scholarly journals Arthropod Biodiversity in Agricultural, Horticultural and Silvicultural Ecosystems with Special Reference to Spiders (Araneae) in Mid-hills of Meghalaya, India

Author(s):  
Jyotim Gogoi ◽  
Kennedy Ningthoujam

Abstract Spiders are the Arthropod and belong to the Phylum: Arthropoda, Class: Arachnida, Order: Araneae. Their occurrence worldwide is about 30,000 species belonging to the 60 families. Totally 4023 arthropods were collected from Silvicultural, Horticultural and Agricultural ecosystem (Maize, Potato and Rice) which belonged to 14 orders and 85 Nos. of different families. Among the ecosystem maximum diversity found in Silvicultural followed by Horticultural and Agricultural ecosystem in terms of alpha diversity such as Shannon Wiener index Simpsons D, Species number, Margelef D, Equitability J, Berger Parker index, Maclntosch U, Brillouin level, Fisher Alpha, Q Statistic and beta diversity such as Whittaker Bw, Cody Bc, Routledge Br, Routledge Bi, Routledge Be and Wilson & Shmida Bt.

2005 ◽  
Vol 137 (1) ◽  
pp. 120-127 ◽  
Author(s):  
Christopher M. Buddle ◽  
Julien Beguin ◽  
Elise Bolduc ◽  
Alida Mercado ◽  
Tara E. Sackett ◽  
...  

AbstractFor over three decades, the importance of taxon sampling curves for comparative biodiversity studies has been repeatedly stated. However, many entomologists (both within Canada and worldwide) continue to publish studies without standardizing their data to take sampling effort into account. We present a case study to illustrate the importance of such standardization, using the collection of spiders (Araneae) by pitfall traps as model data. Data were analyzed using rarefaction to represent one example of a taxon sampling curve, and by a variety of traditional diversity indices to describe alpha diversity. Raw species richness and single-index diversity measures (Shannon–Wiener, Simpson's, and Fisher's α) provided contradictory results. Rarefied species richness standardized to the number of individuals collected enabled more accurate comparisons of diversity and revealed when sampling was insufficient. Focusing on arthropods occurring in forested ecosystems, we also examined the use of taxon sampling curves in current literature by reviewing 133 published articles from 14 journals. Only 26% of the published articles in our review used a taxon sampling curve, and raw species richness and the Shannon–Wiener index of diversity were the most commonly used estimates. There is clearly a need to modify how alpha diversity is measured and compared for arthropod biodiversity studies. We recommend the abandonment of both raw species richness and single-index measures of diversity, and reiterate the need to use rarefaction or a related technique that allows for meaningful comparisons of species richness while taking into account sampling effort.


2014 ◽  
Vol 25 (3-4) ◽  
pp. 53-68
Author(s):  
I. V. Goncharenko ◽  
H. M. Holyk

Cenotic diversity and leading ecological factors of its floristic differentiation were studied on an example of two areas – Kyiv parks "Nivki" and "Teremki". It is shown that in megalopolis the Galeobdoloni-Carpinetum impatientosum parviflorae subassociation is formed under anthropogenic pressure on the typical ecotope of near-Dnieper hornbeam oak forests on fresh gray-forest soils. The degree of anthropogenic transformation of cenofloras can be estimated by the number of species of Robinietea and Galio-Urticetea classes, as well as neophytes and cultivars. Phytoindication for hemeroby index may be also used in calculation. We propose the modified index of biotic dispersion (normalized by alpha-diversity) for the estimation of ecophytocenotic range (beta-diversity) of releves series. We found that alpha-diversity initially increases (due to the invasion of antropophytes) at low level of antropogenic pressure, then it decreases (due to the loss of aboriginal species) secondarily with increasing of human impact. Also we found that beta-diversity (differential diversity) decreases, increasing homogeneity of plant cover, under the influence of anthropogenic factor. Vegetation classification was completed by a new original method of cluster analysis, designated as DRSA («distance-ranked sorting assembling»). The classification quality is suggested to be validated on the "seriation" diagram, which is а distance matrix between objects with gradient filling. Dark diagonal blocks confirm clusters’ density (intracluster compactness), uncolored off-diagonal blocks are evidence in favor of clusters’ isolation (intercluster distinctness). In addition, distinction of clusters (syntaxa) in ordination area suggests their independence. For phytoindication we propose to include only species with more than 10% constancy. Furthermore, for the description of syntaxonomic amplitude we suggest to use 25%-75% interquartile scope instead of mean and standard deviation. It is shown that comparative analysis of syntaxa for each ecofactor is convenient to carry out by using violin (bulb) plots. A new approach to the phytoindication of syntaxa, designated as R-phytoindication, was proposed for our study. In this case, the ecofactor values, calculated for individual releves, are not taken into account, however, the composition of cenoflora with species constancies is used that helps us to minimize for phytoindication the influence of non-typical species. We suggested a syntaxon’s amplitude to be described by more robust statistics: for the optimum of amplitude (central tendency) – by a median (instead of arithmetic mean), and for the range of tolerance – by an interquartile scope (instead of standard deviation). We assesses amplitudes of syntaxa by phytoindication method for moisture (Hd), acidity (Rc), soil nitrogen content (Nt), wetting variability (vHd), light regime (Lc), salt regime (Sl). We revealed no significant differences on these ecofactors among ecotopes of our syntaxa, that proved the variant syntaxonomic rank for all syntaxa. We found that the core of species composition of our phytocenoses consists of plants with moderate requirements for moisture, soil nitrogen, light and salt regime. We prove that the leading factor of syntaxonomic differentiation is hidden anthropogenic, which is not subject to direct measurement. But we detect that hidden factor of "human pressure" was correlated with phytoindication parameters (variables) that can be measured "directly" by species composition of plant communities. The most correlated factors were ecofactors of soil nitrogen, wetting variability, light regime and hemeroby. The last one is the most indicative empirically for the assessment of "human impact". We establish that there is a concept of «hemeroby of phytocenosis» (tolerance to human impact), which can be calculated approximately as the mean or the median of hemeroby scores of individual species which are present in it.


Nutrients ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 820
Author(s):  
Faye Chleilat ◽  
Alana Schick ◽  
Raylene A. Reimer

Background: Consuming a diet high in prebiotic fiber has been associated with improved metabolic and gut microbial parameters intergenerationally, although studies have been limited to maternal intake with no studies examining this effect in a paternal model. Method: Male Sprague Dawley rats were allocated to either (1) control or (2) oligofructose-supplemented diet for nine weeks and then mated. Offspring consumed control diet until 16 weeks of age. Bodyweight, body composition, glycemia, hepatic triglycerides, gastrointestinal hormones, and gut microbiota composition were measured in fathers and offspring. Results: Paternal energy intake was reduced, while satiety inducing peptide tyrosine tyrosine (PYY) gut hormone was increased in prebiotic versus control fathers. Increased serum PYY persisted in female prebiotic adult offspring. Hepatic triglycerides were decreased in prebiotic fathers with a similar trend (p = 0.07) seen in female offspring. Gut microbial composition showed significantly reduced alpha diversity in prebiotic fathers at 9 and 12 weeks of age (p < 0.001), as well as concurrent differences in beta diversity (p < 0.001), characterized by differences in Bifidobacteriaceae, Lactobacillaceae and Erysipelotrichaceae, and particularly Bifidobacterium animalis. Female prebiotic offspring had higher alpha diversity at 3 and 9 weeks of age (p < 0.002) and differences in beta diversity at 15 weeks of age (p = 0.04). Increases in Bacteroidetes in female offspring and Christensenellaceae in male offspring were seen at nine weeks of age. Conclusions: Although paternal prebiotic intake before conception improves metabolic and microbiota outcomes in fathers, effects on offspring were limited with increased serum satiety hormone levels and changes to only select gut bacteria.


Author(s):  
Maciej Chichlowski ◽  
Nicholas Bokulich ◽  
Cheryl L Harris ◽  
Jennifer L Wampler ◽  
Fei Li ◽  
...  

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 &lt; 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).


Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 463
Author(s):  
Mariusz Sikora ◽  
Albert Stec ◽  
Magdalena Chrabaszcz ◽  
Aleksandra Knot ◽  
Anna Waskiel-Burnat ◽  
...  

(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.


2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1907.2-1907
Author(s):  
Y. Tsuji ◽  
M. Tamai ◽  
S. Morimoto ◽  
D. Sasaki ◽  
M. Nagayoshi ◽  
...  

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


2021 ◽  
Vol 9 (11) ◽  
pp. 2339
Author(s):  
Aleksei O. Zverev ◽  
Arina A. Kichko ◽  
Aleksandr G. Pinaev ◽  
Nikolay A. Provorov ◽  
Evgeny E. Andronov

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.


2014 ◽  
Vol 26 (2) ◽  
pp. 129-142 ◽  
Author(s):  
Suelen Cristina Alves da Silva ◽  
Armando Carlos Cervi ◽  
Cleusa Bona ◽  
André Andrian Padial

AIM: Investigate spatial and temporal variation in the aquatic macrophyte community in four urban reservoirs located in Curitiba metropolitan region, Brazil. We tested the hypothesis that aquatic macrophyte community differ among reservoirs with different degrees of eutrophication. METHODS: The reservoirs selected ranged from oligotrophic/mesotrophic to eutrophic. Sampling occurred in October 2011, January 2012 and June 2012. Twelve aquatic macrophytes stands were sampled at each reservoir. Species were identified and the relative abundance of aquatic macrophytes was estimated. Differences among reservoirs and over sampling periods were analyzed: i) through two‑way ANOVAs considering the stand extent (m) and the stand biodiversity - species richness, evenness, Shannon-Wiener index and beta diversity (species variation along the aquatic macrophyte stand); and ii) through PERMANOVA considering species composition. Indicator species that were characteristic for each reservoir were also identified. RESULTS: The aquatic macrophyte stand extent varied among reservoirs and over sampling periods. Species richness showed only temporal variation. On the other hand, evenness and Shannon-Wiener index varied only among reservoirs. The beta diversity of macrophyte stands did not vary among reservoirs or over time, meaning that species variability among aquatic macrophyte stands was independent of the stand extent and reservoir eutrophication. Community composition depended on the reservoir and sampling period. CONCLUSIONS: Our results support our initial expectation that reservoirs of different degrees of eutrophication have different aquatic macrophyte communities. As a consequence, each reservoir had particular indicator species. Therefore, monitoring and management efforts must be offered for each reservoir individually.


2021 ◽  
Vol 8 ◽  
Author(s):  
Robert Valeris-Chacin ◽  
Maria Pieters ◽  
Haejin Hwang ◽  
Timothy J. Johnson ◽  
Randall S. Singer

Infection with Campylobacter species is one of the leading causes of bacterial diarrhea in humans in the US. Chickens, which become colonized on the farm, are important reservoirs of this bacterium. Campylobacter can establish itself in the broiler house via a variety of sources, can survive in the litter of the house, and possibly persist over successive flock cycles. However, the role of the broiler litter microbiome on Campylobacter persistence is not clear. A matched case-control study was conducted to determine whether the broiler litter microbiome composition was associated with Campylobacter isolation within the broiler house. Flocks were classified as cases when either Campylobacter jejuni or Campylobacter coli was isolated in boot sock samples, or as controls otherwise. Case and control flocks were matched at the broiler house level. Composite broiler litter samples were collected and used for DNA extraction and 16S rRNA gene V4 region sequencing. Reads were processed using the DADA2 pipeline to obtain a table of amplicon sequence variants. Alpha diversity and differential bacterial relative abundance were used as predictors of Campylobacter isolation status in conditional logistic regression models adjusting for flock age and sampling season. Beta diversity distances were used as regressors in stratified PERMANOVA with Campylobacter isolation status as predictor, and broiler house as stratum. When Campylobacter was isolated in boot socks, broiler litter microbiome richness and evenness were lower and higher, respectively, without reaching statistical significance. Campylobacter isolation status significantly explained a small proportion of the beta diversity (genus-level Aitchison dissimilarity distance). Clostridium and Anaerostipes were positively associated with Campylobacter isolation status, whereas Bifidobacterium, Anaerosporobacter, and Stenotrophomonas were negatively associated. Our results suggest the presence of bacterial interactions between Campylobacter and the broiler litter microbiome. The negative association of Campylobacter with Bifidobacterium, Anaerosporobacter, and Stenotrophomonas in litter could be potentially exploited as a pre-harvest control strategy.


Author(s):  
Ze Ren ◽  
Hongkai Gao

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.


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