Colonisation of leaf litter by aquatic invertebrates in an Atlantic Forest stream

Riparian vegetation along streams in the Atlantic Forest in Brazil contributes to the formation of a highly heterogeneous leaf litter in streambeds. To investigate the structure and composition of the aquatic invertebrate community during the process of leaf decomposition of two plant species present along the banks of the stream studied, 21 plastic mesh bags containing 2.5g (dry weight) of leaf matter from each species (Alchornea glandulosa (Vell) and Cabralea canjerana End. and Poeppig), for a total of 5.0g, were placed in the streambed. Three bags were removed after 3, 6, 9, 12, 24, 48 and 96 days. The taxonomic density was negatively correlated with the remaining weight. The high density of collector organisms, such as Chironomidae, Oligochaeta and Amphipoda, on the last day of incubation, probably occurred due to the increased amount of fine organic matter in the more advanced decomposition stages. The highest α diversity (Shannon-Wiener) values were observed for the 3rd and 96th days of the experiment, while the β diversity values showed that these days presented the highest variation in the taxonomic composition, thus presenting a different faunistic composition. This study showed that the trophic structure and composition of aquatic invertebrates changes during the decomposition of leaf litter. The faunistic abundance and diversity observed in this study indicate that the entrance of material from plants growing along streams provides favorable conditions for the colonisation and establishment of invertebrates in lower-order streams, and thus points to the need to preserve riparian vegetation.

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Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

Marine Ecology Progress Series ◽

10.3354/meps13419 ◽

2020 ◽

Vol 648 ◽

pp. 19-38

Author(s):

AI Azovsky ◽

YA Mazei ◽

MA Saburova ◽

PV Sapozhnikov

Keyword(s):

Species Abundance ◽

Abundance Ratio ◽

Wave Action ◽

Coarse Grained ◽

Sediment Properties ◽

Β Diversity ◽

Α Diversity ◽

Wide Range ◽

Similar Mode ◽

Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

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Expected impacts of climate change on tree ferns distribution and diversity patterns in subtropical Atlantic Forest

10.1101/2020.01.16.909614 ◽

2020 ◽

Author(s):

André Luís de Gasper ◽

Guilherme Salgado Grittz ◽

Carlos Henrique Russi ◽

Carlos Eduardo Schwartz ◽

Arthur Vinicius Rodrigues

Keyword(s):

Climate Change ◽

Atlantic Forest ◽

Regional Scale ◽

Distribution Area ◽

Study Region ◽

Β Diversity ◽

Forest Sites ◽

Tree Ferns ◽

Α Diversity ◽

Climatic Scenarios

ABSTRACTTree ferns are common elements in the Atlantic Forest domain, sometimes reaching more than half of total dominance at forest sites. Just as most groups, climate change might impact the distribution and diversity of tree ferns. To investigate the extent of these impacts in the subtropical Atlantic Rainforest, we measured the changes in species distribution, α- and β-diversity between current climate and future climatic scenarios for 2050. Most tree ferns species tend to lose their distribution area. Hence, species richness tends to decrease in the future, especially in the Rainforest sites. In general, β-diversity tend to not change on the regional scale, but some sites can change its relative singularity in composition. Our results show that climate change can impact distribution and α-diversity of tree ferns, but with no trend to cause homogenization in the tree ferns of the study area. Protected Areas (PAs) in our study region manage to withhold more α-diversity than areas without PAs — the same applies to β-diversity. Our study offers a new light into the effects of climate change in tree ferns by integrating the evaluation of its impacts on distribution, α- and β-diversity in all study areas and inside PAs.

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Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients: a retrospective cohort study in a Mediterranean area.

10.1101/2021.09.28.461924 ◽

2021 ◽

Author(s):

Maria Paz Ventero ◽

Oscar Moreno-Perez ◽

Carmen Molina-Pardines ◽

Andreu Paytuvi-Gallart ◽

Vicente Boix ◽

...

Keyword(s):

Retrospective Cohort ◽

Invasive Mechanical Ventilation ◽

Fatal Outcome ◽

Mediterranean Area ◽

Taxonomic Composition ◽

Microbiome Composition ◽

Tertiary Centre ◽

Β Diversity ◽

Hospitalised Patients ◽

Α Diversity

Background: There is mounting evidence suggesting that the microbiome composition could be different in COVID-19 patients. However, the relationship between microbiota and COVID-19 severity progression is still being assessed. This study aimed to analyse the diversity and taxonomic composition of the nasopharyngeal microbiota, to determine its association with COVID-19 clinical outcome. Methods and Findings: Samples came from a retrospective cohort of adult patients with COVID-19, hospitalised in a tertiary centre. To study the nasopharyngeal microbiota, we utilized 16S rRNA sequencing. Raw sequences were processed by QIIME2. The associations between the microbiota, invasive mechanical ventilation (IMV), and all-cause mortality were analysed by multiple logistic regression (OR; 95%CI), adjusted for age, gender, and comorbidity. 177 patients were included: median age 68.0 years, 57.6% males, 59.3% had a Charlson comorbidity index ≥3, and 89.2% with pneumonia. The microbiota α diversity indexes were lower in patients with a fatal outcome, and this association persisted after adjustment for the main confounders; whereas the β diversity analysis showed a significant clustering, grouping the patients with a fatal outcome. After multivariate adjustment, the presence of Selenomonas spp., Filifactor spp., Actinobacillus spp., or Chroococcidiopsis spp., was associated with a reduced risk of IMV (adjusted OR 0.06[95%CI 0.01–0.047], p = 0.007). Conclusions: The microbiota diversity and taxonomic composition are related to COVID-19 severity. Higher diversity and the presence of certain genera in the nasopharyngeal microbiota seem to be early biomarkers of a favourable clinical evolution in hospitalised patients with moderate to severe SARS-CoV-2 infections.

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Effects of several in-feed antibiotic combinations on the abundance and diversity of fecal microbes in weaned pigs

Canadian Journal of Microbiology ◽

10.1139/cjm-2016-0681 ◽

2017 ◽

Vol 63 (5) ◽

pp. 402-410 ◽

Cited By ~ 6

Author(s):

Huizhi Li ◽

Tingting Liang ◽

Qingpo Chu ◽

Feilong Xu ◽

Yuan Li ◽

...

Keyword(s):

Experimental Data ◽

High Throughput Sequencing ◽

Antibiotic Administration ◽

Weaned Pigs ◽

Intestinal Microbes ◽

Β Diversity ◽

Α Diversity ◽

Relative Abundances ◽

Abundance And Diversity ◽

Zinc Bacitracin

To characterize the effects of several subtherapeutic antibiotic combinations on the abundance and diversity of fecal microbes, 400 weaned pigs were selected and randomly assigned to 8 groups, where they were continuously fed different antibiotic combinations for 28 days. Then, a total of 48 pigs were randomly selected to collect feces samples for DNA extraction and 16S rRNA high-throughput sequencing. Compared with that of pigs without antibiotic administration, the diversities of fecal microbes were decreased in the pigs fed chlortetracycline (CTC), olaquindox (OLA), and either enramycin (ER) or virginiamycin (VIR), and the relative abundances of members of the phylum Bacteroidetes and the genus Prevotella were increased. Compared with that of pigs without antibiotic administration, the relative abundances of members of the phylum Proteobacteria and the genus Succinivibrio were decreased in the pigs fed CTC, a mixture of zinc bacitracin (ZB) + colistin sulfate (COL), a mixture of CTC+ZB+COL, a mixture of CTC+OLA, or a mixture of CTC+OLA+ER. α-Diversity and β-diversity were decreased (P < 0.05) in the pigs fed ZB+COL or a mixture of CTC+OLA+ER or CTC+OLA+VIR. This study provides experimental data to deepen our understanding on the effects of antibiotic combinations on intestinal microbes.

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ГИГРОТОП И ТРОФОТОП БИОГЕОЦЕНОЗОВ СТЕПНОГО ПРИДНЕПРОВЬЯ КАК ДЕТЕРМИНАНТЫ β-РАЗНООБРАЗИЯ СООБЩЕСТВ ДОЖДЕВЫХ ЧЕРВЕЙ (LUMBRICIDAE)

Biological Bulletin of Bogdan Chmelnitskiy Melitopol State Pedagogical University ◽

10.15421/201651 ◽

2016 ◽

Vol 6 (2) ◽

pp. 188-222 ◽

Cited By ~ 1

Author(s):

A. V. Zhukov ◽

D. B. Shatalin

Keyword(s):

Forest Type ◽

Steppe Zone ◽

Forest Steppe ◽

Ecological Groups ◽

Β Diversity ◽

Α Diversity ◽

Abundance Variation ◽

Abundance And Diversity ◽

Forest Typology

The role of the hygrotope and trophotope of the steppe Pridniprovie biogeoceonosis has been discussed in present article as being determinants of the β-diversity of earthworms (Lumbricidae) communities. Material has been colected to the period 1997-2015. 180 sample polygons have been studied which located in various types of biogeoceonosis. Biogeoceonotic characteristic of the sample polygons have been made on the basis of professor A.L. Belgard forest typology of a steppe zone of Ukraine. Earthworm communities of the steppe Pridniprovie have been established to be presented by 16 species. Hygrotopes, trophotopes and bitope ceonosis features have been shown to be able to explain 72.4 % of a communities’ abundance variation and 73.7 of their % α-diversity by means of second order model. Earthworm communities’ abundance reache their maximum values at a combination of conditions of humidity from hygromesophilous to hygrophilous and conditions of edaphotope trophicity from Dc (linden oakwood) to Dn (elm-ashen oakwood and alder forests). The maximum diversity of earthworm communities has been stated to be characteristic for a combination of mesohygrophilous conditions and a trophicity mode Dc, that there corresponds to forest type a linden oakwood with aegopodium. The coenomorphic structure of the biogeocoenosis is statistically significant predictors of both abundance and α-diversity of earthworm communities. Earthworm communities of marsh monocoenosis, meadow-steppe amphicoenosis and steppe monocoenosis have been found as being characterised by minimum abundance and diversity. Moderate level abundance and diversity are characteristic for meadow-forest amphicoenosis, forest pseudomonocoenosis with elements of transformation to steppe and forest-steppe amphicoenosis. High levels of these indexes are typical for forest monocoenosis. Given other conditions of humidity and edaphotope trophicity being equal in forest monocoenosis abundance and diversity of earthworm communities will be higher than in other biogeocoenosis types. The MDM-analysis (Multinomial Diversity Model) reveals that habitats coenotic features define 12.61 % of all entropy of earthworm communities, hygrotopes – 24.12 %, trophotopes – 12.3 %. The square-law hygrotope member defines 10.93 %, and trophotope – 2.05 %. Hygrotope and trophotope interaction defines 1.53 % of entropy of earthworm communities. Sites (α -diversity) define 36.45 % of entropy. There are other factors which influence a diversity of earthworm communities besides a humidity, trophicity and habitat coenotic features. Steppe Pridniprovie earthworm complexes have been divided into ecological groups on the basis of relation to humidity (hygromorphes) and to edaphotope trophicity (trophocenomorphes). Earthworms hygromorphes are presented by xerophylous (2 species), mesophylous (9 species), hygrophylous (4 species), ultrahygrophylous (1 species). Trophocoenomorphes are presented by oligotrophocoenomorphes (1 species), oligomesotrophocoenomorphes (4 species), mesotrophocoenomorphes (9 species), megatrophocoenomorphes (2 species).

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Taxonomic composition and diversity of the gut microbiota in relation to habitual diet in Korean adults

10.21203/rs.2.22869/v1 ◽

2020 ◽

Author(s):

Hwayoung Noh ◽

Hwan-Hee Jang ◽

Gichang Kim ◽

Semi Zouiouich ◽

Su-Yeon Cho ◽

...

Keyword(s):

Gut Microbiota ◽

Smoking Status ◽

Taxonomic Composition ◽

Alcoholic Beverages ◽

Rrna Gene ◽

Fermented Foods ◽

Korean Adults ◽

Β Diversity ◽

Α Diversity ◽

Habitual Diet

Abstract Background: Little is known of the relationship between the Korean habitual diet and gut microbiota composition. We investigated associations of habitual dietary intake of foods and nutrients with the taxonomic composition and diversity of gut microbiota in 222 Korean adults aged 18-58 years in a cross-sectional study. Gut microbial taxonomic composition and diversity data were obtained by 16S rRNA gene sequencing of bacterial DNA extracted from fecal samples. Habitual diet for the previous year was collected by a validated food frequency questionnaire. Correlations between intakes of food and nutrients and gut microbial taxonomic composition were examined with adjustment for sex, age, body mass index, dietary supplement, smoking status, and sample batch. Specific dietary patterns associated with α-diversity were identified by reduced rank regression. Enterotypes of gut microbiota were explored by principal coordinate analysis based on β-diversity.Results: The intakes of vegetables, fermented legumes, and potatoes were positively associated with the Firmicutes-to-Bacteroidetes (F/B) ratio, while the intakes of noodle products and non-alcoholic beverages were inversely related to the F/B ratio (all P<0.05). A dietary pattern associated with higher α-diversity (HiαDP) was characterized by greater intakes of fermented legumes, vegetables, potatoes, tea, and fruit/fruit juice and lower intakes of non-alcoholic beverages. Among three different enterotypes identified based on the β-diversity, the Ruminococcus enterotype had higher scores of the HiαDP and was more strongly associated with intakes of vegetables and nuts/seeds, compared to the two other enterotypes. Conclusions: We conclude that the habitual diet in Korean adults was associated with gut microbial taxonomic composition and diversity. A higher intake of plant-based and fermented foods was associated with distinct gut microbial enterotypes in Korean adults.

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Transitions in oral and gut microbiome of HPV+ oropharyngeal squamous cell carcinoma following definitive chemoradiotherapy (ROMA LA-OPSCC study)

British Journal of Cancer ◽

10.1038/s41416-020-01253-1 ◽

2021 ◽

Author(s):

Marc Oliva ◽

Pierre H. H. Schneeberger ◽

Victor Rey ◽

Matthew Cho ◽

Rachel Taylor ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Taxonomic Composition ◽

Oropharyngeal Squamous Cell Carcinoma ◽

Oral Microbiome ◽

Metagenomic Sequencing ◽

Α Diversity ◽

16S Rna ◽

The Impact

Abstract Background Oral and gut microbiomes have emerged as potential biomarkers in cancer. We characterised the oral and gut microbiomes in a prospective observational cohort of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) patients and evaluated the impact of chemoradiotherapy (CRT). Methods Saliva, oropharyngeal swabs over the tumour site and stool were collected at baseline and post-CRT. 16S RNA and shotgun metagenomic sequencing were used to generate taxonomic profiles, including relative abundance (RA), bacterial density, α-diversity and β-diversity. Results A total of 132 samples from 22 patients were analysed. Baseline saliva and swabs had similar taxonomic composition (R2 = 0.006; p = 0.827). Oropharyngeal swabs and stool taxonomic composition varied significantly by stage, with increased oral RA of Fusobacterium nucleatum observed in stage III disease (p < 0.05). CRT significantly reduced the species richness and increased the RA of gut-associated taxa in oropharyngeal swabs (p < 0.05), while it had no effect in stool samples. These findings remained significant when adjusted by stage, smoking status and antibiotic use. Conclusions Baseline oral and gut microbiomes differ by stage in this HPV+ cohort. CRT caused a shift towards a gut-like microbiome composition in oropharyngeal swabs. Stage-specific features and the transitions in oral microbiome might have prognostic and therapeutic implications.

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ALLELOPATHIC EFFECTS OF ROSE WOOD, GUAVA, EUCALYPTUS, SACRED FIG AND JAMAN LEAF LITTER ON GROWTH AND YIELD OF WHEAT ( Triticum aestivum L.) IN A WHEAT-BASED AGROFORESTRY SYSTEM

Planta Daninha ◽

10.1590/s0100-83582017350100060 ◽

2017 ◽

Vol 35 (0) ◽

Cited By ~ 3

Author(s):

J. IQBAL ◽

H.A. RAUF ◽

A.N. SHAH ◽

B. SHAHZAD ◽

M.A Bukhari

Keyword(s):

Grain Yield ◽

Leaf Litter ◽

Eucalyptus Camaldulensis ◽

Dry Weight ◽

Triticum Aestivum L ◽

Agroforestry System ◽

Agroforestry Systems ◽

Growth And Yield ◽

Syzygium Cumini ◽

Allelopathic Effects

ABSTRACT Selection of tree species under agroforestry systems is crucial to sustain the productivity of a crop. In present study, allelopathic effects of the leaf litters of 5 trees named Rose wood (Dalbergia sissoo), Guava (Pisidium guajava), Eucalyptus (Eucalyptus camaldulensis), Sacred fig (Ficus religiosa) and Jaman (Syzygium cumini) species on wheat growth and yield was examined. Leaf litter of each tress species was mixed in soil with two doses @ 100 and 200 g of leaves of each species per pot. Higher shoot length, shoot dry weight, number of spikelets per spike and biological yield were recorded in 200 g sun dried Jaman (Syzygium cumini) leaves. Total number of tillers per plant and number of ears per plant were higher under the application of Eucalyptus camaldulensis leaves (200 g sun dried) as compared to other treatments. Spike length, grain yield per pot, number of grains per pot and harvest index were maximum in 200 g sun-dried Sacred fig (Ficu sreligiosa) leaves. Majority of the parameters were promoted at lower doses of leaves per pot, however, at higher doses they started inhibiting the growth and grain yield of wheat.

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Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa141 ◽

2020 ◽

Vol 96 (8) ◽

Author(s):

Judith Mogouong ◽

Philippe Constant ◽

Robert Lavallée ◽

Claude Guertin

Keyword(s):

Population Density ◽

Gut Microbiome ◽

Emerald Ash Borer ◽

Agrilus Planipennis ◽

Economic Damage ◽

Taxonomic Structure ◽

Rrna Gene ◽

Local Conditions ◽

Β Diversity ◽

Α Diversity

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.

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Arthropod community structure in pastures of an island archipelago (Azores): looking for local–regional species richness patterns at fine-scales

Bulletin of Entomological Research ◽

10.1079/ber2004289 ◽

2004 ◽

Vol 94 (2) ◽

pp. 111-121 ◽

Cited By ~ 22

Author(s):

P.A.V. Borges ◽

V.K. Brown

Keyword(s):

Species Richness ◽

Regional Scale ◽

Local Scale ◽

Local Species Richness ◽

Β Diversity ◽

Arthropod Species ◽

Α Diversity ◽

Local Species ◽

Richness Patterns

AbstractThe arthropod species richness of pastures in three Azorean islands was used to examine the relationship between local and regional species richness over two years. Two groups of arthropods, spiders and sucking insects, representing two functionally different but common groups of pasture invertebrates were investigated. The local–regional species richness relationship was assessed over relatively fine scales: quadrats (= local scale) and within pastures (= regional scale). Mean plot species richness was used as a measure of local species richness (= α diversity) and regional species richness was estimated at the pasture level (= γ diversity) with the ‘first-order-Jackknife’ estimator. Three related issues were addressed: (i) the role of estimated regional species richness and variables operating at the local scale (vegetation structure and diversity) in determining local species richness; (ii) quantification of the relative contributions of α and β diversity to regional diversity using additive partitioning; and (iii) the occurrence of consistent patterns in different years by analysing independently between-year data. Species assemblages of spiders were saturated at the local scale (similar local species richness and increasing β-diversity in richer regions) and were more dependent on vegetational structure than regional species richness. Sucking insect herbivores, by contrast, exhibited a linear relationship between local and regional species richness, consistent with the proportional sampling model. The patterns were consistent between years. These results imply that for spiders local processes are important, with assemblages in a particular patch being constrained by habitat structure. In contrast, for sucking insects, local processes may be insignificant in structuring communities.

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