds in total suspended particulates decreased as height increased. The main soluble ions in bioaerosols were Ca²⁺, Na⁺, Cl^-, and SO₄^2-, which ranged from 3.8 to 27.55 μg/m³ in the MWTPs. Water was a main source of intestinal bacteria in bioaerosols from the MWTPs. Bioaerosols in HJK but not in GXQ were closely related. Relative humidity and some ions positively influenced intestinal bacteria in bioaerosols, while wind speed and solar illumination had a negative influence.

A protocol for obtaining DNA barcodes from plant and insect fragments isolated from forensic-type soils

Soil is often collected from a suspect's tire, vehicle, or shoes during a criminal investigation and subsequently submitted to a forensic laboratory for analysis. Plant and insect material recovered in such samples is rarely analyzed, as morphological identification is difficult. In this study, DNA barcoding was used for taxonomic identifications by targeting the gene regions known to permit discrimination in plants [maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL)] and insects [cytochrome oxidase subunit I (COI)]. A DNA barcode protocol suitable for processing forensic-type biological fragments was developed and its utility broadly tested with forensic-type fragments (e.g., seeds, leaves, bark, head, legs; n, 213) isolated from soils collected within Virginia, USA (n, 11). Difficulties with PCR inhibitors in plant extracts and obtaining clean Sanger sequence data from insect amplicons were encountered during protocol development; however, the final protocol produced sequences specific to the expected locus and taxa. The overall quantity and quality of DNA extracted from the 213 forensic-type biological fragments was low (< 15 ng/μL). For plant fragments, only the rbcL sequence data was deemed reliable; thus, taxonomic identifications were limited to the family level. The majority of insect sequences matched COI in both GenBank and Barcode of Life DataSystems; however, they were identified as an undescribed environmental contaminant. Although limited taxonomic information was gleaned from the forensic-type fragments processed in this study, the new protocol shows promise for obtaining reliable and specific identifications through DNA barcoding, which could ultimately enhance the information gleaned from soil examinations.

Bioinformatics Approach to Assess the Biogeographical Patterns of Soil Communities: The Utility for Soil Provenance

Soil DNA profiling has potential as a forensic tool to establish a link between soil collected at a crime scene and soil recovered from a suspect. However, a quantitative measure is needed to investigate the spatial/temporal variability across multiple scales prior to their application in forensic science. In this study, soil DNA profiles across Miami-Dade, FL, were generated using length heterogeneity PCR to target four taxa. The objectives of this study were to (i) assess the biogeographical patterns of soils to determine whether soil biota is spatially correlated with geographic location and (ii) evaluate five machine learning algorithms for their predictive ability to recognize biotic patterns which could accurately classify soils at different spatial scales regardless of seasonal collection. Results demonstrate that soil communities have unique patterns and are spatially autocorrelated. Bioinformatic algorithms could accurately classify soils across all scales with Random Forest significantly outperforming all other algorithms regardless of spatial level.

Forensic genetics and genomics: Much more than just a human affair

While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.

Microbiome Tools for Forensic Science

Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system. In particular, integrating microbiome and metabolomic data has excellent potential to advance microbial forensics.

Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments

The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high-throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments - the nodule endosphere, root endosphere, rhizosphere and root zone - as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged to Ensifer for alfalfa and Ensifer-Bradyrhizobium for soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.

High-throughput Sequencing of Trace Quantities of Soil Provides Reproducible and Discriminative Fungal DNA Profiles

High-throughput sequencing (HTS) offers improved resolution between forensic soil samples by characterizing individual taxa present; however, the heterogeneous distribution of taxa in soils, and limited quantity of material available, may hinder the reliability of HTS in casework. Using HTS of the internal transcribed spacer, we examined the effect of soil mass (50, 150, and 250 mg) on fungal DNA profiles, focusing on reproducibility and discriminatory power between close proximity soils, and samples with similar textural classification. The results show that reduced soil mass had no significant effect on sample differentiation and that 150 mg soil provides the most reproducible DNA profiles across different soil types. In addition, Ascomycota was identified as a robust fungal target for forensic intelligence as this phylum was detected consistently across all samples regardless of sample quantity. Overall, this study highlights the value of trace quantities of soil for use in forensic casework.

Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers

In a rapidly changing world we need methods to efficiently assess biodiversity in order to monitor ecosystem trends. Ecological monitoring often uses plant community composition to infer quality of sites but conventional aboveground surveys only capture a snapshot of the actively growing plant diversity. Environmental DNA (eDNA) extracted from soil samples, however, can include taxa represented by both active and dormant tissues, seeds, pollen, and detritus. Analysis of this eDNA through DNA metabarcoding provides a more comprehensive view of plant diversity at a site from a single assessment but it is not clear which DNA markers are best used to capture this diversity. Sequence recovery, annotation, and sequence resolution among taxa were evaluated for four established DNA markers (matK, rbcL, ITS2, and the trnL P6 loop) in silico using database sequences and in situ using high throughput sequencing of 35 soil samples from a remote boreal wetland. Overall, ITS2 and rbcL are recommended for DNA metabarcoding of vascular plants from eDNA when not using customized or geographically restricted reference databases. We describe a new framework for evaluating DNA metabarcodes and, contrary to existing assumptions, we found that full length DNA barcode regions could outperform shorter markers for surveying plant diversity from soil samples. By using current DNA barcoding markers rbcL and ITS2 for plant metabarcoding, we can take advantage of existing resources such as the growing DNA barcode database. Our work establishes the value of standard DNA barcodes for soil plant eDNA analysis in ecological investigations and biomonitoring programs and supports the collaborative development of DNA barcoding and metabarcoding.

Residual soil DNA extraction increases the discriminatory power between samples

Forensic soil analysis relies on capturing an accurate and reproducible representation of the diversity from limited quantities of soil; however, inefficient DNA extraction can markedly alter the taxonomic abundance. The performance of a standard commercial DNA extraction kit (MOBIO PowerSoil DNA Isolation kit) and three modified protocols of this kit: soil pellet re-extraction (RE); an additional 24-h lysis incubation step at room temperature (RT); and 24-h lysis incubation step at 55°C (55) were compared using high-throughput sequencing of the internal transcribed spacer I ribosomal DNA. DNA yield was not correlated with fungal diversity and the four DNA extraction methods displayed distinct fungal community profiles for individual samples, with some phyla detected exclusively using the modified methods. Application of a 24 h lysis step will provide a more complete inventory of fungal biodiversity, and re-extraction of the residual soil pellet offers a novel tool for increasing discriminatory power between forensic soil samples.