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Background: Small rodents and insectivores are potential reservoirs of many pathogens transmissible to humans, such as bacteria, parasites and viruses responsible for epidemics in sub-Saharan Africa, particularly in West Africa. Few studies on small mammal species in West Africa are available. Our previous findings from a study investigating emerging pathogens in two localities in Mali has determined the prevalence of pathogens in small mammals (rodents and insectivores). We used the data collected from this small mammal population with different eco-climatic characteristics to test hypothesis that small mammal distribution in different eco-climatic settings could explain the diversity and frequency of pathogens they carry. Methods: Sessions of trapping were carried out in December 2016 in Faladjè and Bougouni with "Besançon tous services" (BTS) wire mesh traps baited with peanut butter and/or onion. All animals captured were identified morphologically. Results: Out of 123 small rodents and insectivores captured over 674 trap-nights, 75 (60.97%) were from Faladjè and 48 (39.02%) from Bougouni. Of these, six species of small rodents belonged to the family Muridae (Mastomys erythroleucus, Mastomys natalensis, Rattus rattus, Praomys daltoni, Gerbilliscus gambianus, Taterillus gracilis) and two species of insectivores associated with the genus Crocidura spp. belonged to the family Soricidae and Erinaceidae (Crocidura cf olivieri and Atelerix cf albiventris), respectively. There is low species diversity within these two areas, but the variation in relative abundance is significant (binomial test, p ˂ 0.05) between Faladjè and Bougouni. Mastomys erythroleucus was the most dominant species (57.33%, 43/75) in Faladjè, while R. rattus dominated (37.5%,18/48) in Bougouni. Conclusions: These two species of small mammals potentially involved in the transmission of bacteria, parasites and pathogenic viruses to humans are differently present in two distinct eco-climatic areas in Mali. [ABSTRACT FROM AUTHOR]

The striped field mouse (Apodemus agrarius) is expanding in several European countries, but the details of this process are not always documented due to a lack of long-term studies. We conducted an analysis of changes in relative abundances and proportions of A. agrarius in small mammal communities in nine different habitat groups in Lithuania during 1975–2023. We found an increase in the abundance and proportion of A. agrarius, increasing synanthropization of the species, and tolerance to anthropogenization of habitats. Temporal variations in the relative abundance and proportion of species were observed, with lower values in February–July and higher values in September–January. The main finding is a remarkable increase in species presence in the country after the 1990s, with a peak observed in the 2010s–2020s, confirmed by eight local studies. During these decades, it was the third most abundant species, representing 19.8–20.0% of the individuals caught. It is also important to note that A. agrarius has recently been most abundant in commensal habitats (0.029 ± 0.006 individuals/trap day), with the highest species proportion in agricultural areas (24.8 ± 1.8%). There are many indications that the expansion of A. agrarius in Lithuania is becoming invasive. [ABSTRACT FROM AUTHOR]

Because of their wide distribution, short life cycle, rapid reproduction, and sensitivity to the environment, rodents can indicate changes in habitat quality and climate variables. Long-term studies are needed to verify these changes and assumptions about their causes. We analyzed small mammal trapping data in Lithuania, covering the period 1975–2023, with 1821 trapping sites and 57,426 small mammal individuals, with a focus on the bank vole (Clethrionomys glareolus). The aim of this study was to assess temporal changes in the relative abundance and proportion of this species in small mammal communities in relation to their habitats. With 21,736 captured individuals, C. glareolus was a dominant species in the country; its proportion in general was 37.9%, with 60.0% in forests. Open habitats, meadows and agricultural land were characterized by the lowest species proportions. Our main findings were the confirmation of decreasing abundances and proportions of C. glareolus since the 1990s, the absence of cyclical fluctuations in the relative abundances of the species in general and in forest habitats, and the introduction of a south–north cline in species proportions. The status of this temperate and boreal forest species is subject to change, with implications for the diversity of the mid-latitude small mammal community. [ABSTRACT FROM AUTHOR]

Biting midges belonging to the genus Culicoides are tiny stout-shaped hematophagous insects and are thought to transmit the filarial nematode Mansonella perstans. Little is known about the Culicoides fauna in the rain forest belt of the Littoral Region of Cameroon. This study was designed to investigate the diversity, abundance and distribution of Culicoides spp. and their role as the purported vector(s) of M. perstans. Overnight light trap collections and human landing catches (HLCs) revealed eight species of Culicoides with C. grahamii being the most abundant species followed by C. milnei. Four anthropophilic species (C. inornatipennis, C. grahamii, C. fulvithorax and C. milnei) were determined by the HLCs with a higher abundance in the 4–6 p.m. collections. The drop trap technique and Mp419 LAMP assay confirmed C. milnei to be the most efficient vector in enabling the development of the microfilarial stage to the infective larval form of M. perstans. The LAMP assay also revealed that natural transmission of this nematode is fostered by C. milnei and C. grahamii in the wild. In conclusion, C. milnei was shown to be the main vector of M. perstans in the rain forest belt of the Littoral Region of Cameroon. [ABSTRACT FROM AUTHOR]

The Eurasian harvest mouse (Micromys minutus) is a tiny rodent of the Palearctic and Indomalayan regions, with a distinct regional species status in Europe and irregularly varying local numbers. We analysed the population of M. minutus in Lithuania (Northern Europe) based on trapping data from 1975 to 2022 and owl pellet data from 1986 to 2009. Based on both datasets, the proportion of this species in the small mammal community was similar, 1.13% and 0.62%, respectively. The proportions have remained stable across all decades. Relative abundance was 1.19 ± 0.19 individuals per 1000 trap days, stable over the long term and across the country. Irregular fluctuations in abundance were observed in some of the sites surveyed. The highest average RA was recorded in open sedge habitats, meadows and marshes. The absolute highest RA was 88 individuals per 1000 trap days in floodplain meadows after a major flood. Although the negative impact of habitat anthropogenisation has been confirmed, M. minutus does not require special conservation measures in Lithuania. [ABSTRACT FROM AUTHOR]

Aging is a complex process influenced by genetics and the environment, leading to physiological decline and increased susceptibility to diseases. Cognitive decline is a prominent feature of aging, with implications for different neurodegenerative disorders. The gut microbiome has gained attention for its potential impact on health and disease, including cognitive function. This systematic review and meta-analysis aimed to investigate the relationship between the gut microbiome and cognitive function in the context of aging. Following PRISMA guidelines, a comprehensive search strategy was employed in PubMed, Scopus, and Web of Science databases. Studies exploring the role of the microbiome in cognition and neurodegenerative disorders, published between 2013 and 2023, were included. Data extraction and quality assessment were performed. Quantitative synthesis using statistical analyses was performed to examine microbial diversity and relative abundance in various cognitive conditions. Sixteen studies involving a total of 1303 participants were included in the analysis. The gut microbiota's relative abundance was different in individuals with cognitive impairments such as Alzheimer's disease, Parkinson's disease, and dementia, compared to the healthy controls. The most prevalent phyla affected were Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Meta-analyses indicated substantial heterogeneity among studies focusing on Alzheimer's disease. The overall quality of evidence related to microbial analysis was moderate. The gut microbiome's role in cognitive decline and neurodegenerative disorders warrants investigation. Altered microbial abundance, particularly in specific phyla, is associated with cognitive impairments. However, variations in study findings and methodologies highlight the complexity of the relationship between the gut microbiome and cognitive function. Further studies are needed to better understand the mechanisms underlying this connection and its potential implications for aging and cognitive health. [ABSTRACT FROM AUTHOR]

In Mediterranean, the exploitation and exportation of holothurians as food is increasing during the last 25 years, with Turkey and Greece as leading countries. In Greece, the fishery is expanding by the development of two métiers; however, official monitoring is missing, creating concerns on the future viability of the industry. To evaluate the status and future perspectives of holothurian fisheries, an extensive field survey has been completed (May 2019–July 2021) covering 162 sites dispersed in the Hellenic Seas. Field data included the assessment of the abundance of holothurians (via 100 m transect replicates), and catch per unit of effort (CNPUE and CBPUE, based on 10-min commercial fishing practices). H. tubulosa, H. poli, H. mammata and H. sanctori were fished in 41.35% of the surveyed stations. H. poli (CNPUE 168 specimens, CBPUE 22.24 kg) and H. tubulosa (CNPUE 127 specimens, CBPUE14.51 kg) were the most common species, forming locally dense populations. Mean annual catch was 275 metric tons (2016–2021) according to the processing of the units' data; 62% of the production was made by H. tubulosa and 38% by H. poli. Our results suggest the existence of exploitable grounds in the north Aegean, the central Cyclades, and the north Dodecanese, according to the prevalent environmental conditions (organic load) and fishing pressure. [ABSTRACT FROM AUTHOR]

Afforestation of former agricultural land poses a real challenge for foresters because soil life is often severely limited by the loss of natural soil fungal diversity. In addition, former agricultural soils have low levels of fungal species typical of forest soils, which have a unique microbiome that plays a protective role (antagonists, plant growth promoters, mycorrhizal fungi, etc.). This study aimed to determine the effect of using organic material in the form of bark compost, wood waste, and sawdust to improve the soil mycobiome of soils that have been damaged by their agricultural use. This study used experimental plots established 20 years ago, and we compared the biodiversity of the treated soils with that of the control soils by analysing soil samples with powerful molecular methods. Next-generation sequencing analysis of DNA extracted from soil samples and subsequent analysis of their species composition and biodiversity showed that the mycobiome of soil fungi has been altered by the addition of various forms of organic material. The proportion of fungi belonging to the Ascomycota decreased in favour of species from the Basidiomycota and Mucoromycota. The dominant fungal groups in the soil of the control area were Sagenomella, Wilcoxina, Oidiodendron, Meliniomyces, and Penicillium. Enrichment with organic matter by adding bark compost under the roots led to an increase in Penicillium, Inocybe, and Amphinema. The application of bark compost on the surface led to an increase in the dominance of Inocybe fungi in the soil. The mycobiome of the plant to which woody debris was applied was characterised by a marked dominance of fungi of the genera Russula, Oidiodendron, and Penicillium. Similar ratios were found in the plant to which sawdust was applied, where the fungi Meliniomyces, Penicillium, Oidiodendron, and Russula dominated. A comparative analysis of fungal diversity with the Shannon diversity index showed that the most diverse fungal communities were found in the sawdust plant (6.56), while the control sample (a soil sample from an agricultural area where no organic material was applied) had an index of 5.71. After the treatments, more potential antagonists against pine pathogens and mycorrhizal fungi were found to form beneficial symbiotic relationships with them. In our opinion, the results of this study show that it is worthwhile to introduce different forms of organic matter to post-agricultural land to improve soil biodiversity and mycorrhizal associations of pine roots with fungi to ensure the sustainability of the first generation of forests created. [ABSTRACT FROM AUTHOR]

Research on Bluegills, Lepomis macrochirus R., is abundant but typically focuses on water bodies with similar environmental conditions. We assessed Bluegill density, relative abundance (catch per unit effort [CPUE] by electrofishing), growth, and size structure in 60 lakes with wide-ranging surface areas (2–12,412 ha), trophic states (oligotrophic–hypereutrophic), and macrophyte abundances (0.3–100 percent of lake volume inhabited [PVI]) across Florida, USA. Bluegill density and CPUE increased with lake productivity and decreased with macrophyte abundance. Bluegill growth increased with lake productivity and CPUE of stock-length Florida Bass, Micropterus floridanus L., a Bluegill predator. Bluegill size structure increased with lake productivity and decreased with Bluegill density. Results indicate that Bluegill fisheries with abundant individuals of quality size (≥150 mm) require productive (>25 μg/L chlorophyll-a concentration) lakes with moderate to high macrophyte coverage (PVI 50–100), abundant stock-length Florida Bass (>40 fish/h of electrofishing), and Bluegill densities <300 fish/ha. This study provides an approach to predict Bluegill population demographics based on abiotic and biotic factors, establish fisheries management expectations, and develop regional and lake-specific management tools. [ABSTRACT FROM AUTHOR]

Organic phosphorus (Po) may play a vital role in phosphorus availability via its mineralization by alkaline phosphatase (ALP), being encoded by phoD gene, in calcareous soil. Understanding the effects of long-term fertilization on the community of phoD harboring bacteria and the related alteration of the P availability owing to the changes in ALP secretion may offer a chance to elucidate the Po contribution to soil available P. Based on a long-term experiment, we analyzed the phoD gene harboring microbial diversity, abundance and composition, ALP and Po forms, and their relationship. The treatments involved were control without any fertilizers (CK), synthetic nitrogen and potassium (NK), synthetic nitrogen, phosphorus and potassium (NPK), NPK and crop stalk return (SNPK), and NPK plus organic manure (MNPK). Fertilization increased the abundance and diversity of phoD gene harboring microbial over CK. Those receiving NPK and NPK treatments integrated with organic supplements significantly improved the relative abundance of Proteobacteria but decreased Gemmatimonadetes at the phylum level, while all fertilized treatments appreciably increased the relative abundance of Lysobacter but decreased that of Gemmatirosa and Afipia, at the genus level. SNPK and MNPK treatments noticeably increased the relative abundance of Methylobacter but reduced Pseudomonas and Streptomyces relative to those receiving synthetic fertilizer treatments. Long-term fertilization markedly raised ALP activity, which was significantly and positively correlated with the relative abundance of the phylum Proteobacteria as represented by the genera Methylobacterium and Lysobacter. ALP was closely associated with moderately labile Po, followed by enzyme P, recalcitrant Po, and labile Po. The changes in phoD bacteria and ALP were mainly driven by soil organic carbon, Olsen P and pH. We concluded that the long-term fertilization, especially the addition of organic supplements, profoundly modified the soil properties and subsequently changed the diversity and relative abundance of phoD gene harboring bacteria, which promoted the activity of ALP, and thus the mineralization of various forms of Po (mainly moderately labile Po) to enhance the P availability. [ABSTRACT FROM AUTHOR]

Fruit and berry farms are anthropogenic habitats still inhabited by small mammals, though their presence is constantly affected by agricultural activities. Based on trapping data from 2018–2022, we analyzed the abundance and population structure of the dominant rodent species to assess changes in gender and age ratios by year and habitat, the annual and seasonal dynamics of relative abundance, and the relationship between breeding parameters and abundance. The relative abundance of the dominant species, common vole, yellow-necked mouse, striped field mouse, and bank vole, and their proportion in the investigated community varied according to year, season, and habitat. No outbreaks were recorded during the study period. The abundance of the striped field mouse exhibited a downward trend independently of habitat, while the abundance and proportions of the other three species were habitat-dependent. There was no consistent pattern between litter size and relative abundance in the same or following years. Given the ongoing conflict between biodiversity conservation in Europe and agriculture, the results contribute to a better understanding of the functioning and viability of rodent populations in fruit farms and may be used in agroecology and sustainable farming. [ABSTRACT FROM AUTHOR]

Cormorant colonies are often viewed negatively by fishermen and foresters due to their extremely high impact on aquatic and terrestrial ecosystems. In forests, the habitats of nesting territories are destroyed, with concomitant impacts on the animal communities. In 2011–2022, investigating three colonies of Great Cormorants (Phalacrocorax carbo), we aimed to test whether their effect on small mammals depends on colony size. In the largest colony in Lithuania, a low species richness, lower diversity and relative abundance, as well as poorer body conditions of the most abundant species was found in the nesting zone. However, once the cormorants left the nesting site, all the parameters recovered. Two small colonies had a positive impact, with higher species richness in the territory of the colony (seven and ten species), diversity (H = 1.56 and 1.49), and relative abundance (27.00 ± 2.32 and 25.29 ± 2.91 ind. per 100 trap days) compared with the control habitat (three and eight species; H = 1.65 and 0.99; 12.58 ± 1.54 and 8.29 ± 1.05 ind./100 trap-days). We conclude that up to a certain colony size, cormorant pressure is a driver of habitat succession and has similar effects on the small mammal community as other successions in disturbed habitats. [ABSTRACT FROM AUTHOR]

Tapeworm infection continues to be an important cause of morbidity worldwide. Recent metagenomics studies have established a link between gut microbiota and parasite infection. The identification of gut probiotics is of foremost importance to explore its relationship and function with the parasite in the host. In this study, the gut content of hosts infected with tapeworm Hymenolepis diminuta and non-infected host gut were disected out to determine their Lactic acid bacterial (LAB) population in MRS agar and microbial community was analysed by metagenomics. The bacterial count was calculated on a bacterial counting chamber and their morphology was determined microscopically and biochemically. Further, to determine the safety profile antibiotic resistance test, antimicrobial, hemolytic activity, and adhesion capability were calculated. We found six dominant probiotic strains and a decrease in LAB load from 1.7–2.3 × 107 CFU/mL in the uninfected group to a range of 8.4 × 105 CFU/mL to 3.2 × 105 CFU/mL in the infected groups with respect to an increase in the parasite number from 10–18. In addition, we found a depletion in the probiotic relative abundance of Lactobacillus and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria, and Streptococcus. Phylogenetic analysis of the six probiotics revealed a close similarity with different strains of L. brevis, L. johnsonii, L. taiwansis, L. reuteri, L. plantarum, and L. pentosus. Thus, this study suggests that the parasite inhibits probiotic colonization in the gut during its early establishment of infection inside the host. [ABSTRACT FROM AUTHOR]

We evaluated the effects of a homo-fermentative lactic acid bacteria (homo-LAB) inoculant on the fermentation and microbial communities of alfalfa ensiled at two dry matter (DM) contents of 38 and 46% DM. At both DMs, alfalfa was treated or not with an inoculant containing Pediococcus acidilactici, Enterococcus faecium and Lactobacillus plantarum at a targeted application rate of 165,000 cfu/g of fresh weight and stored for 3, 30 and 60 days. Treatment with the inoculant resulted in a lower drop in pH and, in general, higher lactic acid and lower acetic acid when applied to medium DM silage. For the four most abundant microbial genera, increased abundances of Bacteroides and Lactobacillus (p < 0.05), as well as decreased abundances of Muribaculaceae were observed in high DM and inoculated silages. The abundance of Prevotellaceae-UCG-001 was lower in medium DM control silages than in high DM control silages. Inoculation and DM affected abundances of Vishniacozyma (p < 0.05). Increased abundances of Vishniacozyma, as well as decreased abundances of Leucosporidium were observed in medium DM-inoculated silages. Changes in the relative abundance (RA) of the main populations of bacteria and yeasts did explain the fermentation and nutrition differences among treatments. [ABSTRACT FROM AUTHOR]

Simulating the dynamics of plant species or types in grassland communities remains an open area of research for which the Community Simulation Model (CoSMo) offers novel approaches. The grassland model ModVege was first parameterised based on a functional vegetation typology, in which types "A" and "B" include fast-growing grass species with a phenology-dependent nutrient-capture strategy inherent to fertile grasslands, while the nutrient conservation strategy and late flowering characterise the other types as "b". ModVege was then coupled to the CoSMo rule set to dynamically simulate the relative abundance of plant functional types or individual species, assessed across fertilised and unfertilised, abandoned and mown conditions in a grassland site of the Massif Central of France. While for the simulation of aboveground biomass, model performance is not unambiguously linked to explicit consideration of plant diversity, the simulation of relative abundance for the whole community is satisfactory (relative root mean square error of ~13–25% when simulating functional types and ~28–52% when simulating species). This study extends previous studies by coupling CoSMo, for the first time, to a grassland-specific model and applying it to conditions (long-term observations, extended number of plant species, absence of fertilisation, frequent mowing and abandonment) never investigated before. [ABSTRACT FROM AUTHOR]

Water scarcity and the uneven distribution of water resources in China have resulted in water shortages for agricultural irrigation in arid and semi-arid areas. Reclaimed water used for agricultural irrigation has become an effective solution in the context of the global water shortage. In order to improve soil productivity and solve the shortage of water resources, we carried out reclaimed water irrigation experiments on polluted soil. Compared with full irrigation treatments, the EC value of reclaimed water under deficit irrigation treatments decreased by 2.89–42.90%, and the content of organic matter increased by 6.31–12.10%. The proportion of Acidobacteria community in soils with different cadmium concentration gradients irrigated with reclaimed water ranged from 13.6% to 30.5%, its relative abundance decreased with the increase of soil cadmium concentration. In particular, the relative abundance of Pseudomonas pathogens in deficit irrigation treatments was lower than that of the full irrigation treatments. RDA analysis showed that the environmental factors that played a leading role in the change of microbial community structure were organic matter and pH. Furthermore, the metabolic function potential of the rhizosphere soil bacterial community in deficit irrigation treatments was higher than that of full irrigation treatments with reclaimed water. This study proved that reclaimed water irrigation for cadmium contaminated soil did not aggravate the pollution level and promoted the soil ecological environment with better microbial community diversity. [ABSTRACT FROM AUTHOR]

The metagenomic whole genome shotgun sequencing (mWGS) approach was used to detect signatures of the rhizosphere microbiomes of Dipterygium glaucum and surrounding bulk soil microbiomes, and to detect differential microbial responses due to watering. Preliminary results reflect the reliability of the experiment and the rationality of grouping microbiomes. Based on the abundance of non-redundant genes, bacterial genomes showed the highest level, followed by Archaeal and Eukaryotic genomes, then, the least abundant viruses. Overall results indicate that most members of bacteria have a higher abundance/relative abundance (AB/RA) pattern in the rhizosphere towards plant growth promotion, while members of eukaryota have a higher pattern in bulk soil, most likely acting as pathogens. The results also indicate the contribution of mycorrhiza (genus Rhizophagus) in mediating complex mutualistic associations between soil microbes (either beneficial or harmful) and plant roots. Some of these symbiotic relationships involve microbes of different domains responding differentially to plant root exudates. Among these are included the bacterial genus Burkholderia and eukaryotic genus Trichoderma, which have antagonistic activities against the eukaryotic genus Fusarium. Another example involves Ochrobactrum phage POA1180, its bacterial host and plant roots. One of the major challenges in plant nutrition involves other microbes that manipulate nitrogen levels in the soil. Among these are the microbes that perform contraversal actions of nitrogen fixation (the methanogen Euryarchaeota) and ammonia oxidation (Crenarchaeota). The net nitrogen level in the soil is originally based on the AB/RA of these microbes and partially on the environmental condition. Watering seems to influence the AB/RA of a large number of soil microbes, where drought-sensitive microbes (members of phyla Acidobacteria and Gemmatimonadetes) showed an increased AB/RA pattern after watering, while others (Burkholderia and Trichoderma) seem to be among microbes assisting plants to withstand abiotic stresses. This study sheds light on the efficient use of mWGS in the taxonomic assignment of soil microbes and in their response to watering. It also provides new avenues for improving biotic and abiotic resistance in domestic plant germplasm via the manipulation of soil microbes. [ABSTRACT FROM AUTHOR]

Background: The human microbiome can contribute to pathogeneses of many complex diseases by mediating disease-leading causal pathways. However, standard mediation analysis methods are not adequate to analyze the microbiome as a mediator due to the excessive number of zero-valued sequencing reads in the data and that the relative abundances have to sum to one. The two main challenges raised by the zero-inflated data structure are: (a) disentangling the mediation effect induced by the point mass at zero; and (b) identifying the observed zero-valued data points that are not zero (i.e., false zeros). Methods: We develop a novel marginal mediation analysis method under the potential-outcomes framework to address the issues. We also show that the marginal model can account for the compositional structure of microbiome data. Results: The mediation effect can be decomposed into two components that are inherent to the two-part nature of zero-inflated distributions. With probabilistic models to account for observing zeros, we also address the challenge with false zeros. A comprehensive simulation study and the application in a real microbiome study showcase our approach in comparison with existing approaches. Conclusions: When analyzing the zero-inflated microbiome composition as the mediators, MarZIC approach has better performance than standard causal mediation analysis approaches and existing competing approach. [ABSTRACT FROM AUTHOR]

Tuna fisheries are the most valuable fisheries in the world, with an estimated market value of at least US$42 billion in 2018. Indonesia plays an important role in the global tuna fisheries and has committed to improve its fisheries management; therefore, a pilot of long-term spatial-temporal data bases was developed in 2012, however none have utilized data to have better understanding for management improvement. In this study, the annual and seasonal variation of large (10 kg) Yellowfin Tuna (YFT) catch per unit effort (CPUE) have been investigated and the influence of sea surface temperature (SST) and chlorophyll-a on these variables examined. We used fish landing data fromWest Nusa Tenggara recorded every month between 2012 and 2017 and analyzed using generalized linear models and generalized additive models. We found a seasonal and annual pattern of tuna abundance affected by SST and chlorophyll-a (chl a) and related to upwelling and El Nino event. These results also suggest that a two-month closure to fishing in August and September in southern Lombok is worth considering by the Government to maximize conservation of stocks due to a high abundance of juveniles emerging during the upwelling months from June to August. [ABSTRACT FROM AUTHOR]

Scleractinian corals, the main framework builders of coral reefs, are in serious global decline, although there remains significant uncertainty as to the consequences for individual species and particular regions. We assessed coral species richness and ranked relative abundance across 3075 depth-stratified survey sites, each < 0.5 ha in area, using a standardized rapid assessment method, in 31 Indo-West Pacific (IWP) coral ecoregions (ERs), from 1994 to 2016. The ecoregions cover a significant proportion of the ranges of most IWP reef coral species, including main centres of diversity, providing a baseline (albeit a shifted one) of species abundance over a large area of highly endangered reef systems, facilitating study of future change. In all, 672 species were recorded. The richest sites and ERs were all located in the Coral Triangle. Local (site) richness peaked at 224 species in Halmahera ER (IWP mean 71 species Standard Deviation 38 species). Nineteen species occurred in more than half of all sites, all but one occurring in more than 90% of ERs. Representing 13 genera, these widespread species exhibit a broad range of life histories, indicating that no particular strategy, or taxonomic affiliation, conferred particular ecological advantage. For most other species, occurrence and abundance varied markedly among different ERs, some having pronounced "centres of abundance". Conversely, another 40 species, also with widely divergent life histories, were very rare, occurring in five or fewer sites, 14 species of which are ranked as "Vulnerable" or "Endangered" on the International Union for Conservation of Nature (IUCN) Red List. Others may also qualify in these Threatened categories under criteria of small geographic range and population fragmentation, the utility of which is briefly assessed. [ABSTRACT FROM AUTHOR]

Despite its importance as a component of urban green spaces, as far as we are aware no study has focused on plant diversity in urban green corridors (GCs). Therefore, this study aimed at: (i) characterizing tree and shrub communities in Lisbon's GCs and (ii) assessing whether GCs' users value trees and shrubs. We counted Lisbon's GCs users in the same places where we assessed the tree and shrub community. Along the nine GCs, we observed trees and shrubs belonging to 70 species, distributed across 35 families with most (≥50%) species and plants being trees, exotic, pollinated by insects, with fruit dispersion by animals, evergreen leaves, and producing dry fruits. Most GCs had a similar number of users (20–30 users h−1 survey−1) except for those of Central and Ribeirinho, which were more frequented (60 and 100 users h−1 survey−1, respectively). Most users (≥50%) were adults, walking accompanied, and performing leisure activities. Finally, the number of users was shown to be influenced by: (i) tree and shrub relative abundance, confirming that users preferred greener corridors; and (ii) function(s), showing that users preferred the most multifunctional GCs (i.e., GCs fulfilling ecological, cultural, and recreational functions). Our data suggest that Lisbon's GCs favor more the inclusion of citizens than ecological functionality and resilience. [ABSTRACT FROM AUTHOR]

This study is the first systematic assessment of large herbivore (LH) communities in Limpopo National Park (LNP) in Mozambique, an area where most LH species were extinct until the early 2000s. We investigate whether LH community parameters are linked with the availability of habitat types or the distance between sampling sites and the origin of LH resettlement. We placed camera traps in five habitat types in resettled and not-resettled areas to compare species richness, relative abundance index, grazers–browsers–mixed feeder and naïve occupancy of 15 LH species. While the richness decreased along the distance gradient of LH resettlement, relative abundance index strongly responded to habitat features. The grazer–browser–mixed feeder ratio oscillated, while from resettled to not-resettled areas, the ratio increased. Most species show a wide distribution range. The associations of most LH community parameters with habitat types rather than distance to initial release, together with the species-specific and guild-specific response patterns of LH, suggest LNP to already be in an intermediate stage of restoration. Our results highlight the importance of post-release monitoring of reintroduced wildlife as a tool to assess the success of ecological restoration initiatives in transboundary conservation areas. [ABSTRACT FROM AUTHOR]

Despite growing interest in the environmental impact of microplastics, a standardized characterization method is not available. We carried out a systematic analysis of reliable global data detailing the relative abundance of polymers in freshwaters and estuaries. The polymers were identified according to seven main categories: polyethylene terephthalate, polyethylene, polyvinyl chloride, polypropylene, polystyrene, polyurethane and a final category of miscellaneous plastic. The results show that microplastics comprised of polyvinyl chloride and polyurethane are significantly less abundant than would be expected based on global production, possibly due to their use. This has implications for models of microplastic release into the environment based on production and fate. When analysed by matrix (water, sediment or biota) distinct profiles were obtained for each category. Polyethylene, polypropylene and polystyrene were more abundant in sediment than in biota, while miscellaneous plastics was more frequent in biota. The data suggest that environmental sorting of microplastic particles, influenced by physical, chemical and biological processes, may play a key role in environmental impact, although partitioning among matrices based on density was not realized. The distinct profile of microplastics in biota raises an important question regarding potential selectivity in uptake by organisms, highlighting the priority for more and better-informed laboratory exposure studies.

Soil microbial communities are essential in the cycling of nutrients that affect crop production. Our goal was to characterize the microbial community structure following 34 years of nitrogen (N) fertilization treatments in continuous maize production in highly fertile soils. Using 16S rRNA gene-based analysis of the V4 region via Illumina HiSeq2500 technology with downstream bioinformatics processing and analysis with QIIME 2.0, we aimed to characterize the prokaryotic communities under three increasing N fertilization rates. Factor analyses indicated that a high N level decreased the diversity of soil bacterial and archaeal communities and altered the relative abundance (RA) of the dominant (>1% RA) and minor (<1% RA) phyla. Among the 12 major phyla, we determined increases in Gemmatimonadetes, Proteobacteria, and Euryarchaeota, accompanied by reductions in Cyanobacteria, Chloroflexi, Firmicutes, and Planctomycetes with increasing N. Within the 29 minor phyla, N fertilization led to increases in Aquificae, WPS2, Parvarchaeota, AD3, FCPU426, Armatimonadetes, TM7, Chlamydiae, and OD1, along with reductions of Nitrospirae, WS3, Tenericutes, Lentisphaerae, OP3, Synergistetes, Thermotogae, and prokaryotes that could not be reliably assigned to a phylum (classified as Other). [ABSTRACT FROM AUTHOR]

Simple Summary: For the first time in the Baltic countries, small mammal communities were evaluated in commercial orchards and berry plantations to test for the influence of crop type and intensity of agricultural practices. Out of ten species registered in the fruit farms, the most dominant were common vole and striped field mouse, confirming the spread of the latter species in the country. Small mammal diversity and abundance were not dependent on crop type but decreased in line with the intensity of agricultural practices, not being found in the most intensively cultivated farms. Unexpectedly, small mammal diversity in apple orchards exceeded the diversities found in most types of forests and was significantly higher than in crop fields. Small mammals are not only pests but also an important part of agricultural ecosystems. The common vole is a reference species for risk assessment of plant protection products in the European Union, but no data about the suitability of the species in the Baltic countries are present so far. Using the snap-trap line method, we evaluated species composition, abundance, and diversity of small mammal communities in commercial orchards and berry plantations in Lithuania, testing the predictions that (i) compared with other habitats, small mammal diversity in fruit farms is low, and (ii) the common vole is the dominant species. The diversity of small mammals was compared with control habitats and the results of investigations in other habitats. Out of ten small mammal species registered, the most dominant were common vole and striped field mouse. Small mammal diversity and abundance increased in autumn and decreased in line with the intensity of agricultural practices but were not dependent on crop type. In the most intensively cultivated fruit farms, small mammals were not found. The diversity of small mammal communities in fruit farms was significantly higher than in crop fields and exceeded the diversities found in most types of forests except those in rapid succession. [ABSTRACT FROM AUTHOR]