Impacts of Forest Fire on Understory Species Diversity in Canary Pine Ecosystems on the Island of La Palma

Forest fires are drivers of spatial patterns and temporal dynamics of vegetation and biodiversity. On the Canary Islands, large areas of pine forest exist, dominated by the endemic Canary Island pine, Pinus canariensis C. Sm. These mostly natural forests experience wildfires frequently. P. canariensis is well-adapted to such impacts and has the ability to re-sprout from both stems and branches. In recent decades, however, anthropogenically caused fires have increased, and climate change further enhances the likelihood of large forest fires. Through its dense, long needles, P. canariensis promotes cloud precipitation, which is an important ecosystem service for the freshwater supply of islands such as La Palma. Thus, it is important to understand the regeneration and vegetation dynamics of these ecosystems after fire. Here, we investigated species diversity patterns in the understory vegetation of P. canariensis forests after the large 2016 fire on the southern slopes of La Palma. We analyzed the effect of fire intensity, derived from Sentinel-2 NDVI differences, and of environmental variables, on species richness (alpha diversity) and compositional dissimilarity (beta diversity). We used redundancy analysis (dbRDA), Bray–Curtis dissimilarity, and variance partitioning for this analysis. Fire intensity accounted for a relatively small proportion of variation in alpha and beta diversity, while elevation was the most important predictor. Our results also reveal the important role of the endemic Lotus campylocladus ssp. hillebrandii (Christ) Sandral & D.D.Sokoloff for understory diversity after fire. Its dominance likely reduces the ability of other species to establish by taking up nutrients and water and by shading the ground. The mid- to long-term effects are unclear since Lotus is an important nitrogen fixer in P. canariensis forests and can reduce post-fire soil erosion on steep slopes.

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Robust, data-driven bioregionalizations emerge from diversity concordance

10.1101/2021.08.31.458457 ◽

2021 ◽

Author(s):

Cristian S. Montalvo-Mancheno ◽

Jessie Buettel ◽

Stefania Ondei ◽

Barry W. Brook

Keyword(s):

Species Diversity ◽

Beta Diversity ◽

Alpha Diversity ◽

Data Driven ◽

Conservation Units ◽

Conservation Action ◽

Diversity Patterns ◽

Alpha And Beta Diversity ◽

Terrestrial Vertebrates ◽

Site Diversity

Aim: Despite the increasing interest in developing new bioregionalizations and assessing the most widely accepted biogeographic frameworks, no study to date has sought to systematically define a system of small bioregions nested within larger ones that better reflect the distribution and patterns of biodiversity. Here, we examine how an algorithmic, data-driven model of diversity patterns can lead to an ecologically interpretable hierarchy of bioregions. Location: Australia. Time period: Present. Major taxa studied: Terrestrial vertebrates and vascular plants. Methods: We compiled information on the biophysical characteristics and species occupancy of Australia′s geographic conservation units (bioregions). Then, using cluster analysis to identify groupings of bioregions representing optimal discrete-species areas, we evaluated what a hierarchical bioregionalization system would look like when based empirically on the within- and between-site diversity patterns across taxa. Within an information-analytical framework, we then assessed the degree to which the World Wildlife Fund′s (WWF) biomes and ecoregions and our suite of discrete-species areas are spatially associated and compared those results among bioregionalization scenarios. Results: Information on biodiversity patterns captured was moderate for WWF′s biomes (50–58% for birds′ beta, and plants′ alpha and beta diversity, of optimal discrete areas, respectively) and ecoregions (additional 4–25%). Our plants and vertebrate optimal areas retained more information on alpha and beta diversity across taxa, with the two algorithmically derived biogeographic scenarios sharing 86.5% of their within- and between-site diversity information. Notably, discrete-species areas for beta diversity were parsimonious with respect to those for alpha diversity. Main conclusions: Nested systems of bioregions must systematically account for the variation of species diversity across taxa if biodiversity research and conservation action are to be most effective across multiple spatial or temporal planning scales. By demonstrating an algorithmic rather than subjective method for defining bioregionalizations using species-diversity concordances, which reliably reflects the distributional patterns of multiple taxa, this work offers a valuable new tool for systematic conservation planning.

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The role of alpha and beta diversity in buffering the effects of intensifying natural disturbance regimes

10.5194/egusphere-egu2020-8248 ◽

2020 ◽

Author(s):

Julius Sebald ◽

Timothy Thrippleton ◽

Werner Rammer ◽

Harald Bugmann ◽

Rupert Seidl

Keyword(s):

Climate Change ◽

Forest Management ◽

Species Diversity ◽

Tree Species ◽

Beta Diversity ◽

Alpha Diversity ◽

Tree Species Diversity ◽

Alpha And Beta Diversity ◽

Disturbance Regimes ◽

The Impact

<div> <div> <div> <p>Forests are strongly affected by climatic changes, but impacts vary between tree species and prevailing site conditions. A number of studies suggest that increasing tree species diversity is a potent management strategy to decrease climate change impacts in general, and increase the resilience of forest ecosystems to changing disturbance regimes. However, most studies to date have focused on stand-level diversity in tree species (alpha diversity), which is often difficult to implement in operational forest management. Inter-species competition requires frequent management interventions to maintain species mixture and complicates the production of high-quality stemwood. An alternative option to increasing alpha diversity is to increase tree species diversity between forest stands (beta diversity). Here we quantify the effects of alpha and beta diversity on the impact of forest disturbances under climate change. We conducted a simulation experiment applying two forest landscape models (i.e. iLand and LandClim) in two landscapes with strongly contrasting environmental conditions in Central Europe. Simulations investigate different levels of tree species diversity (no diversity, low diversity and high diversity) in different spatial arrangements (alpha diversity, beta diversity). Subsequently a standard forest management regime and a series of prescribed disturbances are applied over 200 years. By analyzing biomass values relative to a no-disturbance run, variation in biomass over time and the number of trees > 30 cm dbh per hectare, we isolate the effect of tree species diversity on the resistance of forests to disturbances.</p> </div> </div> </div>

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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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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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AB1232 ORAL DYSBIOSIS REFLECTS THE IMMUNOLOGICAL ALTERATION OF RA REGARDING TO ACPA AND HLA DRB1*SE: NAGASAKI ISLAND STUDY

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2020-eular.5147 ◽

2020 ◽

Vol 79 (Suppl 1) ◽

pp. 1907.2-1907

Author(s):

Y. Tsuji ◽

M. Tamai ◽

S. Morimoto ◽

D. Sasaki ◽

M. Nagayoshi ◽

...

Keyword(s):

Beta Diversity ◽

Healthy Subjects ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Enzyme Linked Immunosorbent Assay ◽

Rrna Gene ◽

Oral Microbiota ◽

Unifrac Distance ◽

Alpha And Beta Diversity ◽

The Difference

Background:Anti-citrullinated protein antibody (ACPA) production is observed in several organs even prior to the onset of rheumatoid arthritis (RA), and oral mucosa is considered to be one of the important tissues. The presence of HLA-DRB1*SE closely associates with ACPA production. Saliva is considered to reflect the oral microbiota including periodontal disease. Alteration of oral microbiota of RA becomes to be normalized by DMARDs treatment, however, the interaction of HLA-DRB1*SE, ACPA and oral microbiota of RA patients remains to be elucidated.Objectives:The Nagasaki Island Study, which had started in 2014 collaborating with Goto City, is intended for research of the preclinical stage of RA, including ACPA/HLA genotype screening and ultrasound and magnetic resonance imaging examinations in high-risk subjects. Using the samples accumulated in this cohort, we have tried to investigate the difference of oral microbiota among RA patients and healthy subjects regarding to ACPA and HLA-DRB1*SE.Methods:Blood and salivary samples were obtained from 1422 subjects out of 4276 who have participated in the Nagasaki Island Study from 2016 to 2018. ACPA positivity was 1.7 % in total. Some of RA patients resided in Goto City participated in the Nagasaki Island Study. At this point, we selected 291 subjects, who were ACPA positive non-RA healthy subjects (n=22) and patients with RA (n=33, 11 subjects were ACPA positive and 22 ACPA negative respectively) as the case, age and gender matched ACPA negative non-RA healthy subjects (n=236) as the control. ACPA was measured by an enzyme-linked immunosorbent assay, and HLA genotyping was quantified by next-generation sequencing (Ref.1). The operational taxonomic unit (OUT) analysis using 16S rRNA gene sequencing were performed. The richness of microbial diversity within-subject (alpha diversity) was scaled via Shannon entropy. The dissimilarity between microbial community composition was calculated using Bray-Curtis distance as a scale, and differences between groups (beta diversity) were tested by permutational multivariate analysis of variance (PERMANOVA). In addition, UniFrac distance calculated in consideration of the distance on the phylogenetic tree were performed.Results:Median age 70 y.o., % Female 58.8 %. Among RA and non-RA subjects, not alpha diversity but beta diversity was statistically significance (p=0.022, small in RA). In RA subjects, both alpha and beta diversity is small (p<0.0001), especially significant in ACPA positive RA (Figure 1). Amongt RA subjects, presence of HLA-DRB1*SE did not show the difference but the tendency of being small of alpha diversity (p=0.29).Conclusion:Our study has suggested for the first time the association of oral microbiota alteration with the presence of ACPA and HLA-DRB1*SE. Oral dysbiosis may reflect the immunological status of patients with RA.References:[1]Kawaguchi S, et al. Methods Mol Biol 2018;1802: 22Disclosure of Interests:None declared

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Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

Microorganisms ◽

10.3390/microorganisms9112339 ◽

2021 ◽

Vol 9 (11) ◽

pp. 2339

Author(s):

Aleksei O. Zverev ◽

Arina A. Kichko ◽

Aleksandr G. Pinaev ◽

Nikolay A. Provorov ◽

Evgeny E. Andronov

Keyword(s):

Microbial Communities ◽

Plant Communities ◽

Plant Diversity ◽

Beta Diversity ◽

Mutual Influence ◽

Plant Root ◽

Alpha Diversity ◽

Diversity Indices ◽

Alpha And Beta Diversity ◽

Highly Correlated

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia.

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Impact of intrapartum antibiotics on the infant gastrointestinal microbiome: a narrative review

Archives of Disease in Childhood ◽

10.1136/archdischild-2021-322590 ◽

2021 ◽

pp. archdischild-2021-322590

Author(s):

Laura Diamond ◽

Rachel Wine ◽

Shaun K Morris

Keyword(s):

Gestational Age ◽

Beta Diversity ◽

Mode Of Delivery ◽

Alpha Diversity ◽

First Year ◽

Feeding Method ◽

Alpha And Beta Diversity ◽

Ovid Medline ◽

First Year Of Life ◽

The Impact

BackgroundThe composition of the infant gastrointestinal (GI) microbiome has been linked to adverse long-term health outcomes and neonatal sepsis. Several factors are known to impact the composition of the microbiome, including mode of delivery, gestational age, feeding method and exposure to antibiotics. The impact of intrapartum antibiotics (IPAs) on the infant microbiome requires further research.ObjectiveWe aimed to evaluate the impact of IPAs on the infant GI microbiome.MethodsWe searched Ovid MEDLINE and Embase Classic+Embase for articles in English reporting on the microbiome of infants exposed to IPAs from the date of inception to 3 January 2021. Primary outcomes included abundance and colonisation of Bifidobacterium and Lactobacillus, as well as alpha and beta diversity.Results30 papers were included in this review. In the first year of life, following exposure to IPAs, 30% (6/20) of infant cohorts displayed significantly reduced Bifidobacterium, 89% (17/19) did not display any significant differences in Lactobacillus colonisation, 21% (7/34) displayed significantly reduced alpha diversity and 35% (12/34) displayed alterations in beta diversity. Results were further stratified by delivery, gestational age (preterm or full term) and feeding method.ConclusionsIPAs impact the composition of the infant GI microbiome, resulting in possible reductions Bifidobacterium and alpha diversity, and possible alterations in beta diversity. Our findings may have implications for maternal and neonatal health, including interventions to prevent reductions in health-promoting bacteria (eg, probiotics) and IPA class selection.

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Evidence supporting the microbiota–gut–brain axis in a songbird

Biology Letters ◽

10.1098/rsbl.2020.0430 ◽

2020 ◽

Vol 16 (11) ◽

pp. 20200430

Author(s):

Morgan C. Slevin ◽

Jennifer L. Houtz ◽

David J. Bradshaw ◽

Rindy C. Anderson

Keyword(s):

Gut Microbiome ◽

Beta Diversity ◽

Alpha Diversity ◽

Cloacal Swab ◽

Cognitive Tasks ◽

Captive Population ◽

Wild Populations ◽

Alpha And Beta Diversity ◽

Microbiome Research ◽

Host Development

Recent research in mammals supports a link between cognitive ability and the gut microbiome, but little is known about this relationship in other taxa. In a captive population of 38 zebra finches ( Taeniopygia guttata ), we quantified performance on cognitive tasks measuring learning and memory. We sampled the gut microbiome via cloacal swab and quantified bacterial alpha and beta diversity. Performance on cognitive tasks related to beta diversity but not alpha diversity. We then identified differentially abundant genera influential in the beta diversity differences among cognitive performance categories. Though correlational, this study provides some of the first evidence of an avian microbiota–gut–brain axis, building foundations for future microbiome research in wild populations and during host development.

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Unimodal Relationships of Understory Alpha and Beta Diversity along Chronosequence in Coppiced and Unmanaged Beech Forests

Diversity ◽

10.3390/d12030101 ◽

2020 ◽

Vol 12 (3) ◽

pp. 101 ◽

Cited By ~ 3

Author(s):

Sándor Bartha ◽

Roberto Canullo ◽

Stefano Chelli ◽

Giandiego Campetella

Keyword(s):

Beta Diversity ◽

Management Practices ◽

Multiple Scales ◽

Forest Succession ◽

Spatial Scales ◽

Alpha Diversity ◽

Structural Diversity ◽

Diversity Indices ◽

Alpha And Beta Diversity ◽

Coppice Management

Patterns of diversity across spatial scales in forest successions are being overlooked, despite their importance for developing sustainable management practices. Here, we tested the recently proposed U-shaped biodiversity model of forest succession. A chronosequence of 11 stands spanning from 5 to 400 years since the last disturbance was used. Understory species presence was recorded along 200 m long transects of 20 × 20 cm quadrates. Alpha diversity (species richness, Shannon and Simpson diversity indices) and three types of beta diversity indices were assessed at multiple scales. Beta diversity was expressed by a) spatial compositional variability (number and diversity of species combinations), b) pairwise spatial turnover (between plots Sorensen, Jaccard, and Bray–Curtis dissimilarity), and c) spatial variability coefficients (CV% of alpha diversity measures). Our results supported the U-shaped model for both alpha and beta diversity. The strongest differences appeared between active and abandoned coppices. The maximum beta diversity emerged at characteristic scales of 2 m in young coppices and 10 m in later successional stages. We conclude that traditional coppice management maintains high structural diversity and heterogeneity in the understory. The similarly high beta diversities in active coppices and old-growth forests suggest the presence of microhabitats for specialist species of high conservation value.

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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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