Amphibian Metacommunity Responses to Agricultural Intensification in a Mediterranean Landscape

Agricultural intensification has been associated with biodiversity declines, habitat fragmentation and loss in a number of organisms. Given the prevalence of this process, there is a need for studies clarifying the effects of changes in agricultural practices on local biological communities; for instance, the transformation of traditional rainfed agriculture into intensively irrigated agriculture. We focused on pond-breeding amphibians as model organisms to assess the ecological effects of agricultural intensification because they are sensitive to changes in habitat quality at both local and landscape scales. We applied a metacommunity approach to characterize amphibian communities breeding in a network of ponds embedded in a terrestrial habitat matrix that was partly converted from rainfed crops to intensive irrigated agriculture in the 1990s. Specifically, we compared alpha and beta diversity, species occupancy and abundance, and metacommunity structure between irrigated and rainfed areas. We found strong differences in patterns of species occurrence, community structure and pairwise beta diversity between agricultural management groups, with a marked community structure in rainfed ponds associated with local features and the presence of some rare species that were nearly absent in the irrigated area, which was characterized by a random community structure. Natural vegetation cover at the landscape scale, significantly lower on the irrigated area, was an important predictor of species occurrences. Our results suggest that maintaining both local and landscape heterogeneity is key to preserving diverse amphibian communities in Mediterranean agricultural landscapes.

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Gut microbiota composition is associated with narcolepsy type 1

Neurology Neuroimmunology & Neuroinflammation ◽

10.1212/nxi.0000000000000896 ◽

2020 ◽

Vol 7 (6) ◽

pp. e896

Author(s):

Alexandre Lecomte ◽

Lucie Barateau ◽

Pedro Pereira ◽

Lars Paulin ◽

Petri Auvinen ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiota ◽

Bacterial Communities ◽

Beta Diversity ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Differential Abundance ◽

Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

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Non-crop habitats modulate alpha and beta diversity of flower flies (Diptera, Syrphidae) in Brazilian agricultural landscapes

Biodiversity and Conservation ◽

10.1007/s10531-017-1495-5 ◽

2017 ◽

Vol 27 (6) ◽

pp. 1309-1326 ◽

Cited By ~ 8

Author(s):

Hugo Reis Medeiros ◽

Adriano Thibes Hoshino ◽

Milton Cezar Ribeiro ◽

Mírian Nunes Morales ◽

Felipe Martello ◽

...

Keyword(s):

Beta Diversity ◽

Agricultural Landscapes ◽

Alpha And Beta Diversity ◽

Flower Flies

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Alpha and beta diversity of birds along elevational vegetation zones on the southern slope of Altai Mountains: Implication for conservation

Global Ecology and Conservation ◽

10.1016/j.gecco.2019.e00643 ◽

2019 ◽

Vol 19 ◽

pp. e00643 ◽

Cited By ~ 1

Author(s):

Na Li ◽

Hongjun Chu ◽

Yingjie Qi ◽

Chunwang Li ◽

Xiaoge Ping ◽

...

Keyword(s):

Beta Diversity ◽

Altai Mountains ◽

Southern Slope ◽

Alpha And Beta Diversity ◽

Vegetation Zones

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Ecological Connectivity in Agricultural Green Infrastructure: Suggested Criteria for Fine Scale Assessment and Planning

Land ◽

10.3390/land10080807 ◽

2021 ◽

Vol 10 (8) ◽

pp. 807

Author(s):

Simone Valeri ◽

Laura Zavattero ◽

Giulia Capotorti

Keyword(s):

Land Cover ◽

Green Infrastructure ◽

Rural Areas ◽

Urban Areas ◽

Landscape Heterogeneity ◽

Agricultural Landscapes ◽

Spatial Pattern Analysis ◽

Fine Scale ◽

Unique Type

In promoting biodiversity conservation and ecosystem service capacity, landscape connectivity is considered a critical feature to counteract the negative effects of fragmentation. Under a Green Infrastructure (GI) perspective, this is especially true in rural and peri-urban areas where a high degree of connectivity may be associated with the enhancement of agriculture multifunctionality and sustainability. With respect to GI planning and connectivity assessment, the role of dispersal traits of tree species is gaining increasing attention. However, little evidence is available on how to select plant species to be primarily favored, as well as on the role of landscape heterogeneity and habitat quality in driving the dispersal success. The present work is aimed at suggesting a methodological approach for addressing these knowledge gaps, at fine scales and for peri-urban agricultural landscapes, by means of a case study in the Metropolitan City of Rome. The study area was stratified into Environmental Units, each supporting a unique type of Potential Natural Vegetation (PNV), and a multi-step procedure was designed for setting priorities aimed at enhancing connectivity. First, GI components were defined based on the selection of the target species to be supported, on a fine scale land cover mapping and on the assessment of land cover type naturalness. Second, the study area was characterized by a Morphological Spatial Pattern Analysis (MSPA) and connectivity was assessed by Number of Components (NC) and functional connectivity metrics. Third, conservation and restoration measures have been prioritized and statistically validated. Notwithstanding the recognized limits, the approach proved to be functional in the considered context and at the adopted level of detail. Therefore, it could give useful methodological hints for the requalification of transitional urban–rural areas and for the achievement of related sustainable development goals in metropolitan regions.

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Site‐specific impacts of a major hurricane on alpha and beta diversity in tropical forest seedling communities

Ecosphere ◽

10.1002/ecs2.3651 ◽

2021 ◽

Vol 12 (7) ◽

Author(s):

Samantha J. Worthy ◽

Vanessa E. Rubio ◽

Kirstin Staiger ◽

Boris Ngouajio ◽

Jie Yang ◽

...

Keyword(s):

Tropical Forest ◽

Beta Diversity ◽

Site Specific ◽

Alpha And Beta Diversity ◽

Major Hurricane

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Effect of Bovine MFGM and LF in Infant Formula on Gut Microbiome and Metabolome at Four Months of Age

Current Developments in Nutrition ◽

10.1093/cdn/nzab027 ◽

2021 ◽

Author(s):

Maciej Chichlowski ◽

Nicholas Bokulich ◽

Cheryl L Harris ◽

Jennifer L Wampler ◽

Fei Li ◽

...

Keyword(s):

Infant Formula ◽

Beta Diversity ◽

Milk Fat ◽

Alpha Diversity ◽

Illumina Miseq ◽

Rrna Gene ◽

Term Infants ◽

Linear Discriminant ◽

Alpha And Beta Diversity ◽

Metabolite Profiles

Abstract Background Milk fat globule membrane (MFGM) and lactoferrin (LF) are human milk bioactive components demonstrated to support gastrointestinal (GI) and immune development. Significantly fewer diarrhea and respiratory-associated adverse events through 18 months of age were previously reported in healthy term infants fed a cow's milk-based infant formula with added source of bovine MFGM and bovine LF through 12 months of age. Objectives To compare microbiota and metabolite profiles in a subset of study participants. Methods Stool samples were collected at Baseline (10–14 days of age) and Day 120 (MFGM + LF: 26, Control: 33). Bacterial community profiling was performed via16S rRNA gene sequencing (Illumina MiSeq) and alpha and beta diversity were analyzed (QIIME 2). Differentially abundant taxa were determined using Linear discriminant analysis effect size (LefSE) and visualized (Metacoder). Untargeted stool metabolites were analyzed (HPLC/mass spectroscopy) and expressed as the fold-change between group means (Control: MFGM + LF ratio). Results Alpha diversity increased significantly in both groups from baseline to 4 months. Subtle group differences in beta diversity were demonstrated at 4 months (Jaccard distance; R2 = 0.01, P = 0.042). Specifically, Bacteroides uniformis and Bacteroides plebeius were more abundant in the MFGM + LF group at 4 months. Metabolite profile differences for MFGM + LF vs Control included: lower fecal medium chain fatty acids, deoxycarnitine, and glycochenodeoxycholate, and some higher fecal carbohydrates and steroids (P < 0.05). After applying multiple test correction, the differences in stool metabolomics were not significant. Conclusions Addition of bovine MFGM and LF in infant formula was associated with subtle differences in stool microbiome and metabolome by four months of age, including increased prevalence of Bacteroides species. Stool metabolite profiles may be consistent with altered microbial metabolism. Trial registration: https://clinicaltrials.gov/ct2/show/NCT02274883).

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The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽

10.3390/ani11030745 ◽

2021 ◽

Vol 11 (3) ◽

pp. 745

Author(s):

Michelle Martin de Bustamante ◽

Diego Gomez ◽

Jennifer MacNicol ◽

Ralph Hamor ◽

Caryn Plummer

Keyword(s):

Beta Diversity ◽

High Throughput Sequencing ◽

Illumina Miseq ◽

Diversity Indices ◽

Rrna Gene ◽

Linear Discriminant ◽

Alpha And Beta Diversity ◽

Bacterial Microbiota ◽

Healthy Control ◽

Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

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Partitioning tree diversity patterns to prioritize conservation investments

Environmental Conservation ◽

10.1017/s0376892921000060 ◽

2021 ◽

pp. 1-9

Author(s):

Patrick F McKenzie ◽

Gwenllian D Iacona ◽

Eric R Larson ◽

Paul R Armsworth

Keyword(s):

Protected Areas ◽

Predictive Models ◽

Tree Species ◽

Beta Diversity ◽

Distribution Data ◽

Gamma Diversity ◽

Conservation Practice ◽

Alpha And Beta Diversity ◽

Community Turnover ◽

Data Limitations

Summary The available tools and approaches to inform conservation decisions commonly assume detailed distribution data. We examine how well-established ecological concepts about patterns in local richness and community turnover can help overcome data limitations when planning future protected areas. To inform our analyses, we surveyed tree species in protected areas in the southern Appalachian Mountains in the eastern USA. We used the survey data to construct predictive models for alpha and beta diversity based on readily observed biophysical variables and combined them to create a heuristic that could predict among-site richness in trees (gamma diversity). The predictive models suggest that site elevation and latitude in this montane system explain much of the variation in alpha and beta diversity in tree species. We tested how well resulting protected areas would represent species if a conservation planner lacking detailed species inventories for candidate sites were to rely only on our alpha, beta and gamma diversity predictions. Our approach selected sites that, when aggregated, covered a large proportion of the overall species pool. The combined gamma diversity models performed even better when we also accounted for the cost of protecting sites. Our results demonstrate that classic community biogeography concepts remain highly relevant to conservation practice today.

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Gut Microbiome in Psoriasis: An Updated Review

Pathogens ◽

10.3390/pathogens9060463 ◽

2020 ◽

Vol 9 (6) ◽

pp. 463

Author(s):

Mariusz Sikora ◽

Albert Stec ◽

Magdalena Chrabaszcz ◽

Aleksandra Knot ◽

Anna Waskiel-Burnat ◽

...

Keyword(s):

Gut Microbiome ◽

Beta Diversity ◽

Large Scale ◽

Skin Diseases ◽

Intestinal Barrier ◽

Alpha Diversity ◽

Current Data ◽

Intestinal Microbiome ◽

Microbial Composition ◽

Alpha And Beta Diversity

(1) Background: A growing body of evidence highlights that intestinal dysbiosis is associated with the development of psoriasis. The gut–skin axis is the novel concept of the interaction between skin diseases and microbiome through inflammatory mediators, metabolites and the intestinal barrier. The objective of this study was to synthesize current data on the gut microbial composition in psoriasis. (2) Methods: We conducted a systematic review of studies investigating intestinal microbiome in psoriasis, using the PRISMA checklist. We searched MEDLINE, EMBASE, and Web of Science databases for relevant published articles (2000–2020). (3) Results: All of the 10 retrieved studies reported alterations in the gut microbiome in patients with psoriasis. Eight studies assessed alpha- and beta-diversity. Four of them reported a lack of change in alpha-diversity, but all confirmed significant changes in beta-diversity. At the phylum-level, at least two or more studies reported a lower relative abundance of Bacteroidetes, and higher Firmicutes in psoriasis patients versus healthy controls. (4) Conclusions: There is a significant association between alterations in gut microbial composition and psoriasis; however, there is high heterogeneity between studies. More unified methodological standards in large-scale studies are needed to understand microbiota’s contribution to psoriasis pathogenesis and its modulation as a potential therapeutic strategy.

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