Important Reservoir Research Articles

Integrated environmental and genomic analysis reveals the drivers of fine‐scale divergence and local adaptation in northern populations of two wild rice species in China

Societal Impact StatementCrop wild relatives represent precious genetic resources for crop improvement. Investigating their local adaptation to marginal environments is important for the utilization of wild genetic resources. Oryza officinalis and Oryza granulata are wild relatives of cultivated rice and possess genes that convey resistance to insects, disease, and tolerance to shade and drought. The northern edge for the distribution of these two lies in China where populations are facing habitat destruction. This study found that the northern marginal populations of both species have adapted to local conditions, with specific implications for the conservation and utilization of wild rice.Summary O. officinalis and O. granulata, wild relatives of cultivated rice, represent important gene reservoirs with the potential to improve rice with respect to insect resistance and stress tolerance. However, the northern marginal populations of these two species in China are facing habitat destruction. Here, we investigated the genetic diversity and divergence of northern marginal populations of O. officinalis and O. granulata. The genomic variation of two species was examined by whole‐genome sequencing on 357 individuals. Generalized dissimilarity modeling was applied to investigate the effects of geographic and environmental isolation on population differentiation. Genetic‐environment association analysis and genome‐wide FST outlier scans were used to identify environmentally driven signals of selection. The marginal populations of both species exhibited low genetic diversity and obvious genetic differentiation stemmed from the joint effects of isolation by geographic distance and the environment. Both genomes exhibited specific signals of adaptation to cold environments in the north. Investigation of the divergence and adaptation of marginal populations of O. officinalis and O. granulata will help us to determine how wild rice can adapt to local environments, thus allowing for the development of scientific conservation policies and the identification of new genetic resources for rice with improved resistance.

Examples of Paleokarst in Mesozoic Carbonate Formations in the Carpathian Foreland Area

A paleokarst system developed in the Upper Jurassic–Lower Cretaceous carbonate complex has been recognized in the Carpathian Foreland area. Well logs testing and core data as well as an acoustic imager, a microresistivity scanner and six-arm dipmeter images were used to identify and analyze the character of the paleokarst features. A detailed interpretation of microresistivity and acoustic image logs allowed for the identification of different types of karst forms, such as caverns; multidirectional fractures, including fractures widened by dissolution; and the type of sediments filling them. The analysis of the seismic survey was conducted by linking the paleokarst characteristic features recognized in the seismic image to the karst intervals determined from borehole data. The set of seismic attributes calculated from the analyzed 3D seismic data, including the RMS amplitude, instantaneous frequency, consistent dip, variance, sweetness and relative acoustic impedance, helped to delineate the zones of the paleokarst distribution. Within the interpreted paleokarst surface developed in the carbonate formations in the study area, there are sinkholes, limestone pavements and valleys. Furthermore, in the northwestern part of the analyzed area, the development of paleokarst forms is related to the presence of a relatively deep branch of a paleovalley formed in the Paleogene, as well as to numerous discontinuities developed in carbonate formations. The development of this type of larger karst form was probably controlled primarily by tectonic faults. The research conducted by the authors of this paper showed the widespread presence of paleokarst features in Upper Jurassic–Lower Cretaceous carbonate formations in the study area. A good spatial identification of the paleokarst surface can be important in a regional context, since the highest part of the profile of carbonate formations is the most important reservoir for geothermal or hydrocarbon resources in this region.

Stable isotope geochemistry evidences from fossil carbonate and sulfur minerals on the origin of geothermal water, Kızıldere Geothermal Field, Western Turkey

The Kızıldere geothermal field, located at the eastern part of the Büyük Menderes graben in Western Turkey, is the most important geothermal reservoir suitable for electricity generation. Current and fossil fumaroles and alteration zones are directly related to the tectonic zones influenced by N-S directional extension since Miocene period. Associated to fossil geothermal activities carbonate (calcite, dolomite) and sulfate (gypsum, anhydrite) minerals were occurred in the form of void/crack fill and bands/lenses parallel to bedding of Neogene clastic and carbonate rocks. The carbon (δ13CPDB ‰) and oxygen (δ18OPDB ‰) isotope compositions of hydrothermal calcites and dolomites and sulfur (δ34SCDT) and oxygen (δ18OSMOW) isotope compositions of gypsum and anhydrites are analyzed first time and correlated current geothermal water composition. The carbon and oxygen isotope data of calcites and dolomites have similar carbon but different oxygen isotope composition which increases in the direction of surface calcite – drill cuttings calcite – drill cuttings dolomite – surface dolomite. The isotope compositions of calcite and dolomite minerals range between limestone and marble host rock compositions and indicate the carbonate mineral-forming fluids originated from dissolution of carbonate rocks during the circulation of hot geothermal waters. According to the calcite-CO2 and dolomite-CO2 isotopic fractionation data for the 0–300 °C temperature range, the fossil isotope composition is higher than the composition of current CO2 and reflects relatively lower temperature conditions. The isotope compositions of gypsum and anhydrite minerals indicate that hot thermal waters dissolved terrestrial evaporites and formed a sulfur-rich geothermal solution, and hydrothermal gypsum and anhydrite precipitated from this solution. The δ34SCDT compositions of hydrothermal gypsum and anhydrites are similar to the current geothermal water compositions. Stable isotope geochemistry data of hydrothermal carbonate and sulfate minerals in the Kızıldere geothermal field have shown that the fluids forming these minerals were originated from host rocks instead of magmatic volatiles.

Earth's “Missing” Chlorine May Be in the Core

AbstractThe budget of volatile halogens in the bulk silicate Earth, fluorine and chlorine, differs distinctly from that of chondritic meteorites. Arguably, the bulk silicate Earth shows a low abundance of Cl, while the F budget is in line with the expected volatility trend. One hypothesis for the missing Cl is its sequestration into Earth's core during planetary segregation, but experimental data on partitioning between silicate and metallic melts are limited in pressure and remain inconclusive. Here we use computational quantum mechanical methods to study F and Cl geochemistry during core–mantle differentiation over a wide pressure and temperature range. Our calculations reveal that with increasing pressure and temperature, chlorine shows an enhanced affinity for iron metal. The Cl metal–silicate partition coefficient increase from −1.89 ± 0.84 at 10 GPa and 3000 K to 1.62 ± 0.80 at 130 GPa and 5000 K, while corresponding calculations for F show minimal variations in metal–silicate partitioning across the pressure–temperature conditions investigated, yielding values between −3.61 ± 0.81 and −3.37 ± 0.80. The shift in shows a transition from lithophile to siderophile behavior. Further calculations on isotopic partitioning show negligible fractionation of Cl isotopes (37Cl/35Cl) between the mantle and core. Our results suggest that metallic iron within Earth's mantle and core may serve as an important Cl reservoir, potentially accounting for up to 40% of Earth's overall Cl inventory.

Platform Evolution in an Oligo–Miocene Back‐arc Basin: An Example from the Central Iran Basin

AbstractThe Qom Formation is the most important hydrocarbon reservoir target in Central Iran. The Qom platform developed in a back‐arc basin during the Oligo–Miocene due to the closing of the Tethyan Seaway. This formation consists of a variety of carbonate and non‐carbonate facies deposited on a platform ranging from supratidal to basin. A combination of tectonic and eustatic events led to some lateral and vertical facies variations in the study area. Six third‐order depositional sequences and related surfaces were identified regarding vertical facies changes in the studied sections of this Oligo–Miocene succession. According to all results and data, this succession was initially deposited during the Chattian upon a distally steepened ramp of siliciclastic‐carbonate composition, including the Bouma sequence. Then, from the late Chattian to the Aquitanian, the platform changed into a homoclinal carbonate ramp with a gentle profile. With respect to tectonic activity, this phase was a calm period during the deposition of the Qom Formation. Finally, a drowned carbonate platform and a rimmed shelf emerged during the Burdigalian, terminated by the continental deposits of the Upper Red Formation. Regarding all geological characteristics, three main tectono‐eustatic evolutionary phases have been recognized in the Qom back‐arc basin.

Fluid Contamination Transient Analysis

Successful in-situ fluid cleanup and sampling operations are commonly driven by a fast and reliable analysis of pressure, rate, and fluid contamination measurements. Techniques such as pressure transient analysis (PTA) provide important information to quantify reservoir complexity, while fluid contamination measurements are commonly overlooked for reservoir description purposes. We introduce a new interpretation technique to relate fluid contamination measurements with near-wellbore fluid-transport properties by identifying early- and late-time flow regimes in fluid contamination and its derivative function. The derivative methods used in PTA inspired the development of the new fluid contamination interpretation method. Contamination transient analysis (CTA) evaluates transient measurements acquired during cleanup of mud-filtrate invasion to infer important reservoir flow conditions. Center-point derivative methods are applied to the fluid pumpout volume and time evolution of fluid contamination to identify flow regimes in cases of water-based mud invading either water- or hydrocarbon-bearing formations. We document synthetic examples of the new interpretation method for seven reservoir cases, numerically simulated to obtain contamination data, namely, homogeneous isotropic reservoir, radial boundaries, vertical boundaries, thin-laminated formations, mud-filtrate invasion radius, petrophysical properties, and permeability anisotropy. Single-phase flow and multiphase flow cases are also compared in the analysis. Reservoir boundaries and features are identified in the flow regimes obtained from the combined interpretation of the fluid contamination derivative (FCD) and the log-log plot of the contamination transform. The seven reservoir cases assume fixed reservoir and operational parameters, such as reservoir geometry, rock properties, fluid properties, invasion radius, time of invasion, maximum pumpout rate, and maximum drawdown pressure, to allow for a controlled sensitivity analysis enabling the identification of cleanup trends. It is emphasized that real-time field conditions could trigger certain limitations of the transient techniques developed in this work, such as noisy downhole formation testing measurements, active mud-filtrate invasion, or tool failure. To validate the assumptions, observations, and results of the numerical simulations, a field case is examined to (a) highlight the value of CTA in real-time fluid sampling operations and (b) further investigate its limitations. An alternative validation of the method is performed by applying the derivative directly to the formation testing measurements during fluid cleanup, reducing the uncertainty in the contamination estimation and the interpretation of transient trends. The new approach of the FCD is an alternative to improve fluid cleanup efficiency and to detect the spatial complexity of the reservoir during real-time downhole fluid sampling. Using log-log plots of fluid contamination and the FCD method, we encounter characteristic slopes defining late-time flow regimes. The spherical flow regime gives rise to a slope of –2/3, which has been previously documented by homogeneous isotropic analytical models. Radial flow exhibits a steeper slope of –3 that can be detected when the vertical limits are attained. Boundary effects are evident when the late-time slope of the FCD is equal to –1/3. In addition to the detection of reservoir boundaries, the CTA techniques developed in this paper enable the identification of reservoir fluid type and shale laminations and provide a foundation for the quantification of invasion radius and permeability anisotropy. It is found that cleanup efficiency could be improved based on contamination transient analysis by identifying the flow regimes taking place in the reservoir during filtrate cleanup, hence improving the prediction of the time required to acquire non-contaminated fluid samples.

Characteristics and main controlling factors of intra-platform shoal thin-layer dolomite reservoirs: A case study of Middle Permian Qixia Formation in Gaoshiti–Moxi area of Sichuan Basin, SW China

Based on the study of the distribution of intra-platform shoals and the characteristics of dolomite reservoirs in the Middle Permian Qixia Formation in the Gaoshiti–Moxi area of the Sichuan Basin, SW China, the controlling factors of reservoir development were analyzed, and the formation model of “intra-platform shoal thin-layer dolomite reservoir” was established. The Qixia Formation is a regressive cycle from bottom to top, in which the first member (Qi1 Member) develops low-energy open sea microfacies, and the second member (Qi2 Member) evolves into intra-platform shoal and inter-shoal sea with decreases in sea level. The intra-platform shoal is mainly distributed near the top of two secondary shallowing cycles of the Qi2 Member. The most important reservoir rock of the Qixia Formation is thin-layer fractured-vuggy dolomite, followed by vuggy dolomite. The semi-filled saddle dolomite is common in fracture-vug, and intercrystalline pores and residual dissolution pores combined with fractures to form the effective pore-fracture network. Based on the coupling analysis of sedimentary and diagenesis characteristics, the reservoir formation model of “pre-depositional micro-paleogeomorphology controlling shoal, sedimentary shoal controlling dolomite, penecontemporaneous dolomite benefiting preservation of pores, and late hydrothermal action effectively improving reservoir quality” was systematically established. The “first-order high zone” micro-paleogeomorphology before the deposition of the Qixia Formation controlled the development of large area of intra-platform shoals in Gaoshiti area during the deposition of the Qi2 Member. Shoal facies is the basic condition of early dolomitization, and the distribution range of intra-platform shoal and dolomite reservoir is highly consistent. The grain limestone of shoal facies is transformed by two stages of dolomitization. The penecontemporaneous dolomitization is conducive to the preservation of primary pores and secondary dissolved pores. The burial hydrothermal fluid enters the early dolomite body along the fractures associated with the Emeishan basalt event, makes it recrystallized into medium–coarse crystal dolomite. With the intercrystalline pores and the residual vugs after the hydrothermal dissolution along the fractures, the high-quality intra-platform shoal-type thin-layer dolomite reservoirs are formed. The establishment of this reservoir formation model can provide important theoretical support for the sustainable development of Permian gas reservoirs in the Sichuan Basin.

Lack of mitochondrial introgression and limited genetic connectivity among Manyara tilapia (Oreochromis amphimelas) populations in Tanzanian Saline Rift Valley Lakes

AbstractThe Manyara tilapia (Oreochromis amphimelas), native to the Saline Rift Valley Lakes (SRVLs) in north‐central Tanzania, has recently experienced population declines mainly due to overfishing and severe droughts. This, combined with the introduction of Nile tilapia (O. niloticus), which poses a risk of hybridisation, could potentially erode essential genetic traits necessary for their survival. To address these concerns, our study analysed partial cytochrome oxidase subunit I sequences (627 base pairs) from 139 Manyara tilapia and 79 Nile tilapia specimens collected from the SRVLs to test two hypotheses: (i) whether there is no transfer of mitochondrial DNA between these species, and (ii) whether Manyara tilapia populations in the SRVLs have remained genetically connected despite reported declines. The results revealed six distinct haplotypes for Manyara tilapia and three for Nile tilapia. These haplotypes formed separate clusters for each species, with no shared or closely related haplotypes, indicating limited or no transfer of mitochondrial DNA between them. Additionally, we found evidence of restricted genetic connectivity among Manyara tilapia populations in the SRVLs, with populations in Lakes Manyara and Eyasi displaying limited genetic exchange among themselves and with those in other SRVLs. Our findings highlight the importance of sustained conservation efforts in protected areas around Lake Manyara and Lake Eyasi to safeguard the unique populations of Manyara tilapia in these lakes. However, limited connectivity with other SRVLs suggests that conservation initiatives in these areas may have a limited impact on these lakes. Thus, future efforts should prioritise stocks in Lakes Kindai, Singida and Sulunga, focusing on protecting fish refugia, particularly the rivers connected to these lakes, which serve as critical habitats during the dry season and as important reservoirs for replenishing these populations.

Molybdenum Isotopic Signatures of Forearc Serpentinites: Origin and Contribution to the Subduction Zone Mo Cycle

AbstractSerpentinites, as important reservoirs for volatile and fluid‐mobile elements, have been increasingly recognized as playing a critical role in global geochemical cycles. However, direct evidence for their dominance in the molybdenum (Mo) cycle in subduction zones has been elusive. Here, we address this issue by comprehensively investigating the Mo isotope systematics of serpentinites and accompanying metabasites recovered from the Mariana forearc. Forearc serpentinites under low‐pressure conditions (blue‐ and lizardite‐serpentinites) show substantial enrichments in Mo/Ce ratios (0.42 to 27.34) with high δ98/95Mo values (−0.03‰ to 2.48‰), which arise from not only the incorporation of shallow forearc slab‐derived fluids but also late low‐temperature metasomatism by seawater during clast exhumation. Subducted oceanic crust represented by metabasites has low Mo/Ce ratios (0.004 to 0.049) and δ98/95Mo values (−1.13‰ to −0.61‰), indicating that the loss of Mo during oceanic crust alteration in the early or before subduction stage tends to decrease the Mo isotopic compositions. Combined Mo‐Sr‐Pb isotope systematics indicate that the high δ98/95Mo values in some arc lavas cannot be ascribed simply to the incorporation of slab‐derived fluids at subarc depths; instead, the injection of forearc serpentinite‐derived fluid into their mantle source is noteworthy. We propose that the mobilization of Mo by shallow slab‐derived fluids during the early subduction stage generated forearc lizardite‐bearing serpentinites enriched in heavy Mo isotopes. Subsequently, dehydration and melting of these serpentinites, dragged by the subducting slab down to the subarc region, might have contributed to the Mo systematics in arc lavas. This study demonstrated that forearc serpentinites may be important reservoirs for arc lavas with high Mo isotopic compositions and may contribute to the Mo cycling in subduction zones.

Evolution of guanylate binding protein genes shows a remarkable variability within bats (Chiroptera).

GBPs (guanylate binding proteins), an evolutionary ancient protein family, play a key role in the host's innate immune response against bacterial, parasitic and viral infections. In Humans, seven GBP genes have been described (GBP1-7). Despite the interest these proteins have received over the last years, evolutionary studies have only been performed in primates, Tupaia and rodents. These have shown a pattern of gene gain and loss in each family, indicative of the birth-and-death evolution process. In this study, we analysed the evolution of this gene cluster in several bat species, belonging to the Yangochiroptera and Yinpterochiroptera sub-orders. Detailed analysis shows a conserved synteny and a gene expansion and loss history. Phylogenetic analysis showed that bats have GBPs 1,2 and 4-6. GBP2 has been lost in several bat families, being present only in Hipposideidae and Pteropodidae. GBPs1, 4 and 5 are present mostly as single-copy genes in all families but have suffered duplication events, particularly in Myotis myotis and Eptesicus fuscus. Most interestingly, we demonstrate that GBP6 duplicated in a Chiroptera ancestor species originating two genes, which we named GBP6a and GBP6b, with different subsequent evolutionary histories. GBP6a underwent several duplication events in all families while GBP6b is present as a single copy gene and has been lost in Pteropodidae, Miniopteridae and Desmodus rotundus, a Phyllostomidae. With 14 and 15 GBP genes, Myotis myotis and Eptesicus fuscus stand out as having far more copies than all other studied bat species. Antagonistically, Pteropodidae have the lowest number of GBP genes in bats. Bats are important reservoirs of viruses, many of which have become zoonotic diseases in the last decades. Further functional studies on bats GBPs will help elucidate their function, evolutionary history, and the role of bats as virus reservoirs.

FIRST DATA ON BACTERIAL, FUNGAL AND PARASITIC INFECTIONS OF BLACK RATS (RATTUS RATTUS) FROM THE PALM GROVES OF THE ALGERIAN SAHARA

The present study aimed to detect the parasitic fauna associated with black rats (Rattus rattus) from southeastern Algeria. It showed the presence of seven species of parasitic fungi namely Penicillium sp. (Prevalence Pr=91.3%), Aspergillus niger (Pr=91.3%), Alternaria sp. (Pr=58.7%), Cladosporium sp. (Pr=87%), Microsporum sp. (Pr=19.6%), Trichophyton sp. (Pr=21.7%) and Chrysosporium sp. (Pr=10.9%), noting that saprophytic fungi were the most recorded. On the other hand, according to the richness (S), adults (S = 7) and sub-adults (S = 7) of black rats were the most infested, with leaning for males compared to females, considering all the isolated species as satellites except the Chrysosporium sp. (2.9%) which is presented as a rare species. Concerning parasitic bacteria, aged rats were the most infected followed by adults and sub-adults where total coliforms were present in all individuals of the three classes tested. However, fecal streptococci were noted with a similar infestation rate in all age groups. Unlike this, clostridium sulfite-reducer (CSR) was mostly recorded on aged rats. Concerning the endoparasites found in the intestines of black rats, the pinworms (Syphacia muris, Syphacia obvelata, and Aspiculuris tetraptera) were more abundant than the other species. Hence, the current study allowed us to demonstrate that black rats can be considered an important reservoir of several microorganisms that can hold germs and represent a threat to biomedical and veterinary public health.

Evolutionary game analysis of government, businesses, and consumers in high-standard farmland low-carbon construction

Abstract Soil is an important carbon reservoir, and high-standard farmland construction projects have significant potential to promote low-carbon development. In order to study the management and implementation of low-carbon production in high-standard farmland construction projects, the tripartite evolution game model of government, business, and consumer is constructed based on the tripartite bounded rationality. Then, the behavior strategy of tripartite stakeholders is analyzed with the method of system dynamics. Finally, the evolution process of tripartite interaction behavior is simulated using the MATLAB tool. The results show that: (1) The subsidy and punishment mechanism of the government must be aligned. In addition, the net income of government regulation is higher than the sum of the government’s environmental governance fees and fines of non-regulation; (2) The government, business, and consumers all choose their own behavioral strategies based on their own interests. (3) When the government’s environmental governance fee reaches a particular value, the system will appear imbalanced. In light of this, it is suggested that the government should increase support for business and use media publicity, consumer subsidies, and other measures to promote the consumption of low-carbon products. The business should constantly reduce the cost of carbon emission reduction through technological innovation.

Identification of a novel adenovirus in liver tissue sample of the Great Himalayan leaf-nosed bat (Hipposideros armiger).

Bats are important reservoirs for many zoonotic viruses. To explore and monitor potential novel viruses carried by bats, 21 liver samples of bats (Hipposideros armiger) were collected from Yunnan Province in southern China. Only one (4.8%) of all models was detected with adenovirus. The whole genome strain obtained by the viral metagenomics method combined with PCR was temporarily named YN01. The complete genome of YN01 was 37,676bp, with a G + C content of 55.20% and 28 open reading frames. Phylogenetic analysis indicated that the strain YN01 can be classified as genus Mastadenovirus and was the most similar to the adenovirus isolated from Rhinolophus sinicus in China in 2016. The analysis is needed to verify the possibility of cross-species transmission. This virological investigation has increased our understanding of the ecology of bat-borne viruses in this area and provided a reference for possible future infectious diseases.

Detection of phylogrouping, adhesin, and extended spectrum β-lactamases genes in hospital acquired uropathogenic Escherichia coli isolates.

It has been interesting to compare the levels of antimicrobial resistance and the virulence characteristics of uropathogenic Escherichia coli (UPEC) strains of certain phylogenetic groups. The purpose of this study was to identify the frequency of phylogenetic groups, adhesin genes, antibiotic sensitivity patterns, and extended spectrum-lactamases (ESBLs) genes in hospital-acquired UPEC. After UPEC isolation, the disc diffusion method was used to assess its susceptibility to antibiotics. Combination disc testing confirmed the existence of ESBL producers. Polymerase chain reaction (PCR) was used to detect genes for adhesin and ESBLs. One hundred and twenty-eight E. coli were isolated which had the highest resistance to tetracycline (96%) followed by cefoxitin (93%), cefepime (92%), ceftazidime (79%), aztreonam (77%) and sulfamethoxazole-trimethoprim (75%). About 57% of isolates were phenotypically ESBLs positive and they were confirmed by PCR. B2 phylogroup (41%) was the most frequent in E. coli isolates then group D (30%), group A (18%), and lastly group B1 (11%). ESBLs genes were more significantly prevalent in phylogroups B2 and D than other phylogroups (P < 0.001). Regarding adhesin genes, both fim H and afa were more significantly associated with group B2 than other groups (P < 0.009, < 0.032), respectively. In ESBL-positive isolates, both genes were more significantly detected compared to negative ones (P < 0.001). Phylogroups B2 and D of UPEC are important reservoirs of antimicrobial resistance and adhesion genes. Detection of ESBL-producing E. coli is important for appropriate treatment as well as for effective infection control in hospitals.

Application of phylodynamics to identify spread of antimicrobial-resistant Escherichia coli between humans and canines in an urban environment

The transmission of antimicrobial resistant bacteria in the urban environment is poorly understood. We utilized genomic sequencing and phylogenetics to characterize the transmission dynamics of antimicrobial resistant Escherichia coli (AMR-Ec) cultured from putative canine (caninep) and human feces present on urban sidewalks in San Francisco, California. We isolated a total of fifty-six AMR-Ec isolates from human (n = 20) and caninep (n = 36) fecal samples from the Tenderloin and South of Market (SoMa) neighborhoods of San Francisco. We then analyzed phenotypic and genotypic antimicrobial resistance (AMR) of the isolates, as well as clonal relationships based on cgMLST and single nucleotide polymorphisms (SNPs) of the core genomes. Using Bayesian inference, we reconstructed the transmission dynamics between humans and caninesp from multiple local outbreak clusters using the marginal structured coalescent approximation (MASCOT). Our results provide evidence for multiple sharing events of AMR-Ec between humans and caninesp. In particular, we found one instance of likely transmission from caninesp to humans as well as an additional local outbreak cluster consisting of one caninep and one human sample. Based on this analysis, it appears that non-human feces act as an important reservoir of clinically relevant AMR-Ec within the urban environment for this study population. This work showcases the utility of genomic epidemiology to reconstruct potential pathways by which antimicrobial resistance spreads.

Transport and retention of micro-polystyrene in coarse riverbed sediments: effects of flow velocity, particle and sediment sizes

Riverbed sediments have recently been found to be an important reservoir for microplastics. But the hydrogeological factors that control the abundance of microplastics are complex and conceptual frameworks priorising the parameters affecting their transport and retention during deep riverbed filtration are still missing. In this study a series of saturated column experiments was conducted to investigate the vertical distribution patterns of secondary polystyrene fragments (100–2000 μm) in dependence on their particle size, grain size of the sediment, seepage velocity and duration of infiltration flow. The columns with a length of 50 cm were operated with flow velocities between 1.8 m d−1 and 27 m d−1. Invasive samples obtained after the experiments were density separated and then depth profiles of microplastic concentrations were retrieved using fluorescence imaging analysis. Most polystyrene particles were retained in the upper 20 cm and 15 cm of the medium gravel and coarse sand sediments, respectively. Through the high particle retention riverbed sediments can act as a temporary sink or long term retention site for the transport of microplastic particles (MPPs) from streams to oceans. A small fraction of particles ranging from 100 to 500 μm in size was observed down to infiltration depths of 50 cm suggesting that MPPs at the pore scale have the potential to be advectively transferred via hyporheic exchange or induced bank filtration into coarse riverbed sediments and alluvial aquifers. MPP abundance over column depth follows an exponential relationship with a filter coefficient that was found to depend significantly on the flow rate, MPP and sediment grain size, as indicated by multiple linear regression (R2 = 0.92). The experimentally derived empirical relation allows to estimate particle abundances of initially negatively buoyant MPP in riverbed sediments by surface water infiltration.

El Parque Estatal Cerro de la Tortuga como reservorio de la herpetofauna en la región centro-sur del estado de Morelos

The Cerro de la Tortuga State Park as a herpetofauna reservoir in the central region of Morelos The Cerro de la Tortuga State Park (PECT) in the south-central region of the state of Morelos in Mexico is an important reservoir of amphibian and reptile diversity. The objective of this study is to update the inventory of amphibians and reptiles and to determine the composition, species richness, species-area relationship and similarity of the herpetofauna between reserves with different types of administration. The herpetofauna within the PECT was composed of 28 species, equivalent to 20 % of the herpetofauna of Morelos and 1.97 % of the herpetofauna of Mexico. The Squamata order was the best represented group, with 17 species (60.71 %), followed by Anura with 10 species (35.71 %) and Testudines with 1 species (3.57 %). The agreement with the analysis of the species/area relationship, REBIOSH (3 spp.) and PECT (1 spp.) harbor a greater number of species than expected with respect to CBCH (3 spp.), which harbors a lower number. of species than expected. The similarity of the herpetofaunistic composition of the PECT result is greater between the RESM (50 %) and the REBIOSH (34 %), compared to the CBCH (12 %). Our results indicate that the PECT acts as an important reservoir for the herpetofauna of the south-central region of Morelos, which could structurally be part of the so-called conservation archipelagos. However, in addition to evidence of composition and similarity between reserves, we suggest developers consider habitat quality for corridor identifiers and genetic studies that demonstrate gene flow for species shared between reserves.

The pig intestinal phageome is an important reservoir and transfer vector for virulence genes

Bacteriophages (phages) can significantly influence the composition and functions of their host communities, and enhance host pathogenicity via the transport of phage-encoded virulence genes. Phages are the main component of animal gut viruses, however, there are few reports on the piglet gut phageome and its contribution to virulence genes. Here, a total of 185 virulence genes from 59,955 predicted genes of gut phages in weaned piglets were identified, with 0.688 % of the phage contigs coding for at least one virulence gene. The virulence gene pblA was the most abundant, with various virulence genes significantly correlated with gut phages and their encoded mobile gene element (MGE) genes. Importantly, multiple virulence genes and MGE genes coexist in some phage sequences, and up to 12 virulence genes were detected in a single phage sequence, greatly increasing the risk of phage-mediated transmission of virulence genes into the bacterial genome. In addition, diarrhoea has driven changes in the composition and structure of phage and bacterial communities in the intestinal tract of weaned piglets, significantly increasing the abundance of phage contigs encoding both virulence genes and MGE genes in faecal samples, which potentially increases the risk of phage-mediated virulence genes being transfected into the gut bacterial genome. In summary, this study expands our understanding of the gut microbiome of piglets, advances our understanding of the potential role of phages in driving host pathogenesis in the gut system, and provides new insights into the sources of virulence genes and genetic evolution of bacteria in pig farm environments.

Avian Diversity in and around Wetland of National Importance ‘Pariyej Community Reservoir’, Gujarat, India

The Pariyej Community Reservoir (PCR) is a freshwater reservoir in the Kheda district of Gujarat State, India. The PCR is also listed in Asian Directory of Wetlands. It is an important water storage reservoir; falls in the 4-B Gujarat Rajwara region of Central Gujarat, India. The present study was carried out for the period of one year (March, 2021 to February, 2022) to assess the status of avian diversity in terms of its species richness, abundance, and density. 116 bird species from 20 orders, 51 families, and 100 genera were documented. 75 species (64.4%) were resident, whereas 41 (35.3%) were migratory or seasonal. With respect to abundance, 41species (35.34%) were abundant, 39 species (33.6%) common, and 36 rare species (31.0%). The maximum total abundance (1707 individuals) was found at Site 1 in winter season with mean abundance of 427 individuals, total density (114 individuals/sq.km)and mean density (29 individuals/sq.km). The minimum total abundance (288 individuals) was recorded at Site2 in monsoon season with mean abundance of 72 individuals, total density (19individuals/sq.km) and mean density (5 individuals/sq.km).The present investigation reflects the good species richness of avian specieswith respect to order: family: genera: species ratioi.e., 1: 2.55: 5.0: 5.8. This indicates the flourishing harboring capability of PCR during peak winter period, which could be due to sustenance of rich biotic elements. The PCR has been declared as Sanctum sanctorumfor the refuge of migratory as well as local migrant birds, which is proved to be a wetland of national importance.

Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists.

Habitat type is a strong determinant of microbial composition. Habitat interfaces, such as the boundary between aquatic and terrestrial systems, present unique combinations of abiotic factors for microorganisms to contend with. Aside from the spillover of certain harmful microorganisms from agricultural soils into water (e.g. fecal coliform bacteria), we know little about the extent of soil-water habitat switching across microbial taxa. In this study, we developed a proof-of-concept system to facilitate the capture of putatively generalist microorganisms that can colonize and persist in both soil and river water. We aimed to examine the phylogenetic breadth of putative habitat switchers and how this varies across different source environments. Microbial composition was primarily driven by recipient environment type, with the strongest phylogenetic signal seen at the order level for river water colonizers. We also identified more microorganisms colonizing river water when soil was collected from a habitat interface (i.e. soil at the side of an intermittently flooded river, compared to soil collected further from water sources), suggesting that environmental interfaces could be important reservoirs of microbial habitat generalists. Continued development of experimental systems that actively capture microorganisms that thrive in divergent habitats could serve as a powerful tool for identifying and assessing the ecological distribution of microbial generalists.