Spatial heterogeneity stabilizes predator-prey interactions at the microscale while patch connectivity controls their outcome.

Natural landscapes are both fragmented and heterogeneous, affecting the distribution of organisms, and their interactions. While predation in homogeneous environments increases the probability of population extinction, fragmentation/heterogeneity promotes coexistence and enhances community stability as shown by experimentation with animals and microorganisms, and supported by theory. Patch connectivity can modulate such effects but how microbial predatory interactions are affected by water-driven connectivity is unknown. In soil, patch habitability by microorganisms, and their connectivity depend upon the water saturation degree (SD). Here, using the obligate bacterial predator Bdellovibrio bacteriovorus, and a Burkholderia prey, we show that soil spatial heterogeneity profoundly affects predatory dynamics, enhancing long-term co-existence of predator and prey in a SD-threshold dependent-manner. However, as patches and connectors cannot be distinguished in these soil matrices, metapopulations cannot be invoked to explain the dynamics of increased persistence. Using a set of experiments combined with statistical and physical models we demonstrate and quantify how under full connectivity, predation is independent of water content but depends on soil microstructure characteristics. In contrast, the SD below which predation is largely impaired corresponds to a threshold below which the water network collapses and water connectivity breaks down, preventing the bacteria to move within the soil matrix.

Weight-of-evidence for DNA identification of missing persons and human remains using CODIS.

DNA Identification of unidentified human remains (UHR) is performed in Israel by comparing the UHR's short tandem repeat (STR) profiles to a national database of STR profiles taken from relatives of missing persons. Kinship analysis is performed using the CODIS 7.0 software and results are stated as a Joint Pedigree Likelihood Ratio (JPLR). The weight-of-evidence for JPLR has never been studied, making it difficult to interpret the meaning of specific values in terms of whether UHR are related to specific pedigrees. Therefore, the aim of this study was to statistically determine the practical meaning and context of the JPLR. We used 440 million pairs of simulated DNA profiles and 294 pairs of real ones from known siblings, parent/offspring and unrelated persons. A Score-Based Likelihood Ratio (SBLR) was empirically constructed, validated and compared to both JPLR and the LR produced by CODIS. Our results show that CODIS's JPLR and LR values for single-person pedigrees overestimate the level of support for both "parent/child" and "siblings" propositions relative to the "unrelated" proposition, by up to two orders of magnitude. A practical table is given for correcting this phenomenon, with statistical interpretation (i.e. SBLR) for each JPLR score, including verbal levels of propositional support ranging from "no support" (SBLR<2) to "extremely strong" (SBLR>1 Million).

Bacteria and microeukaryotes are differentially segregated in sympatric wastewater microhabitats.

Wastewater purification is mostly performed in activated sludge reactors by bacterial and microeukaryotic communities, populating organic flocs and a watery liquor. While there are numerous molecular community studies of the bacterial fraction, those on microeukaryotes are rare. We performed a year-long parallel 16S rRNA gene and 18S rRNA-gene based analysis of the bacterial and of the microeukaryote communities, respectively, of physically separated flocs and particle-free liquor samples from three WWTPs. This uncovered a hitherto unknown large diversity of microeukaryotes largely composed of potential phagotrophs preferentially feeding on either bacteria or other microeukaryotes. We further explored whether colonization of the microhabitats was selective, showing that for both microbial communities, different but often closely taxonomically and functionally related populations exhibiting different dynamic patterns populated the microhabitats. An analysis of their between plants-shared core populations showed the microeukaryotes to be dispersal limited in comparison to bacteria. Finally, a detailed analysis of a weather-caused operational disruption in one of the plants suggested that the absence of populations common to the floc and liquor habitat may negatively affect resilience and stability.

Bacterial predation under changing viscosities.

Bdellovibrio and like organisms (BALOs) are largely distributed in soils and in water bodies obligate predators of gram-negative bacteria that can affect bacterial communities. Potential applications of BALOs include biomass reduction, their use against pathogenic bacteria in agriculture, and in medicine as an alternative against antibiotic-resistant pathogens. Such different environments and uses mean that BALOs should be active under a range of viscosities. In this study, the predatory behaviour of two strains of the periplasmic predator B. bacteriovorus and of the epibiotic predator Micavibrio aeruginosavorus was examined in viscous polyvinylpyrrolidone (PVP) solutions at 28 and at 37°C, using fluorescent markers and plate counts to track predator growth and prey decay. We found that at high viscosities, although swimming speed was largely decreased, the three predators reduced prey to levels similar to those of non-viscous suspensions, albeit with short delays. Prey motility and clumping did not affect the outcome. Strikingly, under low initial predator concentrations, predation dynamics were faster with increasing viscosity, an effect that dissipated with increasing predator concentrations. Changes in swimming patterns and in futile predator-predator encounters with viscosity, as revealed by path analysis under changing viscosities, along with possible PVP-mediated crowding effects, may explain the observed phenomena.

Microbial communities and inflammatory response in the endometrium differ between normal and metritic dairy cows at 5-10 days post-partum.

Post-partum metritis is among the most prevalent disease in dairy cows affecting animal welfare and inflicting considerable economic loses. While post-partum contamination of the uterus is rife in dairy cows, only a fraction of these animals will develop metritis. Our main objective was to compare the bacterial communities and the inflammatory response in the endometrium of healthy and metritic dairy cows. Holstein-Friesian cows (n = 35) were sampled immediately following clinical classification as healthy (n = 21), suffering from metritis (n = 13) or septic metritis (n = 1), based on veterinary examination at 5-10 days post-partum. Polymorphonuclear cells (PMN) percentage in endometrial cytology was significantly higher in cows with metritis. Full-thickness uterine biopsy analysis revealed that the luminal epithelium in inter-caruncle areas was preserved in healthy cows, but in metritis it was compromised, with marked PMN infiltration particularly in the apical endometrium. Gram staining revealed that bacterial load and spatial distribution was associated with disease severity. 16S-rDNA bacterial community analysis revealed unique endometrial bacterial community composition in metritic cows, as compared to more diverse communities among healthy cows. The most abundant phyla in healthy cows were Proteobacteria (31.8 ± 9.3%), Firmicutes (27.9 ± 8.4%) and Bacteroidetes (19.7 ± 7.2%), while Bacteroidetes (60.3 ± 10.3%), Fusobacteria (13.4 ± 5.9%) and Firmicutes (10.5 ± 3.3%) were most abundant in the endometrial mucosa of metritic cows. Relative abundance of Bacteroidetes (19.7 ± 7.2% vs. 60.3 ± 10.3%), Fusobacteria (7.5 ± 5.2% vs. 13.4 ± 5.9%) and Proteobacteria (31.8 ± 9.3% vs. 7.3 ± 5.6%) phyla differed significantly between healthy and metritic cows. In summary, endometrial PMN abundance, spatial distribution and bacterial communities differed between healthy and metritic dairy cows at early post-partum.

Cell-cycle progress in obligate predatory bacteria is dependent upon sequential sensing of prey recognition and prey quality cues.

Predators feed on prey to acquire the nutrients necessary to sustain their survival, growth, and replication. In Bdellovibrio bacteriovorus, an obligate predator of Gram-negative bacteria, cell growth and replication are tied to a shift from a motile, free-living phase of search and attack to a sessile, intracellular phase of growth and replication during which a single prey cell is consumed. Engagement and sustenance of growth are achieved through the sensing of two unidentified prey-derived cues. We developed a novel ex vivo cultivation system for B. bacteriovorus composed of prey ghost cells that are recognized and invaded by the predator. By manipulating their content, we demonstrated that an early cue is located in the prey envelope and a late cue is found within the prey soluble fraction. These spatially and temporally separated cues elicit discrete and combinatory regulatory effects on gene transcription. Together, they delimit a poorly characterized transitory phase between the attack phase and the growth phase, during which the bdelloplast (the invaded prey cell) is constructed. This transitory phase constitutes a checkpoint in which the late cue presumably acts as a determinant of the prey's nutritional value before the predator commits. These regulatory adaptations to a unique bacterial lifestyle have not been reported previously.

Host-specific associations affect the microbiome of Philornis downsi, an introduced parasite to the Galápagos Islands.

The composition and diversity of bacteria forming the microbiome of parasitic organisms have implications for differential host pathogenicity and host-parasite co-evolutionary interactions. The microbiome of pathogens can therefore have consequences that are relevant for managing disease prevalence and impact on affected hosts. Here, we investigate the microbiome of an invasive parasitic fly Philornis downsi, recently introduced to the Galápagos Islands, where it poses extinction threat to Darwin's finches and other land birds. Larvae infest nests of Darwin's finches and consume blood and tissue of developing nestlings, and have severe mortality impacts. Using 16s rRNA sequencing data, we characterize the bacterial microbiota associated with P. downsi adults and larvae sourced from four finch host species, inhabiting two islands and representing two ecologically distinct groups. We show that larval and adult microbiomes are dominated by the phyla Proteobacteria and Firmicutes, which significantly differ between life stages in their distributions. Additionally, bacterial community structure significantly differed between larvae retrieved from strictly insectivorous warbler finches (Certhidea olivacea) and those parasitizing hosts with broader dietary preferences (ground and tree finches, Geospiza and Camarhynchus spp., respectively). Finally, we found no spatial effects on the larval microbiome, as larvae feeding on the same host (ground finches) harboured similar microbiomes across islands. Our results suggest that the microbiome of P. downsi changes during its development, according to dietary composition or nutritional needs, and is significantly affected by host-related factors during the larval stage. Unravelling the ecological significance of bacteria for this parasite will contribute to the development of novel, effective control strategies.

An Extended Cyclic Di-GMP Network in the Predatory Bacterium Bdellovibrio bacteriovorus.

UNLABELLED: Over the course of the last 3 decades the role of the second messenger cyclic di-GMP (c-di-GMP) as a master regulator of bacterial physiology was determined. Although the control over c-di-GMP levels via synthesis and breakdown and the allosteric regulation of c-di-GMP over receptor proteins (effectors) and riboswitches have been extensively studied, relatively few effectors have been identified and most are of unknown functions. The obligate predatory bacterium Bdellovibrio bacteriovorus has a peculiar dimorphic life cycle, in which a phenotypic transition from a free-living attack phase (AP) to a sessile, intracellular predatory growth phase (GP) is tightly regulated by specific c-di-GMP diguanylate cyclases. B. bacteriovorus also bears one of the largest complement of defined effectors, almost none of known functions, suggesting that additional proteins may be involved in c-di-GMP signaling. In order to uncover novel c-di-GMP effectors, a c-di-GMP capture-compound mass-spectroscopy experiment was performed on wild-type AP and host-independent (HI) mutant cultures, the latter serving as a proxy for wild-type GP cells. Eighty-four proteins were identified as candidate c-di-GMP binders. Of these proteins, 65 did not include any recognized c-di-GMP binding site, and 3 carried known unorthodox binding sites. Putative functions could be assigned to 59 proteins. These proteins are included in metabolic pathways, regulatory circuits, cell transport, and motility, thereby creating a potentially large c-di-GMP network. False candidate effectors may include members of protein complexes, as well as proteins binding nucleotides or other cofactors that were, respectively, carried over or unspecifically interacted with the capture compound during the pulldown. Of the 84 candidates, 62 were found to specifically bind the c-di-GMP capture compound in AP or in HI cultures, suggesting c-di-GMP control over the whole-cell cycle of the bacterium. High affinity and specificity to c-di-GMP binding were confirmed using microscale thermophoresis with a hypothetical protein bearing a PilZ domain, an acyl coenzyme A dehydrogenase, and a two-component system response regulator, indicating that additional c-di-GMP binding candidates may be bona fide novel effectors. IMPORTANCE: In this study, 84 putative c-di-GMP binding proteins were identified in B. bacteriovorus, an obligate predatory bacterium whose lifestyle and reproduction are dependent on c-di-GMP signaling, using a c-di-GMP capture compound precipitation approach. This predicted complement covers metabolic, energy, transport, motility and regulatory pathways, and most of it is phase specific, i.e., 62 candidates bind the capture compound at defined modes of B. bacteriovorus lifestyle. Three of the putative binders further demonstrated specificity and high affinity to c-di-GMP via microscale thermophoresis, lending support for the presence of additional bona fide c-di-GMP effectors among the pulled-down protein repertoire.

Genome scan for nonadditive heterotic trait loci reveals mainly underdominant effects in Saccharomyces cerevisiae.

The overdominant model of heterosis explains the superior phenotype of hybrids by synergistic allelic interaction within heterozygous loci. To map such genetic variation in yeast, we used a population doubling time dataset of Saccharomyces cerevisiae 16 × 16 diallel and searched for major contributing heterotic trait loci (HTL). Heterosis was observed for the majority of hybrids, as they surpassed their best parent growth rate. However, most of the local heterozygous loci identified by genome scan were surprisingly underdominant, i.e., reduced growth. We speculated that in these loci adverse effects on growth resulted from incompatible allelic interactions. To test this assumption, we eliminated these allelic interactions by creating hybrids with local hemizygosity for the underdominant HTLs, as well as for control random loci. Growth of hybrids was indeed elevated for most hemizygous to HTL genes but not for control genes, hence validating the results of our genome scan. Assessing the consequences of local heterozygosity by reciprocal hemizygosity and allele replacement assays revealed the influence of genetic background on the underdominant effects of HTLs. Overall, this genome-wide study on a multi-parental hybrid population provides a strong argument against single gene overdominance as a major contributor to heterosis, and favors the dominance complementation model.

Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream.

Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics and functions of the microbial communities in highly sewage-impacted rivers is limited, in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem, we show, using 16S and 18S rRNA gene-based community analysis and targeted qPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Hydrolyzers of organics compounds, as well as nitrogen and phosphorus recyclers were lacking, pointing at reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio and like organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify, while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.

Phylogenetic, metabolic, and taxonomic diversities shape mediterranean fruit fly microbiotas during ontogeny.

The Mediterranean fruit fly (medfly) (Ceratitis capitata) lays eggs in fruits, where larvae subsequently develop, causing large-scale agricultural damage. Within its digestive tract, the fly supports an extended bacterial community that is composed of multiple strains of a variety of enterobacterial species. Most of these bacteria appear to be functionally redundant, with most strains sustaining diazotrophy and/or pectinolysis. At least some of these bacteria were shown to be vertically inherited, but colonization, structural, and metabolic aspects of the community's dynamics have not been investigated. We used fluorescent in situ hybridization, metabolic profiling, plate cultures, and pyrosequencing to show that an initial, egg-borne, diverse community expands throughout the fly's life cycle. While keeping "core" diazotrophic and pectinolytic functions, it also harbors diverse and fluctuating populations that express varied metabolic capabilities. We suggest that the metabolic and compositional plasticity of the fly's microbiota provides potential adaptive advantages to the medfly host and that its acquisition and dynamics are affected by mixed processes that include stochastic effects, host behavior, and molecular barriers.

Bdellovibrio exovorus sp. nov., a novel predator of Caulobacter crescentus.

The life cycle, prey range and taxonomic status of a Bdellovibrio-like organism, strain JSS(T), were studied. Strain JSS(T) was isolated from sewage in London, Ontario, Canada, in enrichment culture with Caulobacter crescentus prey cells. During predation, this strain remained attached to the outside of a stalked C. crescentus cell. No periplasmic growth stage was observed and no bdelloplast was formed. The stalked cells of C. crescentus retained their shape and, after predation, were devoid of cytoplasmic content, as shown by transmission electron microscopy. A periplasmic growth stage has been a definitive character in the description of members of the genera Bdellovibrio, Bacteriovorax, Bacteriolyticum and Peredibacter. This is the first description of an epibiotic predator in this group of prokaryotic predators. The G+C content of the genomic DNA of strain JSS(T) was 46.1 mol%. 16S rRNA gene sequence analysis showed that this strain was related to Bdellovibrio bacteriovorus strains HD100(T), 109J, 114 and 127 (90-93 % similarity). Phylogenetic analysis based on 16S rRNA gene sequences grouped strain JSS(T) with the Bdellovibrio cluster, but at a distance from other Bdellovibrio isolates. On the basis of features of the life cycle and phylogenetic data, it was concluded that strain JSS(T) merits classification as the type strain of a novel species, for which the name Bdellovibrio exovorus sp. nov. is proposed (type strain JSS(T) =ATCC BAA-2330(T) = DSM 25223(T)).

Form follows function: Applying photographic content analysis to forensic firearm identification.

Drawing forensic conclusions from an image or a video is known as "photographic content analysis." It involves the analysis of an image, as well as objects, actions, and events depicted in images or video. In recent years, photographic depictions of objects suspected as illegal firearms have substantially increased, appearing on CCTV surveillance footage, captured by mobile phones and shared on social media. However, the law in Israel states that a person can be charged with illegally possessing a firearm only if it can be proven that the object is capable of shooting with lethal bullet energy. This becomes more challenging in cases where the firearm was not physically seized, and the evidence exclusively consists of images and video. In this study, photographic content analysis was applied to images and video where objects suspected as commercial or improvised firearms had been depicted. An image and event sequence reconstruction video databases of both firearms and replicas were created in order to better define firearm-specific functional morphological features. We demonstrate that it is possible to classify an object as a firearm by analyzing the functional, and not only the esthetic, morphology in images and video. It is also shown that event sequence reconstruction in video may be used to infer that an object suspected as a firearm has the capacity to shoot by confirming the occurrence of a shooting act or shooting process. Thus, photographic content analysis may be used to forensically establish that an object depicted in an image or a video is a firearm by ruling out other known scenarios, and without physically seizing it.

Impact of treated wastewater irrigation on antibiotic resistance in agricultural soils.

Antibiotic resistance (AR) is a global phenomenon with severe epidemiological ramifications. Anthropogenically impacted natural aquatic and terrestrial environments can serve as reservoirs of antibiotic resistance genes (ARG), which can be horizontally transferred to human-associated bacteria through water and food webs, and thus contribute to AR proliferation. Treated-wastewater (TWW) irrigation is becoming increasingly prevalent in arid regions of the world, due to growing demand and decline in freshwater supplies. The release of residual antibiotic compounds, AR bacteria, and ARGs from wastewater effluent may result in proliferation of AR in irrigated soil microcosms. The aim of this study was to assess the impact of TWW-irrigation on soil AR bacterial and ARG reservoirs. Tetracycline, erythromycin, sulfonamide, and ciprofloxacin resistance in soil was assessed using standard culture-based isolation methods and culture-independent molecular analysis using quantitative real-time PCR (qPCR). High levels of bacterial antibiotic resistance were detected in both freshwater- and TWW-irrigated soils. Nonetheless, in most of the soils analyzed, AR bacteria and ARG levels in TWW-irrigated soils were on the whole identical (or sometimes even lower) than in the freshwater-irrigated soils, indicating that the high number of resistant bacteria that enter the soils from the TWW are not able to compete or survive in the soil environment and that they do not significantly contribute ARG to soil bacteria. This strongly suggests that the impact of the TWW-associated bacteria on the soil microbiome is on the whole negligible, and that the high levels of AR bacteria and ARGs in both the freshwater- and the TWW-irrigated soils are indicative of native AR associated with the natural soil microbiome.

Preliminary investigation of the ability of fingerprint examiners in detection of sib-sib relationships based upon finger and palm prints similarities.

Variations in biometric parameters such as fingerprints between populations, genders and even twins are wide-ranging issues routinely examined by the forensic community. In this study we tested whether fingerprint examiners can detect if finger and palm prints originate from siblings. In total, 410 finger records and 300 palm records of siblings and non-siblings were examined by seven certified forensic fingerprint examiners with different levels of qualifications and experience. The examiners were asked to determine, based on friction ridge characteristics, if they could detect similarities to such a degree that it was possible to declare a familial relationship (FR) between two prints. The results indicated that among all seven fingerprint examiners, 'true negative' values were very high (95-98%), meaning that in cases where FRs were absent, the examiners' decision was usually correct. In cases where FR was declared by the expert, the probability of a 'true positive' was 25 and 10 times higher than the probability of a 'false positive' for finger prints and palm prints, respectively. We attempt to elucidate the specific fingerprint parameters which facilitate better sibling detection, and conclude that sibling detection by fingerprint similarity may have potential as a novel forensic tool that can be used for intelligence operations.

Identifying protein function and functional links based on large-scale co-occurrence patterns.

OBJECTIVE: The vast majority of known proteins have not been experimentally tested even at the level of measuring their expression, and the function of many proteins remains unknown. In order to decipher protein function and examine functional associations, we developed "Cliquely", a software tool based on the exploration of co-occurrence patterns. COMPUTATIONAL MODEL: Using a set of more than 23 million proteins divided into 404,947 orthologous clusters, we explored the co-occurrence graph of 4,742 fully sequenced genomes from the three domains of life. Edge weights in this graph represent co-occurrence probabilities. We use the Bron-Kerbosch algorithm to detect maximal cliques in this graph, fully-connected subgraphs that represent meaningful biological networks from different functional categories. MAIN RESULTS: We demonstrate that Cliquely can successfully identify known networks from various pathways, including nitrogen fixation, glycolysis, methanogenesis, mevalonate and ribosome proteins. Identifying the virulence-associated type III secretion system (T3SS) network, Cliquely also added 13 previously uncharacterized novel proteins to the T3SS network, demonstrating the strength of this approach. Cliquely is freely available and open source. Users can employ the tool to explore co-occurrence networks using a protein of interest and a customizable level of stringency, either for the entire dataset or for a one of the three domains-Archaea, Bacteria, or Eukarya.

Technical note: The Next Step - a semi-automatic coding and comparison system for forensic footwear impressions.

Footwear impression evidence is a key tool in criminal investigations, connecting suspects to the crime scene; in addition, it may provide valuable forensic intelligence linking different crime scenes in the absence of a suspect. This paper presents the development of a computer database and semi-automatic system for shoeprint comparison. The database is based on structured manual coding of elements by CSI (Crime Scene Investigators). The computer algorithm then compares the pattern information of the query footwear impression to the entire database, returning a list of possible matches ranked by pattern similarity and crime scene geographic proximity. Initial results using a database of 284 footwear impressions from real crime scenes revealed that a "match" (i.e., the same shoe model) was found for 30% of the impressions; in most cases, the "match" ranked within the top five places of the "hit" list generated by the algorithm. Our results confirm that this semi-automatic footwear comparison system is simple, cost-effective and efficient, providing great potential for linking crime scenes.

Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants.

Adding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (Capsicum annuum L.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with the Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes phyla. The relative abundance of members of the Bacteroidetes phylum increased from 12 to 30% as a result of biochar amendment, while that of the Proteobacteria decreased from 71 to 47%. The Bacteroidetes-affiliated Flavobacterium was the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total root-associated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (Chitinophaga and Cellvibrio, respectively) and aromatic compound degraders (Hydrogenophaga and Dechloromonas). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.

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.

The risk of inter-stub contamination during SEM/EDS analysis of gunshot residue particles.

Detecting gunshot residue (GSR) particles on samples collected from individuals or their belongings can connect them to a shooting event. Scanning electron microscopy combined with energy-dispersive X-ray spectrometry (SEM/EDX) is currently the most common forensic method for detecting and characterizing GSR. At the forensic laboratory of the Israel Police, one inch (25 mm) diameter sticky stubs are used to collect samples from suspects' hands, hair, clothes and vehicles. To maximize testing capacity, stubs of samples collected from several different cases and persons may be analyzed side by side in a single run. This has raised concern in court that a clean sample taken from an innocent person may be contaminated during the analysis by GSR particles from an adjacent sample transferred inside the SEM chamber. several experiments were conducted where stubs that were known to contain GSR particles were run adjacent to stubs that were known to be clean. Not a single event of GSR particle transfer was detected, even when a clean stub was surrounded on all sides by stubs containing a total of over 100,000 particles. Thus, the probability of transfer of a single particle is at most 1:100,000. Since the total number of GSR particles found per run is usually three orders of magnitude lower than 100,000, we conclude that the risk of inter-stub contamination is highly negligible.