Old and new challenges in using species diversity for assessing biodiversity

Unveiling Arthropod Responses to Climate Change: A Functional Trait Analysis in Intensive Pastures

This study investigates the impact of elevated temperatures on arthropod communities in intensively managed pastures on the volcanic island of Terceira, Azores (Portugal), using a functional trait approach. Open Top Chambers (OTCs) were employed to simulate increased temperatures, and the functional traits of ground dwelling arthropods were analyzed along a small elevation gradient (180-400 m) during winter and summer. Key findings include lower abundances of herbivores, coprophagous organisms, detritivores, and fungivores at high elevations in summer, with predators showing a peak at middle elevations. Larger-bodied arthropods were more prevalent at higher elevations during winter, while beetles exhibited distinct ecological traits, with larger species peaking at middle elevations. The OTCs significantly affected the arthropod communities, increasing the abundance of herbivores, predators, coprophagous organisms, and fungivores during winter by alleviating environmental stressors. Notably, iridescent beetles decreased with elevation and were more common inside OTCs at lower elevations, suggesting a thermoregulatory advantage. The study underscores the importance of considering functional traits in assessing the impacts of climate change on arthropod communities and highlights the complex, species-specific nature of their responses to environmental changes.

Conservation of more evolutionary unique amphibian communities in Türkiye: The role of protected areas

The alarming decline of amphibians, sometimes marked by sudden extinctions, underlines the urgent need for increased conservation efforts. Conservationists recognize that more action, particularly the setting of national targets, is needed to ensure the future persistence and recovery of species and habitats. Protecting habitats that harbor evolutionarily diverse species preserves divergent genetic information within ecosystems. Türkiye holds 36 amphibian species at the intersection of two continents, creating three biodiversity hotspots and phylogenetic transitional areas. In this study, we aimed to determine the hotspot regions and to evaluate the effectiveness of the protected areas in Türkiye in preserving amphibian populations. First, we estimated four community indexes (species richness and three evolutionary distinctiveness measures) for amphibian communities in Türkiye divided into 371 grid cells with a ca 50 × 50 km size. Then, the spatial extent of protected areas is evaluated from two perspectives: current (has a protection status) and candidate protected areas (Key Biodiversity Areas, not protected) coverage in those grid cells. Finally, these two approaches' effectiveness in protecting areas was assessed by modeling four diversity metrics using GLS models. Current protected areas protect about 6% of the total amphibian distribution in Türkiye, while Key Biodiversity Areas would cover 30% if declared protected areas. We estimated that the coastal areas of Türkiye are identified as hotspots based on the four measured amphibian community indexes. Our study also highlights that Key Biodiversity Areas (KBAs) can contribute to conserving high levels of amphibian richness and evolutionary distinctiveness of species across Türkiye. However, existing protected areas (PAs) networks were insufficient to protect amphibians.

Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber

Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.

Productivity vs. Evenness in the U.S. Financial Market: A Business Ecosystem Perspective

This paper starts by presenting an empirical finding in the U.S. stock market: Between 2001 and 2021, high productivity was achieved when the Shannon evenness-measuring the inverse of concentration-dropped. Conversely, when the Shannon evenness soared, productivity plunged. The same inverse relationship between evenness and productivity has been observed in several ecosystems. This suggests explaining this result by adopting the business ecosystem perspective, i.e., regarding the tangle of interactions between companies as an ecological network, in which companies play the role of species. A useful strategy to model such ecological communities is through ensembles of synthetic communities of pairwise interacting species, whose dynamics is described by the Lotka-Volterra generalized equations. Each community is specified by a random interaction matrix whose elements are drawn from a uniform distribution centered around 0. It is shown that the inverse relationship between productivity and evenness can be generated by varying the strength of the interaction between companies. When the strength increases, productivity increases and simultaneously the market evenness decreases. Conversely, when the strength decreases, productivity decreases and evenness increases. This strength can be interpreted as reflecting the looseness of monetary policy, thus providing a link between interest rates and market structure.

Exposure to diesel exhaust alters the functional metagenomic composition of the airway microbiome in former smokers

The lung microbiome plays a crucial role in airway homeostasis, yet we know little about the effects of exposures such as air pollution therein. We conducted a controlled human exposure study to assess the impact of diesel exhaust (DE) on the human airway microbiome. Twenty-four participants (former smokers with mild to moderate COPD (N = 9), healthy former smokers (N = 7), and control healthy never smokers (N = 8)) were exposed to DE (300 μg/m³ PM_2.5) and filtered air (FA) for 2 h in a randomized order, separated by a 4-week washout. Endobronchial brushing samples were collected 24 h post-exposure and sequenced for the 16S microbiome, which was analyzed using QIIME2 and PICRUSt2 to examine diversity and metabolic functions, respectively. DE exposure altered airway microbiome metabolic functions in spite of statistically stable microbiome diversity. Affected functions included increases in: superpathway of purine deoxyribonucleosides degradation (pathway differential abundance 743.9, CI 95% 201.2 to 1286.6), thiazole biosynthesis I (668.5, CI 95% 139.9 to 1197.06), and L-lysine biosynthesis II (666.5, CI 95% 73.3 to 1257.7). There was an exposure-by-age effect, such that menaquinone biosynthesis superpathways were the most enriched function in the microbiome of participants aged >60, irrespective of smoking or health status. Moreover, exposure-by-phenotype analysis showed metabolic alterations in former smokers after DE exposure. These observations suggest that DE exposure induced substantial changes in the metabolic functions of the airway microbiome despite the absence of diversity changes.

Species Diversity, Distribution, and Abundance of Freshwater Snails in KwaZulu-Natal, South Africa

Disease distribution is correlated to the distribution of the freshwater snails which in turn is influenced by the physicochemical status of the habitats. This study aimed to evaluate freshwater snail species diversity, abundance, and distribution in KwaZulu-Natal (KZN) province, South Africa, between December 2020 to February 2021. A total of 4576 freshwater snails consisting of 8 species were collected from 127 sites in 11 districts. Tarebia granifera snails were the most abundant (n = 2201), while bivalves (n = 95) were the least abundant. The highest and least Shannon–Weiner Simpson’s diversity indices were recorded in Ugu and iLembe districts, respectively. A negative relationship was observed between rainfall, Bulinus tropicus, Lymnaea natalensis, bivalves, and Physa acuta, while temperature had a positive relationship with B. globosus, B. pfeifferi, and T. granifera. A positive relationship was observed between B. globosus and B. pfeifferi (r = 0.713, p < 0.05). Snail presence constitutes potential health and economic risks to humans and animals in contact with the waterbody. Hence, our study described the current distribution, abundance, and species diversity of freshwater snails in the KZN province with insights into the possibilities of snail-based biological control for schistosomes intermediate host snails.

Global Human Consumption Threatens Key Biodiversity Areas

Key biodiversity areas (KBAs) are critical regions for preserving global biodiversity. KBAs are identified by their importance to biodiversity rather than their legal status. As such, KBAs are often under pressure from human activities. KBAs can encompass many different land-use types (e.g., cropland, pastures) and land-use intensities. Here, we combine a global economic model with spatial mapping to estimate the biodiversity impacts of human land use in KBAs. We find that global human land use within KBAs causes disproportionate biodiversity losses. While land use within KBAs accounts for only 7% of total land use, it causes 16% of the potential global plant loss and 12% of the potential global vertebrate loss. The consumption of animal products accounts for more than half of biodiversity loss within KBAs, with housing the second largest at around 10%. Bovine meat is the largest single contributor to this loss, at around 31% of total biodiversity loss. In terms of land use, lightly grazed pasture contributes the most, accounting for around half of all potential species loss. This loss is concentrated mainly in middle- and low-income regions with rich biodiversity. International trade is an important driver of loss, accounting for 22-29% of total potential plant and vertebrate loss. Our comprehensive global, trade-linked analysis provides insights into maintaining the integrity of KBAs and global biodiversity.

Linking Land Use and Plant Functional Diversity Patterns in Sabah, Borneo, through Large-Scale Spatially Continuous Sentinel-2 Inference

Global biodiversity losses erode the functioning of our vital ecosystems. Functional diversity is increasingly recognized as a critical link between biodiversity and ecosystem functioning. Satellite earth observation was proposed to address the current absence of information on large-scale continuous patterns of plant functional diversity. This study demonstrates the inference and spatial mapping of functional diversity metrics through satellite remote sensing over a large key biodiversity region (Sabah, Malaysian Borneo, ~53,000 km2) and compares the derived estimates across a land-use gradient as an initial qualitative assessment to test the potential merits of the approach. Functional traits (leaf water content, chlorophyll-a and -b, and leaf area index) were estimated from Sentinel-2 spectral reflectance using a pre-trained neural network on radiative transfer modeling simulations. Multivariate functional diversity metrics were calculated, including functional richness, divergence, and evenness. Spatial patterns of functional diversity were related to land-use data distinguishing intact forest, logged forest, and oil palm plantations. Spatial patterns of satellite remotely sensed functional diversity are significantly related to differences in land use. Intact forests, as well as logged forests, featured consistently higher functional diversity compared to oil palm plantations. Differences were profound for functional divergence, whereas functional richness exhibited relatively large variances within land-use classes. By linking large-scale patterns of functional diversity as derived from satellite remote sensing to land-use information, this study indicated initial responsiveness to broad human disturbance gradients over large geographical and spatially contiguous extents. Despite uncertainties about the accuracy of the spatial patterns, this study provides a coherent early application of satellite-derived functional diversity toward further validation of its responsiveness across ecological gradients.

Classification and Characterization of the Manoor Valley's (Lesser Himalaya) Vegetation from the Subtropical-Temperate Ecotonal Forests to the Alpine Pastures along Ecological Variables

Plant species are distributed in different types of habitats, forming different communities driven by different sets of environmental variables. Here, we assessed potential plant communities along an altitudinal gradient and their associations with different environmental drivers in the unexplored Manoor Valley (Lesser Himalaya), Pakistan. We have implemented various ecological techniques and evaluated phytosociological attributes in three randomly selected 50 m-transects within each stand (a total of 133) during different seasons for four years (2015-2018). This phytosociological exploration reported 354 plant species representing 93 different families. The results revealed that the Therophytic life form class dominated the flora, whereas Nanophyll dominated the leaf size spectra. There were a total of twelve plant communities identified, ranging from the lowest elevations to the alpine meadows and cold deserts. The maximum number of species were found in Cedrus-Pinus-Parrotiopsis community (197 species), in the middle altitudinal ranges (2292-3168 m). Our results showed that at high altitudes, species richness was reduced, whereas an increase in soil nutrients was linked to progression in vegetation indicators. We also found different clusters of species with similar habitats. Our study clearly shows how altitudinal variables can cluster different plant communities according to different microclimates. Studies such as ours are paramount to better understanding how environmental factors influence ecological and evolutionary aspects.

Tropical forest dung beetle-mammal dung interaction networks remain similar across an environmental disturbance gradient

Conservation outcomes could be greatly enhanced if strategies addressing anthropogenic land-use change considered the impacts of these changes on entire communities as well as on individual species. Examining how species interactions change across gradients of habitat disturbance allows us to predict the cascading consequences of species extinctions and the response of ecological networks to environmental change. We conducted the first detailed study of changes in a commensalist network of mammals and dung beetles across an environmental disturbance gradient, from primary tropical forest to plantations, which varied in above-ground carbon density (ACD) and mammal communities. Mammal diversity changed only slightly across the gradient, remaining high even in oil palm plantations and fragmented forest. Dung beetle species richness, however, declined in response to lower ACD and was particularly low in plantations and the most disturbed forest sites. Three of the five network metrics (nestedness, network specialization, and functionality) were significantly affected by changes in dung beetle species richness and ACD, but mammal diversity was not an important predictor of network structure. Overall, the interaction networks remained structurally and functionally similar across the gradient, only becoming simplified (i.e., with fewer dung beetle species and fewer interactions) in the most disturbed sites. We suggest that the high diversity of mammals, even in disturbed forests, combined with the generalist feeding patterns of dung beetles, confer resilience to the commensalist dung beetle-mammal networks. This study highlights the importance of protecting logged and fragmented forests to maintain interaction networks and potentially prevent extinction cascades in human-modified systems.

Biodiversity and ecosystem functions depend on environmental conditions and resources rather than the geodiversity of a tropical biodiversity hotspot

Biodiversity and ecosystem functions are highly threatened by global change. It has been proposed that geodiversity can be used as an easy-to-measure surrogate of biodiversity to guide conservation management. However, so far, there is mixed evidence to what extent geodiversity can predict biodiversity and ecosystem functions at the regional scale relevant for conservation planning. Here, we analyse how geodiversity computed as a compound index is suited to predict the diversity of four taxa and associated ecosystem functions in a tropical mountain hotspot of biodiversity and compare the results with the predictive power of environmental conditions and resources (climate, habitat, soil). We show that combinations of these environmental variables better explain species diversity and ecosystem functions than a geodiversity index and identified climate variables as more important predictors than habitat and soil variables, although the best predictors differ between taxa and functions. We conclude that a compound geodiversity index cannot be used as a single surrogate predictor for species diversity and ecosystem functions in tropical mountain rain forest ecosystems and is thus little suited to facilitate conservation management at the regional scale. Instead, both the selection and the combination of environmental variables are essential to guide conservation efforts to safeguard biodiversity and ecosystem functions.

What does measuring species diversity in estuarine seagrass systems actually assess?

Relationships between species diversity and other species-density and species-richness metrics were investigated in the seagrass macrobenthos of Knysna estuarine bay, South Africa. Although a wide range of species density occurred across sites, neither Hill-Shannon nor Hill-Simpson diversity showed any significant relationship with it, although they did with species richness. Instead species diversity was very closely related to relative evenness, and (negatively) to overall assemblage abundance. No significant relationship was found between species density and evenness. Whilst there was a clear and marked decrease in species density upstream along the main estuarine channel, only one of the species-diversity indices (the Hill-Shannon) showed a significant equivalent decrease. Relationships depended on how 'species richness' was assessed, and were very strongly influenced by the superabundant local occurrence of a few individual faunal components (three gastropod and one tanaid species). Species-diversity analysis contributes nothing new in such estuarine seagrass meadows and seems best avoided.

Seagrass habitat suitability model for Redang Marine Park using multibeam echosounder data: Testing different spatial resolutions and analysis window sizes

Integrating Multibeam Echosounder (MBES) data (bathymetry and backscatter) and underwater video technology allows scientists to study marine habitats. However, use of such data in modeling suitable seagrass habitats in Malaysian coastal waters is still limited. This study tested multiple spatial resolutions (1 and 50 m) and analysis window sizes (3 × 3, 9 × 9, and 21 × 21 cells) probably suitable for seagrass-habitat relationships in Redang Marine Park, Terengganu, Malaysia. A maximum entropy algorithm was applied, using 12 bathymetric and backscatter predictors to develop a total of 6 seagrass habitat suitability models. The results indicated that both fine and coarse spatial resolution datasets could produce models with high accuracy (>90%). However, the models derived from the coarser resolution dataset displayed inconsistent habitat suitability maps for different analysis window sizes. In contrast, habitat models derived from the fine resolution dataset exhibited similar habitat distribution patterns for three different analysis window sizes. Bathymetry was found to be the most influential predictor in all the models. The backscatter predictors, such as angular range analysis inversion parameters (characterization and grain size), gray-level co-occurrence texture predictors, and backscatter intensity levels, were more important for coarse resolution models. Areas of highest habitat suitability for seagrass were predicted to be in shallower (<20 m) waters and scattered between fringing reefs (east to south). Some fragmented, highly suitable habitats were also identified in the shallower (<20 m) areas in the northwest of the prediction models and scattered between fringing reefs. This study highlighted the importance of investigating the suitable spatial resolution and analysis window size of predictors from MBES for modeling suitable seagrass habitats. The findings provide important insight on the use of remote acoustic sonar data to study and map seagrass distribution in Malaysia coastal water.

Temporary Salt Lakes: Ecosystem Services Shift in a Ramsar Site Over a 50-Year Period

Changes in land use/land cover (LULC) are the key factors driving biodiversity and ecosystem services decline globally. This study examines spatiotemporal LULC changes in a Ramsar coastal temporary wetland (Larnaca Salt Lake) on the island of Cyprus between 1963 and 2015. LULC changes in the area are related to variations in the provision of ecosystem services (ES) namely food provision, climate regulation, avifauna support and landscape aesthetics. LULC mapping was performed based on the interpretation of aerial photos taken in 1963, while 2015 mapping was based on CORINE classification validated by satellite image analysis and fieldwork. We used the following indicators for the ES examined: (1) crops’ yield for the estimation of food supply, (2) carbon storage potential for climate regulation, (3) land cover potential to support avifauna richness and (4) naturalness as a proxy for landscape aesthetics. Quantifications were based on a mixed-methods approach with the use of statistical data, expert opinion and bibliography. Estimates for every service were assigned to CORINE land use classes (CLC) present in the area. Landscape structure was measured using a suite of commonly employed landscape metrics. The results showed that between 1963 and 2015 there has been a significant reduction in food provisioning service by 75%, a 37% reduction in carbon storage capacity, an 11% reduction in the capacity to support avifauna, and a 13% reduction in landscape aesthetics. Increased soil surface sealing, mainly with the construction of the international airport, which resulted in the conversion of natural or semi-natural to artificial surfaces, has been the main reason for the decrease in ES supply over the last fifty years in the study area. The character of the area in terms of land use types richness and diversity remains fairly stable but the dominant land use types have experienced fragmentation. The study sets the basis for a monitoring scheme to evaluate the state of the temporary wetlands with emphasis placed on spatial processes as a link to ES provision.

Measuring diversity from space: a global view of the free and open source rasterdiv R package under a coding perspective

The variation of species diversity over space and time has been widely recognised as a key challenge in ecology. However, measuring species diversity over large areas might be difficult for logistic reasons related to both time and cost savings for sampling, as well as accessibility of remote ecosystems. In this paper, we present a new package - - to calculate diversity indices based on remotely sensed data, by discussing the theory behind the developed algorithms. Obviously, measures of diversity from space should not be viewed as a replacement of in situ data on biological diversity, but they are rather complementary to existing data and approaches. In practice, they integrate available information of Earth surface properties, including aspects of functional (structural, biophysical and biochemical), taxonomic, phylogenetic and genetic diversity. Making use of the package can result useful in making multiple calculations based on reproducible open source algorithms, robustly rooted in Information Theory.

The impact of smoking different tobacco types on the subgingival microbiome and periodontal health: a pilot study

Smoking is a risk factor for periodontal disease, and a cause of oral microbiome dysbiosis. While this has been evaluated for traditional cigarette smoking, there is limited research on the effect of other tobacco types on the oral microbiome. This study investigates subgingival microbiome composition in smokers of different tobacco types and their effect on periodontal health. Subgingival plaques were collected from 40 individuals, including smokers of either cigarettes, medwakh, or shisha, and non-smokers seeking dental treatment at the University Dental Hospital in Sharjah, United Arab Emirates. The entire (~ 1500 bp) 16S rRNA bacterial gene was fully amplified and sequenced using Oxford Nanopore technology. Subjects were compared for the relative abundance and diversity of subgingival microbiota, considering smoking and periodontal condition. The relative abundances of several pathogens were significantly higher among smokers, such as Prevotella denticola and Treponema sp. OMZ 838 in medwakh smokers, Streptococcus mutans and Veillonella dispar in cigarette smokers, Streptococcus sanguinis and Tannerella forsythia in shisha smokers. Subgingival microbiome of smokers was altered even in subjects with no or mild periodontitis, probably making them more prone to severe periodontal diseases. Microbiome profiling can be a useful tool for periodontal risk assessment. Further studies are recommended to investigate the impact of tobacco cessation on periodontal disease progression and oral microbiome.

Combining botanical collections and ecological data to better describe plant community diversity

In this age of rapid biodiversity loss, we must continue to refine our approaches to describing variation in life on Earth. Combining knowledge and research tools from multiple disciplines is one way to better describe complex natural systems. Understanding plant community diversity requires documenting both pattern and process. We must first know which species exist, and where (i.e., taxonomic and biogeographic patterns), before we can determine why they exist there (i.e., ecological and evolutionary processes). Floristic botanists often use collections-based approaches to elucidate biodiversity patterns, while plant ecologists use hypothesis-driven statistical approaches to describe underlying processes. Because of these different disciplinary histories and research goals, floristic botanists and plant ecologists often remain siloed in their work. Here, using a case study from an urban greenway in Colorado, USA, we illustrate that the collections-based, opportunistic sampling of floristic botanists is highly complementary to the transect- or plot-based sampling of plant ecologists. We found that floristic sampling captured a community species pool four times larger than that captured using ecological transects, with rarefaction and non-parametric species estimation indicating that it would be prohibitive to capture the "true" community species pool if constrained to sampling within transects. We further illustrate that the discrepancy in species pool size between approaches led to a different interpretation of the greenway's ecological condition in some cases (e.g., transects missed uncommon cultivated species escaping from nearby gardens) but not others (e.g., plant species distributions among functional groups were similar between species pools). Finally, we show that while using transects to estimate plant relative abundances necessarily trades off with a fuller assessment of the species pool, it is an indispensable indicator of ecosystem health, as evidenced by three non-native grasses contributing to 50% of plant cover along the highly modified urban greenway. We suggest that actively fostering collaborations between floristic botanists and ecologists can create new insights into the maintenance of species diversity at the community scale.

The importance of sharing global forest data in a world of crises

Open access to global forest data, especially ground-measured (in situ) records, is critical for saving the world’s forest systems. Integrated approaches to achieve sustainable data openness will involve legal assurances, shared ethics, innovative funding schemes and capacity development.

Prevalence of Malassezia species on the skin of HIV-seropositive patients

Malassezia is a genus of lipophilic yeasts residing on the skin of warm-blooded animals. The correlation between specific species and their involvement in skin diseases has been well researched. However, only very few studies have investigated the distribution of Malassezia spp. on the healthy skin of patients infected with human immunodeficiency virus (HIV). The purpose of this work was to analyze whether the composition of Malassezia spp. isolated from the skin of the HIV-infected patients differs from that of healthy individuals. The study included a total of 96 subjects, who were divided into two equally sized groups: HIV-seropositive and HIV-seronegative. The specimens were collected from the subjects by swabbing four anatomical sites (face, chest, back, and scalp). Species were identified using phenotype-based methods, and the identification of strains isolated from the HIV-seropositive patients was confirmed by PCR sequencing of the rDNA cluster. Malassezia spp. were isolated from 33 (69%) HIV-seropositive patients and 38 (79%) healthy volunteers. It was found that men were much more likely to have their heads colonized with Malassezia spp. than women. The most prevalent species on the skin of both HIV-seropositive and HIV-seronegative individuals were Malassezia sympodialis, M. globosa, and M. furfur, albeit at different proportions in the two populations. The diversity of Malassezia spp. was the highest on the face of the HIV-seropositive patients (Shannon-Weiner Index H = 1.35) and lowest on the back of the healthy volunteers (H = 0.16). The phenotype- and molecular-based identification methods were congruent at 94.9%. It was observed a tendency that the HIV-seropositive patients had higher CD4+ cell counts, indicating higher colonization with Malassezia spp.

CAMBIOS EN DIVERSIDAD Y DISTRIBUCIÓN DE PECES NATIVOS CON LA PRESENCIA DE DOS ESPECIES INVASORAS EN EL RÍO ATACAMES, NOROCCIDENTE DEL ECUADOR

La interpretación de la diversidad biológica puede resultar muy compleja, ya que existe una dinámica basada en el origen y en la diversificación de las especies, así como en los efectos antrópicos, tales como la introducción de especies invasoras, cuya consecuencia puede conducir a la extinción local de especies nativas. El objetivo de este trabajo fue analizar la variación temporal (2012 y 2017), tanto en composición como en distribución de la ictiofauna a lo largo del río Atacames, noroccidente del Ecuador. En 2012 se registró: 1) la presencia de Astyanax ruberrimus que se extinguió localmente para el 2017; y 2) la presencia de la tilapia (Orechromis niloticus) como única especie introducida a la que se sumó el guppy (Poecilia gillii) para el 2017. Adicionalmente, el aumento en las actividades humanas condujo a un arreglo en la diversidad, abundancia y distribución de peces a lo largo del cauce, lo que determinó además que algunas especies se dispersaran hacia la zona alta de la cuenca.

Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome

RATIONALE

Chronic smoke exposure is associated with weight loss in patients with Chronic Obstructive Pulmonary Disease (COPD). However, the biological contribution of chronic smoking and sex on the cecal microbiome has not been previously investigated.

METHODS

Adult male, female and ovariectomized mice were exposed to air (control group) or smoke for six months using a standard nose-only smoke exposure system. DNA was extracted from the cecal content using the QIAGEN QIAamp® DNA Mini Kit. Droplet digital PCR was used to generate total 16S bacterial counts, followed by Illumina MiSeq® analysis to determine microbial community composition. The sequencing data were resolved into Amplicon Sequence Variants and analyzed with the use of QIIME2®. Alpha diversity measures (Richness, Shannon Index, Evenness and Faith's Phylogenetic Diversity) and beta diversity (based on Bray-Curtis distances) were assessed and compared according to smoke exposure and sex.

RESULTS

The microbial community was different between male and female mice, while ovariectomy made the cecal microbiome similar to that of male mice. Chronic smoke exposure led to significant changes in the cecal microbial community in both male and female mice. The organism, Alistipes, was the most consistent bacteria identified at the genus level in the cecal content that was reduced with chronic cigarette exposure and its expression was positively related to the whole-body weight of these mice.

CONCLUSION

Chronic smoke exposure is associated with changes in the cecal content microbiome; these changes may play a role in the weight changes that are observed in cigarette smokers.

An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample

The human gut microbiome has emerged as a potential key factor involved in the manifestation of physical and mental health. Despite an explosion of cross-disciplinary interest in researching the gut microbiome, there remains to be a gold-standard method for operationalizing gut microbiome alpha diversity. Given researchers' interest in examining the relationships among gut microbiome alpha diversity and health-related outcomes of interest, a way of operationalizing the microbiome that yields a numeric value, which could be used in common statistical approaches, is needed. Thus, the current study aims to provide methodological guidance for how to operationalize microbiome alpha diversity. Findings suggest that alpha diversity of the human gut microbiome is comprised of two sub-constructs (richness and evenness), and we propose a step-by-step method of creating alpha diversity composite measures based on this key insight. Finally, we demonstrate that our empirically derived richness and evenness composite measures are significantly associated with health-related variables of interest (alcohol use, symptoms of depression) among a human clinical sample.

The Introduction of Entropy and Information Methods to Ecology by Ramon Margalef

In ecology and evolution, entropic methods are now used widely and increasingly frequently. Their use can be traced back to Ramon Margalef's first attempt 70 years ago to use log-series to quantify ecological diversity, including searching for ecologically meaningful groupings within a large assemblage, which we now call the gamma level. The same year, Shannon and Weaver published a generally accessible form of Shannon's work on information theory, including the measure that we now call Shannon-Wiener entropy. Margalef seized on that measure and soon proposed that ecologists should use the Shannon-Weiner index to evaluate diversity, including assessing local (alpha) diversity and differentiation between localities (beta). He also discussed relating this measure to environmental variables and ecosystem processes such as succession. Over the subsequent decades, he enthusiastically expanded upon his initial suggestions. Finally, 2019 also would have been Margalef's 100th birthday.

A review of methods and databases for metagenomic classification and assembly

Microbiome research has grown rapidly over the past decade, with a proliferation of new methods that seek to make sense of large, complex data sets. Here, we survey two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly, and we review some of the challenges facing these methods. All of the methods rely on public genome databases, and we also discuss the content of these databases and how their quality has a direct impact on our ability to interpret a microbiome sample.

A review of methods and databases for metagenomic classification and assembly

Microbiome research has grown rapidly over the past decade, with a proliferation of new methods that seek to make sense of large, complex data sets. Here, we survey two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly, and we review some of the challenges facing these methods. All of the methods rely on public genome databases, and we also discuss the content of these databases and how their quality has a direct impact on our ability to interpret a microbiome sample.

Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions

OBJECTIVE

The aim of this study was to use high-resolution whole metagenomic shotgun sequencing to characterize the subgingival microbiome of patients with/without type 2 Diabetes Mellitus and with/without periodontitis.

DESIGN

Twelve subjects, falling into one of the four study groups based on the presence/absence of poorly controlled type 2 Diabetes Mellitus and moderate-severe periodontitis, were selected. For each eligible subject, subgingival plaque samples were collected at 4 sites, all representative of the periodontal condition of the individual (i.e., non-bleeding sulci in subjects without a history of periodontitis, bleeding pockets in patients with moderate-severe periodontitis). The subgingival microbiome was evaluated using high-resolution whole metagenomic shotgun sequencing.

RESULTS

The results showed that: (i) the presence of type 2 Diabetes Mellitus and/or periodontitis were associated with a tendency of the subgingival microbiome to decrease in richness and diversity; (ii) the presence of type 2 Diabetes Mellitus was not associated with significant differences in the relative abundance of one or more species in patients either with or without periodontitis; (iii) the presence of periodontitis was associated with a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in type 2 Diabetes Mellitus patients.

CONCLUSIONS

Whole metagenomic shotgun sequencing of the subgingival microbiome was extremely effective in the detection of low-abundant taxon. Our results point out a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in patients with moderate to severe periodontitis vs patients without history of periodontitis, which was maintained when the comparison was restricted to type 2 diabetics.

Technical quality of fauna monitoring programs in the environmental impact assessments of large mining projects in southeastern Brazil

Biodiversity monitoring is a key element of impact assessment follow-up activities, as it has the potential to generate relevant information about the actual impacts of approved projects on the environment. However, the effectiveness of such monitoring programs depends on issues such as technical quality. The extent to which this issue actually affects biodiversity monitoring is unclear. This knowledge gap was addressed in this study, whose main objective was to analyze the technical quality of fauna monitoring, using empirical data from large-scale mining enterprises in the state of Minas Gerais in southeastern Brazil. More specifically, this study aimed at analyzing: 1) whether license conditions related to fauna monitoring programs were being met by mining companies; 2) the extent to which fauna monitoring programs met a set of technical quality criteria; 3) whether there were significant differences among taxonomic groups; and, finally, 4) how fauna monitoring programs can be made more meaningful to decision-makers. A total of 236 fauna monitoring reports were analyzed. Findings indicated that, while companies complied with all license conditions, their fauna programs met, on average, 32% of the desirable technical requirements, and there were no significant differences among taxonomic groups. The main technical quality gaps were found to be lack of driving questions, hypothesis-testing and conceptual models, as well as lack of comparisons between control and impacted areas. Overall, findings indicated that the data generated in such programs have very limited value to decision-makers as they do not shed sufficient light on the actual impacts of mining activities on biodiversity. The study discusses a number of barriers to more meaningful fauna monitoring programs, and highlights the urgent need for revising current Terms of Reference.

The Time Local Convex Hull method as a tool for assessing responses of fauna to habitat restoration: a case study using the perentie (Varanus giganteus : Reptilia : Varanidae)

Understanding the behavioural responses of animals to habitat change is vital to their conservation in landscapes undergoing restoration. Studies of animal responses to habitat restoration typically assess species presence/absence; however, such studies may be restricted in their ability to show whether restoration is facilitating the return of self-sustaining and functional fauna populations. We present a case study using VHF/GPS tracking of a young adult perentie (Varanus giganteus), to demonstrate the range of applications of the Time Local Convex Hull method of home-range construction in analysing the behavioural responses of fauna to habitat change and restoration. Presence/absence studies provide single point locations of an animal, and the Minimum Convex Polygon method provides an invariant estimate of habitat use across the whole home range. However, the Time Local Convex Hull method provides a useful method for assessing movement and behavioural responses of fauna to habitat change and restoration, and the specific habitat requirements for the long-term support of populations. The breadth and multidimensionality of data generated indicates strongly that understanding the complex interactions between animals and their environment is fundamental to their conservation in the face of ever-increasing rates of human-induced habitat change and degradation.

Phylogenetic study and taxonomic revision of the Xanthoparmeliamexicana group, including the description of a new species (Parmeliaceae, Ascomycota)

Xanthoparmelia (Parmeliaceae, Ascomycota) is the most species-rich genus of lichen-forming fungi. Species boundaries are based on morphological and chemical features, varying reproductive strategies and, more recently, molecular sequence data. The isidiate Xanthoparmeliamexicana group is common in arid regions of North and Central America and includes a range of morphological variation and variable secondary metabolites - salazinic or stictic acids mainly. In order to better understand the evolutionary history of this group and potential taxonomic implications, a molecular phylogeny representing 58 ingroup samples was reconstructed using four loci, including ITS, mtSSU, nuLSU rDNA and MCM7. Results indicate the existence of multiple, distinct lineages phenotypically agreeing with X.mexicana. One of these isidiate, salazinic acid-containing lineages is described here as a new species, X.pedregalensis sp. nov., including populations from xerophytic scrub vegetation in Pedregal de San Angel, Mexico City. X.mexicana s. str. is less isidiate than X.pedregalensis and has salazinic and consalazinic acid, occasionally with norstictic acid; whereas X.pedregalensis contains salazinic and norstictic acids and an unknown substance. Samples from the Old World, morphologically agreeing with X.mexicana, are only distantly related to X.mexicana s. str. Our results indicate that X.mexicana is likely less common than previously assumed and ongoing taxonomic revisions are required for isidiate Xanthoparmelia species.

Studying microbial functionality within the gut ecosystem by systems biology

Humans are not autonomous entities. We are all living in a complex environment, interacting not only with our peers, but as true holobionts; we are also very much in interaction with our coexisting microbial ecosystems living on and especially within us, in the intestine. Intestinal microorganisms, often collectively referred to as intestinal microbiota, contribute significantly to our daily energy uptake by breaking down complex carbohydrates into simple sugars, which are fermented to short-chain fatty acids and subsequently absorbed by human cells. They also have an impact on our immune system, by suppressing or enhancing the growth of malevolent and beneficial microbes. Our lifestyle can have a large influence on this ecosystem. What and how much we consume can tip the ecological balance in the intestine. A "western diet" containing mainly processed food will have a different effect on our health than a balanced diet fortified with pre- and probiotics. In recent years, new technologies have emerged, which made a more detailed understanding of microbial communities and ecosystems feasible. This includes progress in the sequencing of PCR-amplified phylogenetic marker genes as well as the collective microbial metagenome and metatranscriptome, allowing us to determine with an increasing level of detail, which microbial species are in the microbiota, understand what these microorganisms do and how they respond to changes in lifestyle and diet. These new technologies also include the use of synthetic and in vitro systems, which allow us to study the impact of substrates and addition of specific microbes to microbial communities at a high level of detail, and enable us to gather quantitative data for modelling purposes. Here, we will review the current state of microbiome research, summarizing the computational methodologies in this area and highlighting possible outcomes for personalized nutrition and medicine.

Plant recording across two centuries reveals dramatic changes in species diversity of a Mediterranean archipelago

Although islands are model systems for investigating assembly of biological communities, long-term changes in archipelago communities are not well understood because of the lack of reliable data. By using a vast amount of floristic data we assembled a dataset of the plant species occurring on 16 islands of the Tuscan Archipelago, Italy, across two periods, 1830–1950 and 1951–2015. We collected 10,892 occurrence records for 1,831 species. We found major changes in the island plant assemblages between the two periods, with native flora significantly decreasing (−10.7%) and alien flora doubling (+132.1%) in richness. The species–area relationships demonstrated the scale-dependence of the observed changes for native and alien species. The observed floristic changes were dependent on island area, with smaller islands displaying high variability in richness and compositional changes and larger islands having more stable species assemblages. The richness of species associated with open landscapes, that had been maintained for centuries by traditional practices, markedly reduced while the number of woody species, associated with afforestation processes and invasion by alien woody plants, significantly incresed. These results demonstrate the great power of floristic studies, often available in grey literature, for understanding long-term biotic changes in insular ecosystems.

Anticipating species distributions: Handling sampling effort bias under a Bayesian framework

Anticipating species distributions in space and time is necessary for effective biodiversity conservation and for prioritising management interventions. This is especially true when considering invasive species. In such a case, anticipating their spread is important to effectively plan management actions. However, considering uncertainty in the output of species distribution models is critical for correctly interpreting results and avoiding inappropriate decision-making. In particular, when dealing with species inventories, the bias resulting from sampling effort may lead to an over- or under-estimation of the local density of occurrences of a species. In this paper we propose an innovative method to i) map sampling effort bias using cartogram models and ii) explicitly consider such uncertainty in the modeling procedure under a Bayesian framework, which allows the integration of multilevel input data with prior information to improve the anticipation species distributions.