Proteome of spores from biological indicators in sterilization processes: Bacillus pumilus and Bacillus atrophaeus

Bacillus atrophaeus and Bacillus pumilus spores are widely used as biological indicators to assess the effectiveness of decontamination procedures. Spores are intricate, multi-layered cellular structures primarily composed of proteins, which significantly contribute to their extreme resistance. Therefore, conducting a comprehensive proteome analysis of spores is crucial to identify the specific proteins conferring spore resistance. Here, we employed a high-throughput shotgun proteomic approach to compare the spore proteomes of B. atrophaeus DSM675 and B. pumilus DSM492, identifying 1312 and 1264 proteins, respectively. While the overall number of proteins found in both strains is roughly equivalent, a closer examination of a subset of 54 spore-specific proteins revealed noteworthy distinctions. Among these 54 proteins, 23 were exclusively detected in one strain, while others were shared between both. Notably, of the 31 proteins detected in both strains, 10 exhibited differential abundance levels, including key coat layer morphogenetic proteins. The exploration of these 54 proteins, considering their presence, absence, and differential abundance, provides a unique molecular signature that may elucidate the differences in sensitivity/resistance profiles between the two strains.

Species Differences and Tissue Distribution of Heavy Metal Residues in Wild Birds

Birds are useful as bioindicators of metal pollution, but the variety of species and tissue distribution may influence the study of heavy metal burdens in birds. The objective of this study was to determine the levels of heavy metals in wild birds' carcasses to acquire information on species differences and the tissue distribution of metals in wild birds in Thailand. Species differences in metal buildup were observed in the livers and kidneys, but not in the feathers. A significantly higher accumulation of Cd was found in the livers and kidneys of the granivorous birds compared to those in the water birds. In all the groups of birds, the Pb level in the livers (>15 ppm) and feathers (>4 ppm) exceeded the threshold limits, causing potential lead poisoning and disturbing the reproductive success. The Cd accumulation in the kidneys was above 2-8 ppm, indicating increased environmental exposure to Cd in these birds. The Cd, Pb, Ni, Zn, and Fe concentrations in the livers could be estimated using the kidneys, while the Pb level in the liver may be predicted using feathers. Furthermore, water birds' feathers may be potentially appropriate bioindicators for long-term exposure. Research on the origin of metal contamination is needed to reduce the threat of heavy metals to the health of both birds and other wildlife species.

Soil macrofauna communities in Brazilian land-use systems

Background

Soil animal communities include more than 40 higher-order taxa, representing over 23% of all described species. These animals have a wide range of feeding sources and contribute to several important soil functions and ecosystem services. Although many studies have assessed macroinvertebrate communities in Brazil, few of them have been published in journals and even fewer have made the data openly available for consultation and further use. As part of ongoing efforts to synthesise the global soil macrofauna communities and to increase the amount of openly-accessible data in GBIF and other repositories related to soil biodiversity, the present paper provides links to 29 soil macroinvertebrate datasets covering 42 soil fauna taxa, collected in various land-use systems in Brazil. A total of 83,085 georeferenced occurrences of these taxa are presented, based on quantitative estimates performed using a standardised sampling method commonly adopted worldwide to collect soil macrofauna populations, i.e. the TSBF (Tropical Soil Biology and Fertility Programme) protocol. This consists of digging soil monoliths of 25 x 25 cm area, with handsorting of the macroinvertebrates visible to the naked eye from the surface litter and from within the soil, typically in the upper 0-20 cm layer (but sometimes shallower, i.e. top 0-10 cm or deeper to 0-40 cm, depending on the site). The land-use systems included anthropogenic sites managed with agricultural systems (e.g. pastures, annual and perennial crops, agroforestry), as well as planted forests and native vegetation located mostly in the southern Brazilian State of Paraná (96 sites), with a few additional sites in the neighbouring states of São Paulo (21 sites) and Santa Catarina (five sites). Important metadata on soil properties, particularly soil chemical parameters (mainly pH, C, P, Ca, K, Mg, Al contents, exchangeable acidity, Cation Exchange Capacity, Base Saturation and, infrequently, total N), particle size distribution (mainly % sand, silt and clay) and, infrequently, soil moisture and bulk density, as well as on human management practices (land use and vegetation cover) are provided. These data will be particularly useful for those interested in estimating land-use change impacts on soil biodiversity and its implications for below-ground foodwebs, ecosystem functioning and ecosystem service delivery.

New information

Quantitative estimates are provided for 42 soil animal taxa, for two biodiversity hotspots: the Brazilian Atlantic Forest and Cerrado biomes. Data are provided at the individual monolith level, representing sampling events ranging from February 2001 up to September 2016 in 122 sampling sites and over 1800 samples, for a total of 83,085 ocurrences.

Movement of avian predators points to biodiversity hotspots in agricultural landscape

Global agricultural landscapes are witnessing a concerning decline in biodiversity, and this trend is predicted to persist. To safeguard these biodiversity-rich areas, it is crucial to pinpoint hotspots effectively. In doing so, we used various species of avian predators as suitable sentinel animals due to their mobility and dependence on prey diversity and abundance. Between 2019 and 2021, we tracked 62 individuals from four bird of prey species using GPS loggers in Estonian farmland. Dividing the study area into 50 m grids and overlaying them with tracked individuals' locations enabled us to differentiate between hotspots of their activity and control sites. We conducted surveys on amphibian, bird, small mammal and plant abundance and diversity to determine if avian predator activity hotspots correlated with overall biodiversity. Our findings revealed significantly higher diversity and abundance in the surveyed groups within activity hotspots compared to control sites. These hotspots continued to be frequently used by raptors in the subsequent year, albeit not two years later. In conclusion, multispecies GPS telemetry of avian predators emerges as an objective, dependable and spatially accurate biodiversity indicator. With the accumulation of movement data, we anticipate increased interest and adoption of this approach in biodiversity monitoring.

Screening of Phytoplankton Dynamics: Assessing Reservoir Ecosystem Health under Thermal Pollution from an Electrical Power Plant in the Pechora River Basin, European North

For the first time, we investigated species composition, phytoplankton community structure, and hydrochemical parameters in the artificial cooling reservoir of a major thermal power plant (TPP) in northeastern Europe located in the Pechora River basin (Komi Republic). Our research, conducted during June and August, revealed a total of 81 species of algae and cyanobacteria, with cyanobacteria predominating. Among these cyanobacteria and microalgae (Bacillariophyta and Chlorophyta), algae that serve as reliable indicators of water quality were identified. The assessment of water quality based on abundance and species composition of indicator phytoplankton species revealed that the waters of the Pechorskoe Reservoir belong to the III class (β-mesosaprobic or moderately polluted). This indicates that water quality is satisfactory, and the reservoir retains the ability to self-purify. The power plant's discharges heat the surface layers, increasing plankton communities' diversity, abundance, and biomass. Such stable warming in the upper layers throughout the season, uncommon for natural water bodies in the north, results in a slight increase in the trophic status of the studied reservoir, supported by hydrochemical analysis. These results provide valuable information about ecosystem functioning under temperature increasing for predicting changes in the phototrophic biota of small northern reservoirs facing the impacts of climate change.

Lake Avernus Has Turned Red: Bioindicator Monitoring Unveils the Secrets of "Gates of Hades"

Lake Avernus is a volcanic lake located in southern Italy. Since ancient times, it has inspired numerous myths and legends due to the occurrence of singular phenomena, such as coloring events. Only recently has an explanation been found for them, i.e., the recurring color change over time is due to the alternation of cyanobacterial blooms that are a consequence of natural nutrient inputs as well as pollution resulting from human activities. This current report specifically describes the red coloring event that occurred on Lake Avernus in March 2022, the springtime season in this region of Italy. Our innovative multidisciplinary approach, the 'Fast Detection Strategy' (FDS), was devised to monitor cyanobacterial blooms and their toxins. It integrates remote sensing data from satellites and drones, on-site sampling, and analytical/bioinformatics analyses into a cohesive information flow. Thanks to FDS, we determined that the red color was attributable to a bloom of Planktothrix rubescens, a toxin-producing cyanobacterium. Here, we report the detection and identification of 14 anabenopeptins from this P. rubescens strain, seven of which are known and seven are newly reported herein. Moreover, we explored the mechanisms and causes behind this cyclic phenomenon, confirming cyanobacteria's role as reliable indicators of environmental changes. This investigation further validates FDS's effectiveness in detecting and characterizing cyanobacterial blooms and their associated toxins, expanding its potential applications.

Send nudis: An assessment of nudibranch diversity in Sodwana Bay, South Africa

Climate change is posing unprecedented pressure onto marine ecosystems worldwide. This makes it imperative to monitor the effects that are being experienced in these environments. Nudibranchs are benthic marine organisms that possess characteristics that have the potential to act as indicators of change within ecosystems such as coral reefs. Therefore, these species have the ability to provide valuable information on fine-scale changes in environmental conditions. It is thus essential for studies, such as this, to establish baseline analyses from which changes within nudibranch populations can be examined in order to investigate their ability to act as bioindicators. Recommendations can also be made for future sampling procedures through investigating environmental and experimental parameters that influence nudibranch communities. Nudibranch populations were sampled on Two-Mile Reef in Sodwana Bay, South Africa, through SCUBA where individuals were photographed and later identified. Data were collected within a sample-based dataset, as well as by citizen scientists within an incidence-based dataset. Across both datasets, a total of 85 species were identified. Nudibranch populations showed high levels of diversity within an uneven, unstable community. Citizen scientist data provided imperative information to the baseline assessment and, therefore, the inclusion of these data increased the robustness of this study. Environmental and experimental variables investigated did not influence the outcomes of this study and should therefore not be heavily focused on in designing future experiments. Future monitoring studies should continue to record oceanic pH in order to detect any possible changes due to ocean acidification. It is recommended that sampling events should be increased in order to capture all species present in these localities. These events should also encompass an extended temporal scale in order to cover a larger temperature range. Research on bioindicators is essential within today's rapidly changing climate, mainly due to human activities, particularly within an extremely vulnerable habitats such as coral reefs.

The conversion of native savannah into pasturelands does not affect exclusively species diversity: Effects on physiological condition of a highly abundant dung beetle species

Dung beetles are efficient indicators to obtain responses regarding the effects of land use change on biodiversity. Although the biological consequences of Cerrado conversion into pasture have been observed at the assemblage scale, there are no cues regarding the effects of tropical savanna conversion into pasture on physiological condition of dung beetle individuals. In this study, we evaluated whether native and non-native habitats in Cerrado affect the physiological condition and body traits of males and females of Phanaeus palaeno. The individuals were collected from a Cerrado fragment (sensu stricto) and an exotic pasture (Urochloa spp.). Physiological condition was assessed through the estimation of individuals' dry body mass, fat mass, and muscle mass. Body traits were estimated through individual body size and males' horn length. We did not find differences between dung beetle morphological traits between Cerrado and pastures. However, individuals collected in exotic pastures had lower dry mass and fat mass, but higher muscle mass, than in conserved Cerrado. Understanding how the land use change affects individuals' body condition is essential to maintain abundant and healthy populations of dung beetles in human-modified landscapes. Although the estimation of physiological condition is logistically more complex than species body traits, future studies aiming to present complex and finer ecological responses of dung beetles should incorporate physiological data to their approaches.

Caddisflies (Trichoptera) of Protected Calcareous Fen Habitats: Assemblages, Environmental Drivers, Indicator Species, and Conservation Issues

The caddisflies (Trichoptera) of calcareous fen habitats, in contrast to those of other peatland types, have been poorly researched. We thus conducted a two-year study in south-eastern Poland encompassing four types of such habitats-drained and undrained fens and water bodies (pools and ditches) located within the fens-in order to define trichopteran reference assemblages (PCoA), indicator species (IndVal analysis), and the drivers (both natural and those associated with landscape management, including area protection) responsible for caddisfly species distribution (CCA). The most important environmental driver was habitat persistence. Distance-based RDA analysis revealed a distinct pattern in the distribution of species with or without diapause along the persistence gradient. Environmental drivers associated with plants were also crucial for both fens and water bodies. The key factor influencing the caddisfly assemblages of pools and ditches was the use and management of the surrounding land, whereas in the fens, it was the level of area protection. Physical and chemical water parameters had no statistically significant impact on the assemblages. Some factors can be modified by humans (e.g., water level regulation, vegetation, and landscape management) to maintain healthy ecosystems for aquatic insects.

Biogeographical patterns of the soil fungal:bacterial ratio across France

Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.

Changes in Diversity of Silica-Scaled Chrysophytes during Lake-River-Reservoir Transition (Baikal-Angara-Irkutsk Reservoir)

Hydroelectric dams create new ecosystems such as reservoirs. Several hydroelectric dams forming shallow reservoirs were built on the Angara River flowing out of Lake Baikal. The first of them in downstream Angara is Irkutsk Reservoir, with several shallow bays. Since silica-scaled chrysophytes are effective bioindicators for aquatic ecosystems, this paper aimed to determine their distribution, taxonomic structure and species richness in South Baikal and Irkutsk Reservoir, which have different environmental parameters. Thirty-one species were found using scanning and transmission electron microscopy. Only seven of them inhabited South Baikal in June 2023 at 3.66-4.51 °C and pH 7.80-8.24, with Chrysosphaerella baicalensis, Spiniferomonas trioralis f. cuspidata and Mallomonas alpina being prevalent. Only one species (M. alpina) was dominant in Irkutsk Reservoir at all stations at a water temperature of 5.33-11.55 °C and pH 8.10-8.52, alongside three other abundant species, Synura cf. glabra, Mallomonas acaroides and M. crassisquama. The maximum number of species (23) was found in a shallow bay of the reservoir at maximal values of temperature (11.5 °C) and pH (8.57) and minimal values of phosphate and nitrate concentrations during the study. The enrichment of Irkutsk Reservoir in species of silica-scaled chrysophytes was due both to cosmopolitan widespread and polyzonal species as well as to rare boreal, arctic-boreal, and unknown, possibly new species.

Metabolite Profiling of Conifer Needles: Tracing Pollution and Climate Effects

In the face of escalating environmental challenges, understanding the intricate relationship between plant metabolites, pollution stress, and climatic conditions is of paramount importance. This study aimed to conduct a comprehensive analysis of metabolic variations generated through 1H and 13C NMR measurements in evergreen needles collected from different regions with varying pollution levels. Multivariate analyses were employed to identify specific metabolites responsive to pollution stress and climatic factors. Air pollution indicators were assessed through ANOVA and Pearson correlation analyses. Our results revealed significant metabolic changes attributed to geographical origin, establishing these conifer species as potential indicators for both air pollution and climatic conditions. High levels of air pollution correlated with increased glucose and decreased levels of formic acid and choline. Principal component analysis (PCA) unveiled a clear species separation, largely influenced by succinic acid and threonine. Discriminant analysis (DA) confirmed these findings, highlighting the positive correlation of glucose with pollution grade. Beyond pollution assessment, these metabolic variations could have ecological implications, impacting interactions and ecological functions. Our study underscores the dynamic interplay between conifer metabolism, environmental stressors, and ecological systems. These findings not only advance environmental monitoring practices but also pave the way for holistic research encompassing ecological and physiological dimensions, shedding light on the multifaceted roles of metabolites in conifer responses to environmental challenges.

Exploring the Impact of Contaminants of Emerging Concern on Fish and Invertebrates Physiology in the Mediterranean Sea

In this historical context, the Mediterranean Sea faces an increasing threat from emerging pollutants such as pharmaceuticals, personal care products, heavy metals, pesticides and microplastics, which pose a serious risk to the environment and human health. In this regard, aquatic invertebrates and fish are particularly vulnerable to the toxic effects of these pollutants, and several species have been identified as bio-indicators for their detection. Among these, bivalve molluscs and elasmobranchs are now widely used as bio-indicators to accurately assess the effects of contaminants. The study focuses on the catshark Scyliorhinus canicular and on the Mediterranean mussel Mytilus galloprovincialis. The first one is a useful indicator of localised contamination levels due to its exposure to pollutants that accumulate on the seabed. Moreover, it has a high trophic position and plays an important role in the Mediterranean Sea ecosystem. The bivalve mollusc Mytilus galloprovincialis, on the other hand, being a filter-feeding organism, can acquire and bioaccumulate foreign particles present in its environment. Additionally, because it is also a species of commercial interest, it has a direct impact on human health. In conclusion, the increasing presence of emerging pollutants in the Mediterranean Sea is a serious issue that requires immediate attention. Bivalve molluscs and elasmobranchs are two examples of bio-indicators that must be used to precisely determine the effects of these pollutants on the marine ecosystem and human health.

Major drivers of biodiversity loss and their impacts on helminth parasite populations and communities

The world's biodiversity is in peril. The major threats to biodiversity globally are habitat change, overexploitation, climate change, invasive species and pollution. Not only do these stressors impact free-living organisms, but they affect parasitic ones as well. Herein, this perspective examines the potential consequences of these anthropogenic perturbations on helminth populations and communities, with emphasis on significant developments over the past decade. Furthermore, several case studies are examined in more detail for each of these threats to biodiversity. While effects are widespread and diverse, for the most part all these environmental stressors have negative effects on parasite populations and communities. Those parasites with complex life cycles that are trophically transmitted are often more at risk, although larval parasites with a wide host spectrum, and directly transmitted ectoparasites, appear less threatened and may even benefit. However, differential effects on hosts and parasites, on parasite life cycle stages and on host-parasite interactions made specific predictions difficult and context-dependent. Experimental laboratory and mesocosm studies on specific parasites that test effects on the different life cycle stages, hosts and host-parasite interactions, permitting the determination of net effects of an environmental stressor, yield insightful and sometimes counterintuitive results, although they remain a simplification of real-world complexity. Recent advances in the use of parasites as bioindicators of effects also are discussed.

A first insight into haemocytes of Pinctada imbricata radiata: A morpho-functional characterization

The pearl oyster Pinctada imbricata radiata (Leach, 1814), from the Pacific Ocean, was one of the first species to reach via Suez the Mediterranean, colonizing the eastern basin and recently spreading to the western. The species showed to be able to adapt to a wide range of climatic, hydrological, and ecological conditions. Since 2000 it reached the Strait of Messina, where is now infesting the transitional waters of the oriented natural reserve "Laguna di Capo Peloro." Due to such resistance and adaptation ability, various assays were performed. Haemocyte morpho-functional aspects were evaluated in haemolymph samples fixed with 1% and 2% glutaraldehyde for optical and electron microscopy (TEM). The following assays were carried out: cell characterization using several dyes, detection of intra- and extracellular lipids, the capability of phagocytosis using the yeast Saccharomyces cerevisiae and to produce superoxide anion (O^2- ). Detection of several enzymes, such as acid and alkaline phosphatase, arylsulfatase, chloro-acetylesterase and β-glucuronidase was also assessed. Cell count was demonstrated to be abundant with a mean of 8.263 × 106 mm²  ± 0.935 × 106 (SD). Two main cell populations were noticed: granulocytes and hyalocytes, both competent for phagocytosis, to produce O^2- , and characterized by lipids. Based on the granule analysis, enzymatic activity was also demonstrated. The observations under TEM confirmed all the results obtained. This study supports the hypothesis that P. imbricata radiata can be usefully employed as a model organism in environmental biomonitoring. Moreover, since the species represent potential threats to native species and ecosystems, further insights into its biological adaptations in invaded ecosystems are recommended.

Microplastics in Terrestrial Domestic Animals and Human Health: Implications for Food Security and Food Safety and Their Role as Sentinels

Terrestrial domestic animals are exposed to microplastics, therefore, contaminating the food chain, in the case of livestock, or acting as sentinels for human exposure, in the case of companion animals. The aim of this review was to address the importance of terrestrial domestic animals on human exposure to microplastics. Animal products may already show some microplastics contamination, which may occur during their lifetime, possibly also compromising productivity, and during processing, originating from equipment and packaging. Moreover, release of microplastics in animal feces (or manure) leads to the contamination of agricultural fields, with possible impacts and internalization in plants. Therefore, microplastics pose a threat to food security, compromising food productivity, and food safety, by being a foreign material found in animal products. Conversely, in urban environments, companion animals (cats and dogs) may be relevant sentinels for human exposure. While oral exposure may vary in pets compared to humans, due to indiscriminate ingestion and chewing or licking behaviors, airborne exposure is likely to be a good indicator for human exposure. Therefore, future studies should address the importance of terrestrial domestic animals for human exposure of microplastics, both in the food chain and as sentinels for environmental exposure.

Relationship between serum thyroid hormones and their associated metabolites, and gene expression bioindicators in the back skin of Rana [Lithobates] catesbeiana tadpoles and frogs during metamorphosis

Anuran metamorphosis is characterized by profound morphological changes including remodeling of tissues and organs. This transition is initiated by thyroid hormones (THs). However, the current knowledge of changing levels of THs during metamorphosis relies on pooled samples using methods known for high variability with sparse reporting of measured variation. Moreover, establishing a clear linkage between key gene expression bioindicators and TH levels throughout the metamorphic process is needed. Using state-of-the-art ultra-high performance liquid chromatography isotope-dilution tandem mass spectrometry, we targeted 12 THs and metabolites in the serum of Rana [Lithobates] catesbeiana (n=5-10) across seven distinct postembryonic stages beginning with premetamorphic tadpoles (Gosner stage 31-33) and continuing through metamorphosis to a juvenile frog (Gosner stage 46). TH levels were related to TH-relevant gene transcripts (thra, thrb, and thibz) in back skin of the same individual animals. Significant increases from basal levels were observed for thyroxine (T4) and 3,3',5-triiodothyronine (T3) at Gosner stage 41, reaching maximal levels at Gosner stage 44 (28 ± 10 and 2.3 ± 0.5 ng/mL, respectively), and decreasing to basal levels in juvenile frogs. In contrast, 3,5-diiodothyronine (T2) increased significantly at Gosner stage 40 and was maintained elevated until stage 44. While thra transcript levels remained constant and then decreased at the end of metamorphic climax, thrb and thibz were induced to maximal levels at Gosner stage 41, followed by a decrease to basal levels in the froglet. This exemplifies the exquisite timing of events during metamorphosis as classic early response genes are transcribed in anticipation of peak TH concentrations. The distinct T2 concentration profile suggests a biological role of this biomolecule in anuran postembryonic development and an additional aspect that may be a target of anthropogenic chemicals that can disrupt anuran metamorphosis and TH signalling. Hence, as a second aim of the study, we set out to find additional bioindicators of metamorphosis, which can aid future investigations of developmental disruption. Using a sensitive nanoLC-Orbitrap system an untargeted analysis workflow was applied. Among 6,062 endogenous metabolites, 421 showed metamorphosis-dependent concentration dynamics. These potential bioindicators included several carnitines, prostaglandins and some steroid hormones.

Impact of different environmental pollution processes on bacterial key-indicators in tropical rivers: scoping review

Freshwater ecosystems are an essential resource for human use and natural populations, but they are exposed to different sources of man-made pollution. This study analyses how different environmental pollution processes influence the structure of bacterial communities in tropical rivers. A scoping review was performed to characterize the bacterial communities in freshwater ecosystems in tropical regions that have been reported to be associated with pollution of different kinds. The statistical analyses allowed us to categorize the genera found into three large groups (pollution generalists, middle types, and pollution specialists) according to the types of pollutants with which they were associated. The results show that Escherichia has a greater association with fecal contamination, while Enterococcus is more associated with domestic wastewater and organic and synthetic chemicals. The present study proposes Streptomyces as a potential indicator of waters with microbial contamination, as well as some other genera as possible indicators of waters with heavy metal contamination.

Roe Deer (Capreolus capreolus) Hair as a Bioindicator for the Environmental Presence of Toxic and Trace Elements

The return to pasture use as an alternative to intensive livestock farming implies some risks with the lack or the excessive presence of potentially toxic elements; in this regard, wild animals have been used as bioindicators for decades. Thus, the purpose of this study is quantifying Cu, Cr, Mn, Zn, Se, As, Cd, Ni, Pb, Al, Fe, and Mg in fur from roe deer and understanding if it is a valid bioindicator tool. Hair was collected from 39 hunted roe deer and divided by age (<36 months old/≥36 months old), sex (male/female), and area of origin (urbanized/rural area). The mean concentrations of Fe, Mg, Mn, Al, Cr, and Pb were higher (p < 0.05) in the urbanized group; the mean levels of Mg and Cr were higher (p < 0.05) in older animals; and Cu, Fe, Mg, Cd, and Cr showed a higher accumulation in females. Our findings showed an age-related variation of elements, with higher concentrations in adult animals and females. In conclusion, our findings prove that hair is a valid matrix for this type of survey, and wild animals are good bioindicators for monitoring the presence of trace elements in pastures.

Ecological Preferences and Indication Potential of Freshwater Bryophytes-Insights from Croatian Watercourses

A comprehensive survey of Croatian watercourses covering the whole of the national territory and investigating inherent watercourse heterogeneity was conducted to explore the ecological responses of the most frequent freshwater bryophytes with respect to water chemistry variables and land use within the catchment area. Direct multivariate ordination (CCA) of vegetation data paired with 18 environmental variables revealed that freshwater bryophytes and their assemblages were segregated along the gradients of water chemistry and the proportion of natural and urban area within the catchment. Generalized additive models (GAM) were employed to explore the ecological responses of individual species. The results showed that most of the investigated species preferred natural, clean, well-oxygenated watercourses, with low nutrient and organic matter content, as well as with low electrical conductivity. Species such as Palustriella falcata, Eucladium vertcillatum, Dichodontium flavescens and Jungermannia atrovirens had narrow ecological niches and were restricted to pristine watercourses, while the most frequent and widely distributed species, such as Fontinalis antipyretica, Rhynchostegium riparioides, Cratoneuron filicinum, Fissidens crassipes, Cinclidotus fontinaloides and C. riparius, had a wide ecological tolerance. Riccia fluitans and Leptodyctium riparium had wide ecological ranges, but with optima in hypereutrophic waters with high nutrient and organic content, as well as high electrical conductivity. Furthermore, these two species were frequently associated with a high share of intensive agriculture and a low share of natural land within the catchment.

Using Trait-Based Approaches to Assess the Response of Epedaphic Collembola to Organic Matter Management Practices: A Case Study in a Rubber Plantation in South-Eastern Côte d'Ivoire

We used trait-based approaches to reveal the functional responses of springtails communities to organic matter inputs in a rubber plantation in Côte d’Ivoire. Pitfall traps were used to sample springtails in each practice. The results showed that the total abundance of springtails increased significantly with the amount of organic matter (R0L0 < R2L1). Larger springtails (body length, furca and antennae) were observed in plots with high organic matter. Practices with logging residues and legume recorded the highest functional richness. The principal coordinate analysis showed different functional composition patterns between practices with logging residues (R1L1 and R2L1) and those without inputs (R0L0 and R0L1). This difference in functional composition (PERMANOVA analysis) was related to the effect of practices. These results highlight the pertinence of the functional trait approach in the characterization of springtail communities, a bioindicator of soil health, for organic matter management practice.

The multi-isotope biogeochemistry (S, C, N and Pb) of Hypogymnia physodes lichens: air quality approach in the Świętokrzyski National Park, Poland

The isotope biogeochemistry of bioindicators has widely demonstrated its added value in environmental issues by allowing to precisely identify sources of contamination. Most of the studies are based on studying one or two isotope systematics. Here, we are presenting an innovative multi-proxy approach that combines chemistry with both stable (C, S, N) and radiogenic (Pb) isotope systematics. Using Hypogymnia physodes bioindicators, we evaluated air quality in the complex environment of the Świętokrzyski National Park (ŚNP, Poland) with the ultimate objective of isotopically identifying the sources responsible for the observed contamination. Combining the isotope systematics showed that home heating is a major source of contamination in winter, whereas the contribution of road traffic increases during the summer. Pb isotope ratios identified industrial activities as the major source of this metal in the atmosphere.

Blood biomarkers in white stork (Ciconia ciconia) nestlings show different responses in several areas of Croatia

White stork nestlings can provide quantitative data on the quality of the environment, as they are dependent on their parents that provide locally foraged food. Blood was sampled from the brachial vein (n = 109) and the sampling was performed in parallel with ringing during breeding season 2020 from five areas in eastern Croatia: Lonjsko polje, Jelas polje, Slavonski Brod-east, Podunavlje, and Donje Podravlje. In the present study, for the first time in Croatia, the following enzymatic biomarkers were assessed in white stork nestlings: activities of acetylcholinesterase (AChE), carboxylesterase (CES), glutathione S-transferase (GST), and glutathione reductase (GR), as well as nonenzymatic biomarkers: levels of glutathione (GSH) and reactive oxygen species (ROS). All endpoints were measured in two blood fractions: plasma and a postmitochondrial fraction (S9). Nestlings from Podunavlje and Donje Podravlje, areas known for intensive agriculture, showed lower AChE and CES activity when compared to the other investigated areas, indicating the presence of inhibitory xenobiotics. Higher oxidative stress was observed in Slavonski Brod-east, an area surrounded by metal and engineering industry, and Podunavlje compared to the other sampling areas. Hence, this study shows the impact of pollutants from the surrounding metal, petroleum, and agricultural industry might have on the biomarkers in white stork nestlings, which are often seen as early-warning signals.

Bee Products: A Representation of Biodiversity, Sustainability, and Health

Biodiversity strengthens the productivity of any ecosystem (agricultural land, forest, lake, etc.). The loss of biodiversity contributes to food and energy insecurity; increases vulnerability to natural disasters, such as floods or tropical storms; and decreases the quality of both life and health. Wild and managed bees play a key role in maintaining the biodiversity and in the recovery and restoration of degraded habitats. The novelty character of this perspective is to give an updated representation of bee products’ biodiversity, sustainability, and health relationship. The role of bees as bioindicators, their importance in the conservation of biodiversity, their ecosystem services, and the variety of the bee products are described herein. An overview of the main components of bee products, their biological potentials, and health is highlighted and detailed as follows: (i) nutritional value of bee products, (ii) bioactive profile of bee products and the related beneficial properties; (iii) focus on honey and health through a literature quantitative analysis, and (iv) bee products explored through databases. Moreover, as an example of the interconnection between health, biodiversity, and sustainability, a case study, namely the “Cellulose Park”, realized in Rome (Italy), is presented here. This case study highlights how bee activities can be used to assess and track changes in the quality of agricultural ecosystems—hive products could be valid indicators of the quality and health of the surrounding environment, as well as the changes induced by the biotic and abiotic factors that impact the sustainability of agricultural production and biodiversity conservation in peri-urban areas.

Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956

Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.

Environmental controls on butterfly occurrence and species richness in Israel: The importance of temperature over rainfall

Butterflies are considered important indicators representing the state of biodiversity and key ecosystem functions, but their use as bioindicators requires a better understanding of how their observed response is linked to environmental factors. Moreover, better understanding how butterfly faunas vary with climate and land cover may be useful to estimate the potential impacts of various drivers, including climate change, botanical succession, grazing, and afforestation. It is particularly important to establish which species of butterflies are sensitive to each environmental driver. The study took place in Israel, including the West Bank and Golan Heights. To develop a robust and systematic approach for identifying how butterfly faunas vary with the environment, we analyzed the occurrence of 73 species and the abundance of 24 species from Israeli Butterfly Monitoring Scheme (BMS-IL) data. We used regional generalized additive models to quantify butterfly abundance, and generalized linear latent variable models and generalized linear models to quantify the impact of temperature, rainfall, soil type, and habitat on individual species and on the species community. Species richness was higher for cooler transects, and also for hilly and mountainous transects in the Mediterranean region (rendzina and Terra rossa soils) compared with the coastal plain (Hamra soil) and semiarid northern Jordan Vale (loessial sierozem soil). Species occurrence was better explained by temperature (negative correlation) than precipitation, while for abundance the opposite pattern was found. Soil type and habitat were insignificant drivers of occurrence and abundance. Butterfly faunas responded very strongly to temperature, even when accounting for other environmental factors. We expect that some butterfly species will disappear from marginal sites with global warming, and a large proportion will become rarer as the region becomes increasingly arid.

The applicability of the Sludge Biotic Index in a facility treating sugar refinery effluents and municipal wastewater

Protozoans are valuable indicators of the wastewater biological treatment process and are used in a variety of water resource recovery facilities (WRRF). The aim of this study was to determine the applicability of the Sludge Biotic Index (SBI) as an indicator of activated sludge purification efficiency during different influent loadings: municipal wastewater (M) and municipal wastewater combined with industrial wastewater from a sugar refinery (M + S). Despite the higher organic load during the M + S period, purification efficiency was higher for BOD₅ , compared with the M period. SBI values were high during both periods, indicating stable sludge, excellent biological activity, and good to very good performance. According to the share of indicator taxa, better conditions of activated sludge were found during the M + S period. Protozoan abundance differed between the two study periods, as well as purification efficiency for some parameters. Certain taxa showed a significant correlation with purification efficiency for specific parameters. Although SBI is a useful tool for estimating activated sludge health, it should be used in combination with additional indicator metrics and/or a species-specific approach. PRACTITIONER POINTS: Activated sludge can have high purification efficiency during the co-treatment of industrial and municipal wastewater. The Sludge Biotic Index is applicable as an indicator of activated sludge condition during the treatment of municipal and sugar refinery wastewaters. A combination of indicators and a species-specific approach can give better estimation of the health of activated sludge.

Aquatic Macrophytes Occurrence in Mediterranean Farm Ponds: Preliminary Investigations in North-Western Sicily (Italy)

Mediterranean wetlands are severely affected by habitat degradation and related loss of biodiversity. In this scenario, the wide number of artificial farm ponds can play a significant role in the biodiversity conservation of aquatic flora. In the present contribution we show the preliminary results of a study on Mediterranean farm ponds of north-western Sicily (Italy), aimed to investigating the environmental factors linked to the occurrence of submerged macrophytes (vascular plants and charophytes). We studied the aquatic flora of 30 ponds and determined the chemical and isotopic composition of their water bodies on a subset of the most representative 10 sites. Results show that (1) farm ponds host few but interesting species, such as Potamogeton pusillus considered threatened at regional level; (2) Chara vulgaris, C. globularis and P. pusillus behave as disturbance-tolerant species, occurring both in nitrates-poor and nitrates-rich waters, whereas Stuckenia pectinata and Zannichellia palustris occur only in nitrates-poor waters. Although farm ponds are artificial and relatively poor habitats, these environments seem to be important for the aquatic flora and for the conservation of the local biodiversity, and can give useful information for the use of macrophytes as bioindicators in the Mediterranean area.

Treatment of effluent containing thiamethoxam and efficiency evaluation of toxicity reduction

The treatment of seeds using pesticides is a widely employed technique that generates effluents with high contamination potential. In the present study, our objective was to characterize and evaluate the toxicity of washing wastewater from corn seed treaters that contained the pesticide thiamethoxam. Effluents were treated by adsorption using several adsorbent materials, namely activated vegetable carbon, corn straw, and soybean hulls, different pH, and distinct mass concentrations for each material. The activated carbon promoted a greater reduction in the chemical oxygen demand (COD). In the coagulation-flocculation treatment, with ferric chloride (FeCl₃) and poly-aluminum chloride (PAC), and using factorial planning with the concentration of FeCl₃ and the sedimentation time as independent variables, the best COD removal occurred with 850 mg L^-1 FeCl₃ and 120 min sedimentation. The treatments C (coagulation), CACA (coagulation followed by adsorption with activated vegetable carbon), and CACS (coagulation followed by adsorption with corn straw) presented the most efficacious physicochemical parameter changes. The CACA treatment showed the best result for removing thiamethoxam. Nevertheless, raw and treated effluents showed high toxicity to the bioindicators Artemia salina L. (immobility/mortality test), Eisenia fetida (avoidance test), and Allium cepa L. (cytotoxicity test). The effluents also produced a mutagenic effect for A. cepa, due to the presence of chromosomal changes. The results demonstrated the risk that this effluent can cause to the environment. These data highlight the need to investigate new technologies to reduce the physicochemical parameters, the agrochemical levels, and, in particular, the final effluent toxicity.

Effects of Landscape Patterns and Their Changes to Species Richness, Species Composition, and the Conservation Value of Odonates (Insecta)

Simple Summary

In this study, we aimed to evaluate the relationship between human transformations of land use/land cover and adult dragonfly diversity. Based on previous studies, we assumed that with increasing rates of environmental degradation and declining levels of naturalness, the representation of species with high conservation value would significantly decrease, which, however, would not affect the regional alpha diversity. Our results have shown that species richness did not correspond to habitat naturalness, but the occurrence of endangered species was significantly positively correlated with increasing naturalness; thus, habitat degradation and/or the level of naturalness significantly affected species composition, while species richness remained unchanged. Based on our analyses, it is evident that most natural areas, and therefore the least affected areas, provide suitable conditions for the largest number of endangered species. This research extends our knowledge about the impact of human activities, especially the conversion and degradation of habitats, on the composition of odonates and freshwater animals at the regional scale.

Abstract

Understanding the impact of the changing proportion of land-use patterns on species diversity is a critical issue in conservation biology, and odonates are good bioindicators of these environmental changes. Some freshwater ecosystems that have been modified due to human activities can serve as important secondary habitats for odonate assemblages; however, the majority of studies addressing the value of secondary habitats in industrial and urban areas for adult dragonfly diversity have been limited to the local scale, and the value of such habitats for gamma diversity is still unclear. The aim of this study was to determine the relationship between human transformations of land use/land cover and dragonfly diversity. We interpolated the information based on dragonfly occurrence per grid cell and land cover data, indicating naturalness and degradation in 677 grid cells in the Czech Republic. Species richness did not correspond to habitat naturalness, but the occurrence of endangered species was significantly positively correlated with increasing naturalness; thus, habitat degradation and/or the level of naturalness significantly affected species composition, while species richness remained unchanged. Threatened species that occur predominantly in natural areas and threatened species with a dominant occurrence in degraded squares were also separated, which indicated that the conservation of the latter should be prioritised.

Bacterial Communities in Concrete Reflect Its Composite Nature and Change with Weathering

Concrete is an extreme but common environment and is home to microbial communities adapted to alkaline, saline, and oligotrophic conditions. Microbes inside the concrete that makes up buildings or roads have received little attention despite their ubiquity and capacity to interact with the concrete. Because concrete is a composite of materials which have their own microbial communities, we hypothesized that the microbial communities of concrete reflect those of the concrete components and that these communities change as the concrete ages. Here, we used a 16S amplicon study to show how microbial communities change over 2 years of outdoor weathering in two sets of concrete cylinders, one prone to the concrete-degrading alkali-silica reaction (ASR) and the other having the risk of the ASR mitigated. After identifying and removing taxa that were likely laboratory or reagent contaminants, we found that precursor materials, particularly the large aggregate (gravel), were the probable source of ∼50 to 60% of the bacteria observed in the first cylinders from each series. Overall, community diversity decreased over 2 years, with temporarily increased diversity in warmer summer months. We found that most of the concrete microbiome was composed of Proteobacteria, Firmicutes, and Actinobacteria, although community composition changed seasonally and over multiyear time scales and was likely influenced by environmental deposition. Although the community composition between the two series was not significantly different overall, several taxa, including Arcobacter, Modestobacter, Salinicoccus, Rheinheimera, Lawsonella, and Bryobacter, appear to be associated with ASR.

IMPORTANCE Concrete is the most-used building material in the world and a biologically extreme environment, with a microbiome composed of bacteria that likely come from concrete precursor materials, aerosols, and environmental deposition. These microbes, though seeded from a variety of materials, are all subject to desiccation, heating, starvation, high salinity, and very high pH. Microbes that survive and even thrive under these conditions can potentially either degrade concrete or contribute to its repair. Thus, understanding which microbes survive in concrete, under what conditions, and for how long has potential implications for biorepair of concrete. Further, methodological pipelines for analyzing concrete microbial communities can be applied to concrete from a variety of structures or with different types of damage to identify bioindicator species that can be used for structural health monitoring and service life prediction.

Fresh-Water Mollusks as Biomonitors for Ecotoxicity of Nanomaterials

The use of different nanoparticles (NPs) is growing every year since discoveries of their unique properties. The wide use of nanomaterials has raised concerns about their safety and possible accumulation in the aquatic environment. Mussels are being considered as one of the most suitable organisms for bioaccumulation monitoring. Within our study, we focused on developing the method that can be applied in field studies of ecotoxicity and can be nondestructive and informative at early times of exposure, while at the same time being based on changes of physiological parameters of fresh water mussels. The changes in the cardiovascular and neural systems of mollusks (Anodonta anatina and Unio tumidus) were measured as biomarkers of toxic effects. Different monometallic and bimetallic NPs, silicon NPs with various ligands were applied as test substances. Changes in cardiovascular and neural functions were in good correlation with accumulation tests for all tested NPs.

Quantification of the covariation of lake microbiomes and environmental variables using a machine learning-based framework

It is known that microorganisms are essential for the functioning of ecosystems, but the extent to which microorganisms respond to different environmental variables in their natural habitats is not clear. In the current study, we present a methodological framework to quantify the covariation of the microbial community of a habitat and environmental variables of this habitat. It is built on theoretical considerations of systems ecology, makes use of state-of-the-art machine learning techniques and can be used to identify bioindicators. We apply the framework to a data set containing operational taxonomic units (OTUs) as well as more than twenty physicochemical and geographic variables measured in a large-scale survey of European lakes. While a large part of variation (up to 61%) in many environmental variables can be explained by microbial community composition, some variables do not show significant covariation with the microbial lake community. Moreover, we have identified OTUs that act as "multitask" bioindicators, i.e., that are indicative for multiple environmental variables, and thus could be candidates for lake water monitoring schemes. Our results represent, for the first time, a quantification of the covariation of the lake microbiome and a wide array of environmental variables for lake ecosystems. Building on the results and methodology presented here, it will be possible to identify microbial taxa and processes that are essential for functioning and stability of lake ecosystems.

Contamination of polychlorinated biphenyls in honey from the Brazilian state of Rio Grande do Sul

Persistent organic pollutants are characterised by their chemical structure, environmental persistence and toxicity to human and wildlife populations. The production of these chemicals is regulated and restricted. However, they continue to be detected in the environment. In this study, the occurrence of 11 congeners of polychlorinated biphenyls (PCBs 28, 52, 77, 81, 101, 118, 126, 138, 153, 169, and 180) was investigated in 90 honey samples produced in the Brazilian state of Rio Grande do Sul. The samples were from different municipalities, production systems and floral origins. Extraction was performed using the modified QuEChERS method (Quick, Easy, Cheap, Effective, Rugged and Safe) followed by gas chromatography with micro-electron capture detector. The results showed the presence of four congeners (PCBs 28, 77, 81, 101) in 15 honey samples confirming the environmental contamination in Southern Brazil. Among the contaminated samples, no significant differences were identified regarding the production system and floral origin.

Monitoring of Nitrification in Chloraminated Drinking Water Distribution Systems With Microbiome Bioindicators Using Supervised Machine Learning

Many drinking water utilities in the United States using chloramine as disinfectant treatment in their drinking water distribution systems (DWDS) have experienced nitrification episodes, which detrimentally impact the water quality. Identification of potential predictors of nitrification in DWDS may be used to optimize current nitrification monitoring plans and ultimately helps to safeguard drinking water and public health. In this study, we explored the water microbiome from a chloraminated DWDS simulator operated through successive operational schemes of stable and nitrification events and utilized the 16S rRNA gene dataset to generate high-resolution taxonomic profiles for bioindicator discovery. Analysis of the microbiome revealed both an enrichment and depletion of various bacterial populations associated with nitrification. A supervised machine learning approach (naïve Bayes classifier) trained with bioindicator profiles (membership and structure) were used to classify water samples. Performance of each model was examined using the area under the curve (AUC) from the receiver-operating characteristic (ROC) and precision-recall (PR) curves. The ROC- and PR-AUC gradually increased to 0.778 and 0.775 when genus-level membership (i.e., presence and absence) was used in the model and increased significantly using structure (i.e., distribution) dataset (AUCs = 1.000, p < 0.01). Community structure significantly improved the predictive ability of the model beyond that of membership only regardless of the type of data (sequence- or taxonomy-based model) we used to represent the microbiome. In comparison, an ATP-based model (bulk biomass) generated a lower AUCs of 0.477 and 0.553 (ROC and PR, respectively), which is equivalent to a random classification. A combination of eight bioindicators was able to correctly classify 85% of instances (nitrification or stable events) with an AUC of 0.825 (sensitivity: 0.729, specificity: 0.894) on a full-scale DWDS test set. Abiotic-based model using total Chlorine/NH₂Cl and NH₃ generated AUCs of 0.740 and 0.861 (ROC and PR, respectively), corresponding to a sensitivity of 0.250 and a specificity of 0.957. The AUCs increased to > 0.946 with the addition of NO₂^– concentration, which is indicative of nitrification in the DWDS. This research provides evidence of the feasibility of using bioindicators to predict operational failures in the system (e.g., nitrification).

Biomonitoring of Polycyclic Aromatic Hydrocarbon Deposition in Greenland Using Historical Moss Herbarium Specimens Shows a Decrease in Pollution During the 20th Century

Although most point sources of persistent organic pollutants (POPs), including polycyclic aromatic hydrocarbons (PAHs), are at lower latitudes, the Arctic region is contaminated. In particular, PAHs now dominate the POP body burden of the region's marine biota at the lower trophic levels. Greenlandic Inuits have the most elevated levels of POPs in their blood compared to any other population, due to their consumption of seal meat and other marine mammals. PAHs, the by-products of the incomplete combustion of petroleum products, are known carcinogens and have been shown to affect the immune system, reproduction, endocrine functions, and the nervous system. With industrial activities and climate change set to increase local PAH emissions, it is paramount to document changes in atmospheric PAH deposition to further investigate PAH exposure in the region and attribute contaminations to their sources. As a measure of atmospheric pollution, we sampled bryophyte herbarium specimens of three common and widespread species collected in Greenland between the 1920s and 1970s after which time new collections were not available. They were analyzed for 19 PAHs using GC-MS (gas chromatography mass spectrometry). The presence of more low-molecular-weight PAHs than high-molecular-weight PAHs is evidence that the PAH contamination in Greenland is due to long-range transport rather than originating from local sources. The results show peaks in PAH atmospheric deposition in the first part of the 19th century followed by a trend of decrease, which mirror global trends in atmospheric pollution known from those periods. PAHs associated with wood and fossil-fuel combustion decrease in the 1970s coinciding with the disappearance of charcoal pits and foundries in Europe and North America, and a shift away from domestic heating with wood during the 19^th century. The results highlight the value of bryophytes as bioindicators to measure PAH atmospheric pollution as well as the unrealized potential of herbaria as historical records of environmental change.

Wild Micromammals as Bioindicators of Antibiotic Resistance in Ecopathology in Northern Italy

Antimicrobial resistance (AMR) is an increasing threat to human health and an important issue also in the natural environment. For this study, an ecopathological approach was applied to the monitoring of the antimicrobial resistance in the province of Parma, Northern Italy. Fourteen monitoring sites and seventy-four faecal samples from four species of wild micromammals (Apodemus sylvaticus, Microtus savii, Mus domesticus and Suncus etruscus) were collected. Samples were subjected to bacteriological examination and antimicrobial susceptibility testing. Antibiotics belonging to 13 different antibiotic classes were tested. Collected data showed a prevalence of multi-drug resistant (MDR) strains of 55.13% and significant differences in the prevalence of MDR strains among the different micromammal species, while sex, age and anthropization level did not significantly affected MDR strains prevalence. Moreover, a high prevalence of bacterial strains resistant to colistin (95%), gentamicin (87%) and amikacin (83%) was observed. To our knowledge, this is the first report on antibiotic resistance in wild micromammals in the province of Parma.

Effect of Sporulation Conditions Following Submerged Cultivation on the Resistance of Bacillus atrophaeus Spores against Inactivation by H2O2

The resistance formation of spores in general and of Bacillus atrophaeus in particular has long been the focus of science in the bio-defense, pharmaceutical and food industries. In the food industry, it is used as a biological indicator (BI) for the evaluation of the inactivation effects of hydrogen peroxide in processing and end packaging lines’ sterilization. Defined BI resistances are critical to avoid false positive and negative tests, which are salient problems due to the variable resistance of currently available commercial BIs. Although spores for use as BIs have been produced for years, little is known about the influence of sporulation conditions on the resistance as a potential source of random variability. This study therefore examines the dependence of spore resistance on the temperature, pH and partial oxygen saturation during submerged production in a bioreactor. For this purpose, spores were produced under different sporulation conditions and their resistance, defined by the D-value, was determined using a count reduction test in tempered 35% liquid hydrogen peroxide. The statistical analysis of the test results shows a quadratic dependence of the resistance on the pH, with the highest D-values at neutral pH. The sporulation temperature has a linear influence on the resistance. The higher the temperature, the higher the D-value. However, these factors interact with each other, which means that the temperature only influences the resistance when the pH is within a certain range. The oxygen partial pressure during sporulation has no significant influence. Based on the data obtained, a model could be developed enabling the resistance of BIs to be calculated, predicted and standardized depending on the sporulation conditions. BI manufacturers could thus produce BIs with defined resistances for the validation of sterilization effects in aseptic packaging/filling lines for the reliable manufacture of shelf-stable and safe food products.

Response of aquatic microbial communities and bioindicator modelling of hydraulic fracturing flowback and produced water

The response of microbial communities to releases of hydraulic fracturing flowback and produced water (PW) may influence ecosystem functions. However, knowledge of the effects of PW spills on freshwater microbiota is limited. Here, we conducted two separate experiments: 16S rRNA gene sequencing combined with random forests modelling was used to assess freshwater community changes in simulated PW spills by volume from 0.05% to 50%. In a separate experiment, live/dead cell viability in a freshwater community was tested during exposure to 10% PW by volume. Three distinct patterns of microbial community shifts were identified: (i) indigenous freshwater genera remained dominant in <2.5% PW, (ii) from 2.5% to 5% PW, potential PW organic degraders such as Pseudomonas, Rheinheimera and Brevundimonas became dominant, and (iii) no significant change in the relative abundance of taxa was observed in >5% PW. Microbial taxa including less abundant genera such as Cellvibrio were potential bioindicators for the degree of contamination with PW. Additionally, live cells were quickly damaged by adding 10% PW, but cell counts recovered in the following days. Our study shows that the responses of freshwater microbiota vary by spill size, and these responses show promise as effective fingerprints for PW spills in aquatic environments.

Environmental Distribution of AR Class 1 Integrons in Upper Adige River Catchment (Northern Italy)

The source of antibiotic residuals can be directly related to the presence of municipal or industrial wastewater and agricultural activities. Antibiotics can trigger the dissemination of antibiotic resistance genes within bacterial communities. The mobile genetic elements Class 1 integrons (intl1 region) has been already found to be correlated with a wide range of pollutants (i.e., antibiotics, heavy metals), and hence, it has been proposed as a proxy for environmental health. This study aimed to assess the presence of intl1 in different environmental matrices, including agricultural and forest soils, freshwater and unpolluted sediments in the upper Adige River catchment (N Italy), in order to identify the spread of pollutants. Intl1 was detected by direct PCR amplification at different frequencies. The urban and agricultural areas revealed the presence of intl1, except for apple orchards, where it was below the detection limit. Interestingly, intl1 was found in a presumed unpolluted environment (glacier moraine), maybe because of the high concentration of metal ions in the mineral soil. Finally, intl1 was absent in forest fresh-leaf litter samples and occurred with low rates in soil. Our results provide new data in supporting the use of intl1 to detect the environmental health of different land-use systems.

Evaluation of acute toxicity of vinasse by means of Daphnia magna and Aliivibrio fischeri: a comparative study

In the bioethanol industry, per liter of the produced alcohol 9 to 14 liters of vinasse are obtained as a byproduct. If the vinasse is directly shed into bodies of water without an adequate treatment, it may have negative effects on the existing biota and human health due to its high turbidity and color, low pH and high content of organic material. The purpose of this study was to assess the acute toxicity of vinasse by means of a rapid test with Aliivibrio fischeri and compare it with a standard immobilization assay with Daphnia magna. The standard assay of D. magna by means of its EC₅₀ of 4.7% showed that organism was more sensitive to the contaminant, in comparison with the 69.6% obtained with the A. fischeri which suggests that it should be continuesly used as one of the organisms of first choice for the evaluation of the acute toxicity of this effluent.

Higher plants as bioindicators of metal contamination from Shangdong abandoned karst bauxite, southwestern China

Bauxite mining on karst generates numerous ecological and environmental problems, including metal pollution, water and soil erosion and destruction of vegetation. Among these, the most important environmental problem is soil metal pollution. Higher plants have a great ability to adsorb metals and can be used as biological indicators. However, the study of bioindicators for soil contamination in karst bauxite is not clear. Plants and their soil were collected from an abandoned karst bauxite area at Shangdong, Guizhou Province, southwestern China. Plants were collected and identified as Pteris vittata, Pinus massoniana, Miscanthus floridulus, Coriaria nepalensis, Artemisia argyi and Senecio scandens. The content of metals in plant roots were in the order: P. vittata > M. floridulus > C. nepalensis, other plants roots had no consistent pattern. Concentrations of metal in plants (P. vittata and M. floridulus) and soil were: soil > root > leaf > stem. Levels of metals in soil samples easily exceeded background values, indicating that soil had been contaminated. Al and Fe were highest in soil samples of P. vittata, with a good correlation. Results show that the metal content determined in plants is relatively high, particularly in P. vittata. Data also suggest that P. vittata colonies were able to tolerate and accumulate high levels of metal elements, which evidences their suitability for use as bioindicatord of soil metal contamination caused by mining activities.

Soil Health and Arthropods: From Complex System to Worthwhile Investigation

The dramatic increase in soil degradation in the last few decades has led to the need to identify methods to define not only soil quality but also, in a holistic approach, soil health. In the past twenty years, indices based on living communities have been proposed alongside the already proven physical-chemical methods. Among them, some soil invertebrates have been included in monitoring programs as bioindicators of soil quality. Being an important portion of soil fauna, soil arthropods are involved in many soil processes such as organic matter decomposition and translocation, nutrient cycling, microflora activity regulation and bioturbation. Many studies have reported the use of soil arthropods to define soil quality; among taxa, some have been explored more in depth, typically Acari and Collembola, while generally less abundant groups, such as Palpigradi or Embioptera, have not been investigated much. This paper aims to evaluate and compare the use of different soil microarthropod taxa in soil degradation/quality studies to highlight which groups are the most reported for soil monitoring and which are the most sensitive to soil degradation. We have decided not to include the two most present and abundant taxa, Acari and Collembola, in this paper in consideration of the vast amount of existing literature and focus the discussion on the other microarthropod groups. We reported some studies for each taxon highlighting the use of the group as soil quality indicator. A brief section reporting some indices based on soil microarthropods is proposed at the end of this specific discussion. This paper can be considered as a reference point in the use of soil arthropods to estimate soil quality and health.

Checklist of marine mammal parasites in New Zealand and Australian waters

Marine mammals are long-lived top predators with vagile lifestyles, which often inhabit remote environments. This is especially relevant in the oceanic waters around New Zealand and Australia where cetaceans and pinnipeds are considered as vulnerable and often endangered due to anthropogenic impacts on their habitat. Parasitism is ubiquitous in wildlife, and prevalence of parasitic infections as well as emerging diseases can be valuable bioindicators of the ecology and health of marine mammals. Collecting information about parasite diversity in marine mammals will provide a crucial baseline for assessing their impact on host and ecosystem ecology. New studies on marine mammals in New Zealand and Australian waters have recently added to our knowledge of parasite prevalence, life cycles and taxonomic relationships in the Australasian region, and justify a first host-parasite checklist encompassing all available data. The present checklist comprises 36 species of marine mammals, and 114 species of parasites (helminths, arthropods and protozoans). Mammal species occurring in New Zealand and Australian waters but not included in the checklist represent gaps in our knowledge. The checklist thus serves both as a guide for what information is lacking, as well as a practical resource for scientists working on the ecology and conservation of marine mammals.

Using Mosses as Bioindicators of Potentially Toxic Element Contamination in Ecologically Valuable Areas Located in the Vicinity of a Road: A Case Study

This study analyzed the impact of road transportation on the concentration of Zn, Ni, Pb, Co, and Cd in moss (Pleurozium schreberi). The study was carried out over five years near a national road running from the north to the east (Poland) in the area of Natura 2000 sites. Samples were collected at three significantly different locations: (1) near a sharp bend, (2) near a straight section of the road in a woodless area, and (3) in a slightly wooded area. At each location, moss samples were collected from sites situated 2, 4, 6, 8, 10, 12, and 14 m from the road edge. The highest Zn and Cd contents in the moss were recorded 6 m from the road edge near a sharp bend (where vehicles brake sharply and accelerate suddenly). At the same location, at a distance of 2 m, the highest Pb concentration was noted, and at a distance of 4 m from the road, the highest Ni concentration was noted. The Co concentration in the moss was the highest near the woodless straight section at a distance of 2 and 12 m from the road. The concentrations of Zn, Pb, Ni, Co (only at the woodless location), and Cd (at all locations) were significantly and negatively correlated with distance from the road.

Long-term declines of European insectivorous bird populations and potential causes

Evidence of declines in insect populations has recently received considerable scientific and societal attention. However, the lack of long-term insect monitoring makes it difficult to assess whether declines are geographically widespread. By contrast, bird populations are well monitored and often used as indicators of environmental change. We compared the population trends of European insectivorous birds with those of other birds to assess whether patterns in bird population trends were consistent with declines of insects. We further examined whether declines were evident for insectivores with different habitats, foraging strata, and other ecological preferences. Bird population trends were estimated for Europe (1990-2015) and Denmark (1990-2016). On average, insectivores declined over the study period (13% across Europe and 28% in Denmark), whereas omnivores had stable populations. Seedeaters also declined (28% across Europe; 34% in Denmark), but this assessment was based on fewer species than for other groups. The effects of insectivory were stronger for farmland species (especially grassland species), for ground feeders, and for cold-adapted species. Insectivory was associated with long-distance migration, which was also linked to population declines. However, many insectivores had stable populations, especially habitat generalists. Our findings suggest that the decline of insectivores is primarily associated with agricultural intensification and loss of grassland habitat. The loss of both seed and insect specialists indicates an overall trend toward bird communities dominated by diet generalists.

Separating the effects of water quality and urbanization on temperate insectivorous bats at the landscape scale

Many local scale studies have shown that bats respond to water quality degradation or urbanization in a species-specific manner. However, few have separated the effects of urbanization versus water quality degradation on bats, in single city or single watershed case studies. Across North Carolina, USA, we used the standardized North American Bat Monitoring Program mobile transect protocol to survey bat activity in 2015 and 2016 at 41 sites. We collected statewide water quality and urban land cover data to disentangle the effects of urbanization and water quality degradation on bats at the landscape scale. We found that statewide, water quality degradation and urbanization were not correlated. We found that bats responded to water quality degradation and urbanization independently at the landscape scale. Eptesicus fuscus and Lasiurus cinereus negatively responded to water quality degradation. Lasiurus borealis and Perimyotis subflavus positively responded to water quality degradation. Lasionycteris noctivagans did not respond to water quality degradation but was more active in more urbanized areas. Tadarida brasiliensis positively responded to urbanization and was less active in areas with degraded water quality. We show that bat-water quality relationships found at the local scale are evident at a landscape scale. We confirm that bats are useful bioindicators for both urbanization and water quality degradation. We suggest that water quality can be used to predict the presence of bat species of conservation concern, such as P. subflavus, in areas where it has not been studied locally.

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity

In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.

Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria. Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.

IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.

A follow-up study of selected biomarkers of health in cod Gadus morhua L. collected from the southern Baltic off the Polish coast

Selected biomarkers of health were examined in 50 post-spawning cod Gadus morhua collected in November 2015 from the southern Baltic. The biomarkers included condition factor (CF), macroscopic lesions, histopathology of spleen, liver and gonads, and morphometry of follicular atresia and hepatic and splenic melanomacrophage cells (MMC). All fish appeared in good body condition. One fish had a dermal ulcer, and in seven, macroscopic nematodes were noted within body cavity. Microscopic lesions in the liver included biliary myxozoanosis, microsporidial and necrocentric granulomas, parasitic hepatitis, multifocal necrosis, foci of cellular alterations, spongiosis, peliosis and cytoplasmic fibrillar inclusions. The spleen and gonads had microsporidial and/or necrocentric granulomas. Some of the biomarkers showed differences as compared to spawning cod collected in May from the same location in 2012, most importantly values an order of magnitude lower for splenic MMC in post-spawning fish. In post-spawning fish, there were statistically significant correlations between MMC, CF, follicular atresia, parasitic hepatitis and microsporidiosis. This is the first comparison of biomarkers of health in post-spawning and spawning Baltic cod. Future studies need to examine the relationships of biomarkers to levels of pollutants in the environment and in tissues of cod.