Non-metric Dimensional Scaling Research Articles

The Effects of Salinity and Genotype on the Rhizospheric Mycobiomes in Date Palm Seedlings.

Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, 'Zabad', and the tolerant cultivar, 'Umsila'. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool. The sequencing of 12 mycobiome libraries yielded 905,198 raw sequences of 268,829 high-quality reads that coded for 135 unique and annotatable operational taxonomic units (OTUs). An OTU analysis revealed differences in the rhizofungal community structures between the treatments regardless of genotype, and non-metric dimensional scaling (N-MDS) analyses demonstrated distinct separations between the cultivars under saline stress. However, these differences were not detected under the control environmental conditions, i.e., no salinity. The rhizospheric fungal community included four phyla (Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota), with differences in the abundances of Aspergillus, Clonostachys, and Fusarium genera in response to salinity, regardless of the genotype. Differential pairwise comparisons showed that Fusarium falciforme-solani and Aspergillus sydowii-versicolor increased in abundance under saline conditions, providing potential future in vitro isolation guidelines for plant growth-promoting fungi. This study highlights the intricate dynamics of the rhizosphere microbial communities in date palms and their responses to salt stress. Additionally, we found no support for the hypothesis that indigenous epiphytic fungal communities are significantly involved in salinity tolerance in date palms.

Beneath the Surface: Investigating soil microbial and metazoa communities at various depths in a natural desert ecosystem inhabited by Karelinia caspia

Soil organisms play a pivotal role in terrestrial ecosystems, sparking growing curiosity about the comprehensive diversity of subterranean biota across large ecological levels. Soil inhabitants’ exhibit varied responses to soil physicochemical properties (SPPs) across desert ecosystem. Yet, the knowledge of their population dynamics across different soil depths (SDs) in the indigenous natural dominant zone of Karelinia caspia, a primary desert shrub in China, remains limited. This study employed advanced illumina sequencing to assess soil bacteria, fungi, archaea, protist, and metazoa populations across six distinct SDs (0 to 100 cm) within the K. caspia desert landscape. Our findings indicate a descending alpha diversity pattern in bacteria, archaea, and protists as soil depth increases, contrary to fungi and metazoa, which exhibit the opposite trend. SDs significantly shape soil biota beta diversity, notably impacting bacteria, protists, and fungi, as revealed by Non-Metric Dimensional Scaling. Prominent classes include Actinobacteria, Sordariomycetes, Nitrososphaeria, Spirotrichea, and Nematoda for soil bacteria, fungi, archaea, protists, and metazoa, respectively. Correlation analysis between predominant biotic communities' vertical distribution and SPPs variations revealed total potassium (TK) and pH's pronounced influence on bacteria, while fungi were affected by total nitrogen (TN) and soil water content (SWC). Archaea exhibit sensitivity to SWC, available potassium (AK), and available phosphorus (AP); protists respond to C/N-Ratio, nitrate (NO3), and total phosphorus (TP); metazoa correlate with SWC, pH, and NO3. Overall, these findings offer valuable insights regarding population fluctuations of soil biota within naturally established K. caspia across vertical soil strata within China's desert ecosystem.

Characterisation of Milk Microbiota from Subclinical Mastitis and Apparently Healthy Dairy Cattle in Free State Province, South Africa.

Bovine mastitis is an inflammation of the udder tissue of the mammary gland brought on by microbial infections or physical damage. It is characterised by physical, chemical, and biological changes in the udder and milk. While several different bacterial species have been identified as causative agents of mastitis, many subclinical mastitis (SCM) cases remain culture-negative. The aim of this study was to characterise milk microbiota from SCM and apparently healthy dairy cows (non-SCM) by 16S rRNA sequencing. Alpha-diversity metrics showed significant differences between SCM cows and non-SCM counterparts. The beta-diversity metrics in the principal coordinate analysis significantly clustered samples by type (PERMANOVA test, p < 0.05), while non-metric dimensional scaling did not (PERMANOVA test, p = 0.07). The overall analysis indicated a total of 95 phyla, 33 classes, 82 orders, 124 families, 202 genera, and 119 bacterial species. Four phyla, namely Actinobacteriota, Bacteroidota, Firmicutes, and Proteobacteria collectively accounted for more than 97% of all sequencing reads from SCM and non-SCM cow samples. The most abundant bacterial classes were Actinobacteria, Bacilli, Bacteroidia, Clostridia, and Gammaproteobacteria in non-SCM cow samples, whilst SCM cow samples were mainly composed of Actinobacteria, Alphaproteobacteria, Bacilli, Clostridia, and Gammaproteobacteria. Dominant bacterial species in non-SCM cow samples were Anthropi spp., Pseudomonas azotoformans, P. fragi, Acinetobacter guillouiae, Enterococcus italicus, Lactococcus lactis, whilst P. azotoformans, Mycobacterium bovis, P. fragi, Acinetobacter guillouiae, and P. koreensis were dominant in the SCM cow samples. The current study found differences in bacterial species between SCM and non-SCM cow milk; hence, the need for detailed epidemiological studies.

Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination.

16S rRNA gene sequencing is widely used to characterize human and environmental microbiomes. Sequencing at scale facilitates better powered studies but is limited by cost and time. We identified two areas in our 16S rRNA gene library preparation protocol where modifications could provide efficiency gains, including (1) pooling of multiple PCR amplifications per sample to reduce PCR drift and (2) manual preparation of mastermix to reduce liquid handling. Using nasal samples from healthy human participants and a serially diluted mock microbial community, we compared alpha and beta diversity, and compositional abundance where the PCR amplification was conducted in triplicate, duplicate or as a single reaction, and where manually prepared or premixed mastermix was used. One hundred and fifty-eight 16S rRNA gene sequencing libraries were prepared, including a replicate experiment. Comparing PCR pooling strategies, we found no significant difference in high-quality read counts and alpha diversity, and beta diversity by Bray-Curtis index clustered by replicate on principal coordinate analysis (PCoA) and non-metric dimensional scaling (NMDS) analysis. Choice of mastermix had no significant impact on high-quality read and alpha diversity, and beta diversity by Bray-Curtis index clustered by replicate in PCoA and NMDS analysis. Importantly, we observed contamination and variability of rare species (<0.01 %) across replicate experiments; the majority of contaminants were accounted for by removal of species present at <0.1 %, or were linked to reagents (including a primer stock). We demonstrate no requirement for pooling of PCR amplifications or manual preparation of PCR mastermix, resulting in a more efficient 16S rRNA gene PCR protocol.

Response of total belowground soil biota in Alhagi sparsifolia monoculture at different soil vertical profiles in desert ecosystem

The soil organisms are extremely important for the land-based ecosystem. There is a growing interest in studying the variety and composition of the entire underground soil organism community at a large ecological scale. Soil organisms show different patterns in relation to soil physiochemical properties (SPPs) in various ecosystems. However, there is limited knowledge regarding their response to soil vertical profiles (SVPs) in monoculture of Alhagi sparsifolia, which is the primary shrub in the deserts of China, and is well-known for its contributions to sand dune stabilization, traditional Chinese medicine, and forage. Here, we investigated the population dynamics of soil bacteria, fungi, archaea, protists and metazoa across six different SVPs ranging from 0 to 100 cm in monoculture of A. sparsifolia, in its natural desert ecosystem. Our findings indicate that the soil biota communities displayed a declining pattern in the alpha diversity of bacteria, protists, and metazoa with an increase in soil depth. However, the opposite trend was observed for fungi and archaea. The beta diversity of soil biota was significantly affected by SVPs, particularly for metazoa, fungi and protists as revealed by Non-Metric Dimensional Scaling. The most prevalent soil bacterial, fungal, archaeal, protist, and metazoa classes were Actinobacteria, Sordariomycetes, Nitrososphaeria, Filosa-Sarcomonadea, and Nematoda, respectively. The correlation among vertical distribution of the most abundant biotic communities and variations in SPPs exhibited that the variations in total carbon (TC) and total nitrogen (TN) had the most significant influence on bacterial changes, while available potassium (AK) had an impact on fungi. Archaea were affected by TC and pH, protists by the C/N-Ratio and TP, and metazoa by TN, AK, and soil water capacity (SWC). Collectively, our findings provide a new perspective on the vertical distribution and distinct response patterns of soil biota in A. sparsifolia monoculture under natural desert ecosystem of China.

Dynamics of rhizosphere bacterial communities and soil physiochemical properties in response to consecutive ratooning of sugarcane.

Ratooning in sugarcane often leads to soil problems such as degradation, acidification, and soil-borne diseases that negatively impact agriculture output and sustainability. Understanding the alteration in bacterial communities, activities, and their diversity connected to the plant and soil under consecutive ratooning still needs to be clarified. To address this gap, multidisciplinary approaches such as Illumina sequencing and measurement of soil nutrients and enzymes were used in this study to analyze soil samples in a field with three consecutive ratooning sugarcane crops. The results revealed a decline in crop yield and significant changes (P < 0.05) in soil nutrients and bacterial diversity. Ratooning resulted in an acidic environment that potentially affected soil nutrients and enzyme activity responsible for the cycling of carbon, nitrogen, and phosphorous. Non-metric dimensional scaling (NMDS) confirmed the effect of ratooning on soil attributes. Moreover, a positive correlation between soil physiochemical properties and soil enzymes was observed. Alpha diversity indices indicated greater bacterial diversity in ratooning sugarcane. Bacterial diversity varied throughout the ratooning crop, and significant (P < 0.05) changes in the relative abundance of specific phyla were observed. For example, the relative abundance of Proteobacteria was decreased, and Acidobacteria was increased. Furthermore, the relative abundance of bacterial phyla was strongly correlated with soil attributes (enzymes and nutrients). Additionally, ratooning results in the depletion or enrichment of important agriculture microbial genera such as Sphingomonas, Burkholderia, and Acidothermus (P < 0.05), respectively. In conclusion, ratooning led to soil acidification, decreased fertility, and altered microbial structure and activity. Thus, restraining soil acidity by means of liming or biofertilizers to maintain soil nutrients, enzymatic activities, and microbial structure could benefit plants and soil to help create a long-term eco-friendly sugarcane cropping system.

Is the soil seed bank a reliable source for passive restoration of intensive grazed habitats in river riparian areas of western Iran?

Soil seed banks serve as reservoirs of seeds for subsequent regeneration of plants particularly in areas prone to disturbance, such as intensive grazed areas along rivers. The potential of soil seed bank (SSB) for vegetation restoration was assessed in overgrazed riparian areas in Gamasyab river, Iran. Therefore, SSB composition, density and diversity and, its relationship with aboveground vegetation (AGV) were investigated along the river. Fifteen transects were set perpendicular to the river and along each transect, 6 plots (1 m × 1 m) were established, in total 90 plots. In each plot, soil was collected for SSB experiments and AGV was sampled during the growing season. The similarity between SSB and AGV was estimated by the Jaccard similarity index and non-metric dimensional scaling (NMDS). Spatial beta diversity was calculated by the mean Bray-Curtis index for the SSB and vegetation compositions, separately. A total of 136, 108 and 134 species were identified in the upper (0–5 cm) and lower (5–10 cm) soil layers and, AGV, respectively. Annual and perennial grasses were dominant in SSB composition at 0–5 cm depth while the frequency of perennial grasses was highest in SSB at deeper depth and vegetation composition. The beta diversity of AGV was significantly higher than for SSB. Similarity between SSB and vegetation was low (7.92%–22.40%), nevertheless, most species in AGV were found frequently in the SSB. So, we argued that restoration of degraded vegetation in our riparian could rely on SSB. It is expected that after grazing exclosure, vegetation would restore mostly with perennial grasses through SSB and vegetative growth.

Implementing voluntary assisted dying laws in healthcare: Exploring beliefs to identify implementation hurdles.

The number of countries introducing voluntary assisted dying (VAD) laws is increasing. Actively taking steps to end a person's life is contentious so implementing these laws into healthcare services presents unique challenges. Theoretically underpinned by the Advocacy Coalition Framework, this study identified the beliefs of classes of stakeholders who engaged with the parliamentary process associated with the introduction of VAD laws in Queensland, Australia. Submissions about VAD made to a parliamentary inquiry were allocated to a class and qualitatively analysed to identify underlying beliefs. The data were then subjected to statistical analysis including nonmetric dimensional scaling and one-way analysis of similarity. Data visualisation techniques were used to generate a chord map and heatmap, to identify the belief types, as well as similarities and differences between beliefs and among classes. Fourteen different beliefs were identified in the 91 reviewed submissions. Six were deep core beliefs and eight were policy core beliefs. Beliefs could be associated with a positive or negative sentiment toward VAD. In this study, the class of Health Services expressed more negative sentiments to VAD than neutral or positive sentiments. The sentiments expressed by the class of Health Professionals were equally divided between positive, neutral and negative. These findings provide important insights for implementors as laws become operational. In particular, for organisations that provide health services, clear articulation of their stance in relevant policy and guidance documents is recommended.

Genetic diversity and community composition of arbuscular mycorrhizal fungi associated with root and rhizosphere soil of the pioneer plant Pueraria phaseoloides.

The pioneering plant Pueraria phaseoloides had a strong modulation effect on arbuscular mycorrhizal fungi (AMF) communities. Irrespective of geographical location, community composition of AMF in rhizosphere soil differed from that of the root. Co-occurrence network analysis revealed two AMF keystone species in rhizosphere soil (Acaulospora) and roots (Rhizophagus) of P. phaseoloides.

Exploration and comparison of bacterial communities present in bovine faeces, milk and blood using 16S rRNA metagenomic sequencing.

Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most abundant phyla overall. A total of 58 genus-level taxa occurred concurrently between the body sites. The important taxa could be categorized into four potentially pathogenic clusters i.e. arthropod-borne; food-borne and zoonotic; mastitogenic; and metritic and abortigenic. A number of taxa were significantly differentially abundant (DA) between sites based on the Wald test implemented in DESeq2 package. Majority of the DA taxa (i.e. Romboutsia, Paeniclostridium, Monoglobus, Akkermansia, Turicibacter, Bacteroides, Candidatus_Saccharimonas, UCG-005 and Prevotellaceae_UCG-004) were significantly enriched in faeces in comparison to milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the largest microbial genus in the entire analysis. This study provides insights into the microbial community composition of the sampled body sites and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the community of Waaihoek in KwaZulu-Natal, Republic of South Africa pertaining to their unsanitary practices associated with the use of cattle by-products.

Exploring the diversity and structural response of sediment-associated microbiota communities to environmental pollution at the siangshan wetland in Taiwan using environmental DNA metagenomic approach

One of the most crucial struggles for the aquatic ecosystem and modern society is environmental pollution. New approaches, such as the environmental DNA Metagenomic approach, have become a powerful tool to investigate the abundance and diversity of sediment-associated microbiota communities. Nevertheless, information on the response of microbial populations to heavy metals (HMs) in the coastal sediments of Taiwan is scarce. 44 sediment samples were collected from the Siangshan wetland in Taiwan (Taiwan Strait) at two different depths (surface and sub-surface) to measure various environmental variables viz., heavy metals, total organic matters, and sediment composition. Moreover, the abundance and structure of sediment-associated microbiota were examined using high-throughput 16S rRNA gene (V3-V4) next-generation sequencing, to explore the response of the microbiota community to environmental variables. According to the computed pollution indices viz., sediment quality guidelines (SQGs), enrichment factor (EF), geo-accumulation index (Igeo), pollution index (PI), and pollution load index (PLI), the studied sites were classified as unpolluted, moderately polluted, and extremely polluted. Our results revealed that the majority of high-quality reads were assigned to bacteria (~ 95.05%), Archaea (~ 4.83%), and 0.13% were unclassified. Study sites were dominated largely by Proteobacteria with a total of 38.02% across all sediment samples, followed by Bacteroidota (7.18%), Desulfobacterota (6.97%), Actinobacterota (6.68%), Cyanobacteria (5.84%), Chloroflexota (4.18%), Planctomycetota (4.16%), and Firmicutes (3.69%). Beta diversity (Non-metric dimensional scaling analysis, nMDS) explained that surface and sub-surface groups had significantly different microbial community compositions (p = 0.01). Meanwhile, polluted sites exhibited more richness and diversity than unpolluted sites. Redundancy analysis (RDA) illustrated that Mn, Cu, Al, Co, Ni, Sand, and Cr had a sizable effect on the structure of microbiota communities (at the class level). This work highlights the potential responsibility of environmental variables in shaping the sedimentary microbiota of the Siangshan wetland via integrating various ecological variables with alteration of the microbiota composition.

Soil macrofauna and microbial communities respond in similar ways to management drivers in an irrigated maize system of Colorado (USA)

The adoption of conservation agriculture has gained considerable attention due to growing interest in managing soil biological diversity and overall soil health. However, there is limited understanding of how practices such as conservation tillage and residue retention affect soil biota across different spatial scales and are associated with alterations to other soil properties. In this study, we examined changes in soil physicochemical properties, soil macrofauna, and microbial communities at two soil depths (0–10 cm, and 10–20 cm) in a 6-year field experiment manipulating tillage and maize residue management. The following treatments were included in the experiment: no-till with residue retention; no-till with residue harvest; conventional tillage with residue retention; and conventional tillage with residue harvest. Macrofauna taxa were identified and estimated visually, while bacterial and fungal communities were identified and analyzed using high throughput sequencing and multivariate statistics including non-metric dimensional scaling and indicator species analysis. Soil physicochemical properties measured include soil carbon and nitrogen, soil moisture, permanganate oxidizable carbon, available soil phosphate, pH, electrical conductivity and aggregate stability. Residue retention increased macrofauna abundance and diversity across soil depths and tillage treatments. Fungal diversity was also highest under residue retention in the topsoil (0–10 cm), while bacterial diversity was generally higher under conventional tillage. Residue retention was the main driver of macrofauna and microbial community composition, while an interaction between tillage and residue management indicated that the effect of tillage on microbial communities was most pronounced when residues were retained. Soil carbon and nitrogen, aggregate stability, permanganate oxidizable carbon, soil moisture content, available soil phosphate and soil electrical conductivity were all enhanced under residue retention in the topsoil. Indicator species analysis suggested that macrofauna taxa belonging to Annelida, Aranaea and Chilopoda together with bacterial phyla Fibrobacteres and fungal phyla Rozellomycota were indicators for no-till combined with residue retention, while Coleoptera, Spirochaetae and Basidiomycota were indicators for conventional tillage with residue retention. Multivariate analyses suggested that total macrofauna abundance, soil carbon and pH were strongly associated with bacterial and fungal community composition in the topsoil layer. Co-inertia analysis indicated significant covariation between soil physicochemical, macrofauna, bacterial and fungal datasets, suggesting a strong association between different soil parameters and cascading effects of management on multiple soil properties. Our findings demonstrate that residue retention enhances soil biological, physical and chemical properties and that communities of soil macro- and microorganisms tend to respond in similar ways to these management interventions.

Changes in Lake Sturgeon Gut Microbiomes Relative to Founding Origin and in Response to Chemotherapeutant Treatments

Antibiotics, drugs, and chemicals (collectively referred to as chemotherapeutants) are widely embraced in fish aquaculture as important tools to control or prevent disease outbreaks. Potential negative effects include changes in microbial community composition and diversity during early life stages, which can reverse the beneficial roles of gut microbiota for the maintenance of host physiological processes and homeostatic regulation. We characterized the gut microbial community composition and diversity of an ecologically and economically important fish species, the lake sturgeon (Acipenser fulvescens), during the early larval period in response to weekly treatments using chemotherapeutants commonly used in aquaculture (chloramine-T, hydrogen peroxide, and NaCl2 followed by hydrogen peroxide) relative to untreated controls. The effects of founding microbial community origin (wild stream vs. hatchery water) were also evaluated. Gut communities were quantified using massively parallel next generation sequencing based on the V4 region of the 16S rRNA gene. Members of the phylum Firmicutes (principally unclassified Clostridiales and Clostridium_sensu_stricto) and Proteobacteria were the dominant taxa in all gut samples regardless of treatment. The egg incubation environment (origin) and its interaction with chemotherapeutant treatment were significantly associated with indices of microbial taxonomic diversity. We observed large variation in the beta diversity of lake sturgeon gut microbiota between larvae from eggs incubated in hatchery and wild (stream) origins based on nonmetric dimensional scaling (NMDS). Permutational ANOVA indicated the effects of chemotherapeutic treatments on gut microbial community composition were dependent on the initial source of the founding microbial community. Influences of microbiota colonization during early ontogenetic stages and the resilience of gut microbiota to topical chemotherapeutic treatments are discussed.

Bladder Microbiota Are Associated with Clinical Conditions That Extend beyond the Urinary Tract.

Background. Since the discovery of the human urinary microbiota (UM), alterations in microbial community composition have been associated with various genitourinary conditions. The aim of this exploratory study was to examine possible associations of UM with clinical conditions beyond the urinary tract and to test some of the conclusions from previous studies on UM. Methods. Catheterised urine samples from 87 men were collected prior to endoscopic urological interventions under anaesthesia. The composition of the bacterial community in urine was characterized using the hypervariable V4 region of the 16S rRNA gene. Samples from 58 patients yielded a sufficient amount of bacterial DNA for analysis. Alpha diversity measures (number of operational taxonomic units, ACE, iChao2, Shannon and Simpson indices) were compared with the Kruskal–Wallis test. Beta diversity (differences in microbial community composition) was assessed using non-metric dimensional scaling in combination with the Prevalence in Microbiome Analysis algorithm. Results. Differences in bacterial richness and diversity were observed for the following variables: age, diabetes mellitus, dyslipidemia, smoking status and single-dose preoperative antibiotics. Differences in microbial community composition were observed in the presence of chronic kidney disease, lower urinary tract symptoms and antibiotic prophylaxis. Conclusions. UM appears to be associated with certain clinical conditions, including those unrelated to the urinary tract. Further investigation is needed before conclusions can be drawn for diagnostics and treatment.

Grouped SPME Comparison of Floral Scent as a Method of Unlocking Phylogenetic Patterns in Volatiles

Global crop production rate has exceeded the availability of pollination services provided by managed honeybees, and habitat loss remains a key factor in the loss of wild pollinators. Revegetation of agricultural land and wild pollination may provide a solution; however, the collection of floral trait data that are correlated to pollinator preferences remains an under studied and complex process. Here, we demonstrate a method for scent analysis, ordination [non-metric dimensional scaling (NMDS)], and clustering outputs that provides a fast and reproducible procedure for a broad grouping of flora based on scent and unlocking characteristic inter-floral patterns. We report the floral profiles of 15 unstudied native Australian plant species and the extent to which they match the commonly cultivated seed crops of Daucus carota L and Brassica rapa L. Through solid-phase microextraction (SPME) paired with gas chromatography–mass spectrometry (GC-MS), we identify a set of inter-family shared, common floral volatiles from these plant species as well as unique and characteristic patterns.

Field investigation of topsoil moisture and temperature as drivers for decomposition or germination of sclerotia (Sclerotinia sclerotiorum) under winter-killed cover crops

ABSTRACT Cover cropping provides versatile benefits for sustainable agriculture, but many cover crops are potential host plants for pathogens such as Sclerotinia sclerotiorum (Lib.) de Bary. Therefore, 14 cover crops were investigated for their interaction with sclerotia, topsoil moisture and temperature in two consecutive field trials in East Austria. In July, after the cover crops were sown, sclerotia were inoculated at 3 cm soil depth in two mesh tubes per plot with 1×1 mm and 3×10 mm mesh size and remained until March. Cover crops did not affect decay of sclerotia, but sclerotia declined faster in 3×10 mm mesh compared to 1×1 mm (75.7 and 54.7%; respectively). Degree days reached the required 500 °C for apothecia development in September in both years, but only in year 1 was topsoil moisture sufficient for apothecia development. Nonmetric dimensional scaling revealed that, among others, topsoil temperature in March was significant for sclerotia germination in spring and was independent of plant biomass. There are indications that Poaceae such as sorghum × Sudan grass and Sudan grass can stimulate early germination under cover crops, causing vulnerability of sclerotia to degradation. This could reduce the pathogen pressure for the subsequent irrigated cash crops.

Influence of environmental factors on tree species diversity and composition in the Indian western Himalaya

Understanding patterns in forest communities and its driving factors play a critical role in ecological studies. In view of this, present study attempts to understand the role of environmental and anthropogenic factors towards shaping species diversity and composition along the altitudinal gradient (700–3800 m asl) in Indian western Himalaya. A total of 51 tree species (28 families) were recorded; Pinaceae (5) and Fagaceae (5) were the species rich families. α-diversity indices i.e., Margalef's richness index (R), Shannon index (Hʹ) and Simpson index showed a humped shaped distribution, whereas Evenness index (E) showed an inverted humped shaped distribution along the altitude range. Based on non-metric dimensional scaling (NMDS), four different community types were identified. Redundancy analysis (RDA) revealed a strong relationship of tree species composition with environmental (41.73% variation) and anthropogenic factors (17.35% variation). RDA further indicated that the bulk density (BD), disturbance index (DI), mean diurnal temperature range (Bio2) and solar radiation (SR) are significantly associated with sub-tropical (below 1200 m) and lower temperate forest (1200–1700 m) types. Likewise, soil organic carbon (SOC), precipitation of the driest quarter (Bio17) and pH were significantly associated with upper temperate (1700–2900 m), and subalpine forest composition (>2900 m). Both NMDS classification and RDA ordination clearly demonstrate spatial variability in composition of tree community and environmental properties.

Palaeobotanical experiences of plant diversity in deep time. 2: How to measure and analyse past plant biodiversity

Determining the diversity of past floras helps with interpreting both the history and predicting the future of vegetation change. For global-scale and regional-scale diversity studies especially, secondary data are often used but local-scale studies tend to be based on survey data that require rigorous sampling. The correct sampling strategies depend on the types of fossils being investigated, including their physical size, and whether the aim is to determine taxonomic richness or relative abundance. Describing and comparing diversities can use a range of different metrics, depending on whether binary presence/absence or abundance data are available. Each metric provides a different insight into the diversities and the choice of which to use depends on the research question being investigated. Various numerical approaches are available for identifying spatial and stratigraphical diversity patterns, mainly classificatory techniques (e.g., cluster and parsimony analyses) and ordination (e.g., Detrended Correspondence Analysis, Nonmetric Dimensional Scaling). The choice of technique again depends on the research question, but often it has proved useful to run both types of analysis in tandem. This article is illustrated by past biodiversity case studies from throughout the fossil record, dealing with floras ranging in age from the Devonian to the last few centuries.

Effect of different shrub species on their sub‐canopy soil and vegetation properties in semiarid regions

AbstractShrubs are one of the most dominant plant types in semiarid ecosystems all over the world. What remains to be investigated is how soil and vegetation characteristics vary under canopy of different species of shrubs in these regions. Thus, this study aimed to compare the effect of three shrub species (Amygdalus scoparia, Ebenus stellata, and Daphne mezereum) on soil and vegetation characteristics under their canopies in semiarid rangelands in Iran for restoration purposes of degraded areas. Fifteen sites were selected in such three shrub species, which were found close to each other in each site. Soil and vegetation characteristics were measured under the shrubs, comparing with outside the shrub canopies (control). One‐way ANOVA and nonmetric dimensional scaling were used to clarify the differences of the effects of different shrub species on sub‐canopy soil and plants. The results indicated that the effect of different species of shrubs on soil properties was not equal, more pronounced by A. scoparia. Similarly, the highest value of Shannon‐Wiener diversity was recorded under A. scoparia (2.07) as compared with D. mezerum (1.76), E. stellata (1.41) (F = 32.25, p &lt; 0.01). The highest and lowest values of Menhinick richness index were observed under A. scoparia (3.43) and E. stellata (1.46), respectively (1.41) (F = 13.30, p &lt; 0.01). Compared with two other shrubs, a taller canopy in A. scoparia (3.50 m vs. 2.60 m and 1.83 m) probably led to greater litter input by the shrub. Different effects of different species of shrubs on sub‐canopy soil and vegetation should be considered in the restoration projects of degraded semiarid rangelands.

Selenium: a sole treatment for erosive oral lichen planus (randomized controlled clinical trial)

Objectives Oral lichen planus (OLP) is a chronic disease with immune-mediated pathogenesis. Selenium (Se), an antioxidant, plays a role in modulating immunity. The aim of this clinical trial was to evaluate 2 Se forms (novel topical hydrogel and oral capsules), solely, in treating erosive OLP based on clinical evaluation and salivary oxidative stress markers. To date, to our knowledge, this is the first study to evaluate the role of Se solely in treating erosive lesions associated with erosive OLP. This clinical trial has been registered in the Cochrane Database under registry number PACTR201901531815403. Methods Patients were allocated into 1 of 3 groups: group I, topical corticosteroids and topical antifungal as an adjunctive therapy; group II, novel topical Se hydrogel; or group III, systemic Se. Treatment lasted for 6 weeks. Patients were clinically evaluated at baseline and at 6 and 12 weeks for reduction in pain scores and clinical lesion size. Biochemical analysis was performed for salivary malondialdehyde (MDA) and total antioxidant capacity (TAC) levels at baseline and 6 weeks. Correlation between clinical signs and symptoms and salivary oxidative stress markers was measured at 6 weeks. Two-way analysis of variance (ANOVA) followed by a post hoc Tukey test was performed to assess for significant differences in mean pain scores, clinical lesion size, and salivary MDA and TAC levels at 6 weeks. One-way ANOVA was used to test for significant variations in clinical parameters at 12-week follow-up. Principal component analysis and nonmetric dimensional scaling were performed to test for correlation and possible relationships between clinical parameters and salivary oxidative stress markers. Results There was a significant reduction in signs and symptoms in response to all treatment modalities. However, there was no significant difference among the 3 groups at 6 weeks. At 12 weeks, group II had significantly lower pain scores than group I. Salivary MDA levels showed a significant decrease in patients in group I and group III. TAC levels showed no significant difference in response to treatment. Conclusions Se can be proposed as a treatment for OLP. Salivary MDA levels can be a biomarker for OLP disease severity. Oral lichen planus (OLP) is a chronic disease with immune-mediated pathogenesis. Selenium (Se), an antioxidant, plays a role in modulating immunity. The aim of this clinical trial was to evaluate 2 Se forms (novel topical hydrogel and oral capsules), solely, in treating erosive OLP based on clinical evaluation and salivary oxidative stress markers. To date, to our knowledge, this is the first study to evaluate the role of Se solely in treating erosive lesions associated with erosive OLP. This clinical trial has been registered in the Cochrane Database under registry number PACTR201901531815403. Patients were allocated into 1 of 3 groups: group I, topical corticosteroids and topical antifungal as an adjunctive therapy; group II, novel topical Se hydrogel; or group III, systemic Se. Treatment lasted for 6 weeks. Patients were clinically evaluated at baseline and at 6 and 12 weeks for reduction in pain scores and clinical lesion size. Biochemical analysis was performed for salivary malondialdehyde (MDA) and total antioxidant capacity (TAC) levels at baseline and 6 weeks. Correlation between clinical signs and symptoms and salivary oxidative stress markers was measured at 6 weeks. Two-way analysis of variance (ANOVA) followed by a post hoc Tukey test was performed to assess for significant differences in mean pain scores, clinical lesion size, and salivary MDA and TAC levels at 6 weeks. One-way ANOVA was used to test for significant variations in clinical parameters at 12-week follow-up. Principal component analysis and nonmetric dimensional scaling were performed to test for correlation and possible relationships between clinical parameters and salivary oxidative stress markers. There was a significant reduction in signs and symptoms in response to all treatment modalities. However, there was no significant difference among the 3 groups at 6 weeks. At 12 weeks, group II had significantly lower pain scores than group I. Salivary MDA levels showed a significant decrease in patients in group I and group III. TAC levels showed no significant difference in response to treatment. Se can be proposed as a treatment for OLP. Salivary MDA levels can be a biomarker for OLP disease severity.