BIODIVERSITY OF FRUIT-BEARING FOREST SPECIES IN THE PROTECTED LANDSCAPE "KONJUH"

UDK: 634.2:574.4]:502(497.6 “Konjuh“) The area of the protected landscape "Konjuh" is distinguished by quality forest ecosystems, featuring diverse fruit-bearing forest species, which contributes to the conservation of biodiversity of the protected landscape "Konjuh". The aim of the paper is to assess the state of biodiversity of fruit-bearing species in the forest ecosystems of the study area, with the emphasis on determining the genus richness as a basis for conservation (in/ex situ), breeding and economic use. During the vegetation season in 2015 and 2016, several relevés (phytosociological plot) were made in the Protected Landscape "Konjuh". The results of the research indicate the high level of variability for most of the species according to characteristics of biology, pomology, and ecology. The fruit trees, like the noble hardwood, are wild cherry, (Prunus avium L.), wild pear (Pyrus communis L.), wild apples (Malus sylvestris Mill.), Breccia (Torminalis clusii M. Roem.), Sorbus aria L. et all, Wild cherry, Vrapcarka (Prunus avium L.) is the most famous forest fruit grower, occurs as a single tree or in smaller groups (Noćajević, 2009). The benefits of fruit-bearing forest species are emphasized in the bloom and the fruiting time, when "decorated" forest provide a rich bee pasture and feeding nutriment for forest fauna (Orešković et al. 2006). Fruit-bearing Forest species are significant as the genera of the varieties and as a basis for the grafting for high-grade varieties. Also, they are important for humans from the aspect of ecology, nutrition, dietotherapy, pharmacology and bioenergy balance.

Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns

The human gut microbiome has been extensively studied, but its diversity scaling (changes or heterogeneities) along the digestive tract (DT) as well as their inter-individual heterogeneities have not been adequately addressed to the best of our knowledge. Here we fill the gap by applying the diversity-area relationship (DAR), a recent extension to the classic species-area relationship (SAR) in biogeography, by reanalyzing a dataset of over 2000 16s-rRNA microbiome samples obtained from 10 DT sites of over 200 individuals. We sketched out the biogeography “maps” for each of the 10 DT sites by cross-individual DAR analysis, and the intra-DT distribution pattern by cross-DT-site DAR analysis. Regarding the inter-individual biogeography, it was found that all DT sites have the invariant (constant) scaling parameter—all sites possessing the same diversity change rate across individuals, but most sites have different potential diversities, which include the portions of diversity that may be absent locally but present regionally. In the case of this study, the potential diversity of each DT site covers the total diversity of the respective site from all individuals in the cohort. In terms of the genus richness, an average individual hosts approximately 20% of the population-level genus richness (total bacterial genus of a human population). In contrast, in terms of community biodiversity, the percentages of individual over population may exceed 90%. This suggests that the differences between individuals in their DT microbiomes are predominantly in the composition of bacterial species, rather than how their abundances are distributed (i.e., biodiversity). Regarding the intra-DT patterns, the scaling parameter (z) is larger—suggesting that the intra-DT biodiversity changes are larger than inter-individual changes. The higher intra-DT heterogeneity of bacteria diversity, as suggested by larger intra-DT z than the inter-individual heterogeneity, should be expected since the intra-DT heterogeneity reflects the functional differentiations of the DT tract, while the inter-individual heterogeneity (z) reflects the difference of the same DT site across individuals. On average, each DT site contains 21–36% of the genus diversity of the whole DT, and the percentages are even higher in terms of higher taxon levels.

When fossil clades ‘compete’: local dominance, global diversification dynamics and causation

Examining the supposition that local-scale competition drives macroevolutionary patterns has become a familiar goal in fossil biodiversity studies. However, it is an elusive goal, hampered by inadequate confirmation of ecological equivalence and interactive processes between clades, patchy sampling, few comparative analyses of local species assemblages over long geological intervals, and a dearth of appropriate statistical tools. We address these concerns by reevaluating one of the classic examples of clade displacement in the fossil record, in which cheilostome bryozoans surpass the once dominant cyclostomes. Here, we analyse a newly expanded and vetted compilation of 40 190 fossil species occurrences to estimate cheilostome and cyclostome patterns of species proportions within assemblages, global genus richness and genus origination and extinction rates while accounting for sampling. Comparison of time-series models using linear stochastic differential equations suggests that inter-clade genus origination and extinction rates are causally linked to each other in a complex feedback relationship rather than by simple correlations or unidirectional relationships, and that these rates are not causally linked to changing within-assemblage proportions of cheilostome versus cyclostome species.

Large-Scale Patterns of Soil Nematodes across Grasslands on the Tibetan Plateau: Relationships with Climate, Soil and Plants

Soil nematodes are important contributors to soil biodiversity. Nonetheless, the distribution patterns and environmental drivers of soil nematode communities are poorly understood, especially at the large scale, where multiple environmental variables covary. We collected 520 soil samples from 104 sites representing alpine meadow and steppe ecosystems. First, we explored the soil nematode community characteristics and compared community patterns between the ecosystems. Then, we examined the contributions of aboveground and belowground factors on these patterns. The genus richness and abundance of nematodes on the Tibetan Plateau are lower than other alpine ecosystems, but are comparable to desert or polar ecosystems. Alpine meadows supported a higher nematode abundance and genus richness than alpine steppes; bacterial-based energy channels were pre-dominant in both the ecosystems. Soil factors explained the most variation in the soil nematode community composition in the alpine meadows, while plant factors were as essential as soil factors in the alpine steppes. Unexpectedly, the climate variables barely impacted the nematode communities. This is the first study to explore the spatial patterns of soil nematode compositions on the Tibetan Plateau, and we found that the contributions of climate, plants, and soil properties on soil nematodes community were essentially different from the previous knowledge for well-studied plant and animal communities.

Gut microbiota changes after metabolic surgery in adult diabetic patients with mild obesity: a randomised controlled trial

Background Roux-en-Y gastric bypass (RYGB) surgery is one of the most efficient procedures for the treatment of obesity, also improving metabolic and inflammatory status, in patients with mild obesity. The underlying mechanisms have not been fully understood, but gut microbiota is hypothesized to play a key role. Our aim was to evaluate the association between gut microbiota changes and anthropometric, metabolic and inflammatory profiles after metabolic surgery compared with medical therapy, in type 2 diabetic (T2DM) adults with mild obesity (BMI 30–35 kg/m2). Methods DM2 was an open-label, randomised controlled clinical trial (RCT: ISRCTN53984585) with 2 arms: (i) surgical, and (ii) medical. The main outcome was gut microbiota changes after: metabolic surgery (Roux-en-Y gastric bypass—RYGB) versus standard medical therapy. Secondary outcomes included anthropometric, metabolic and inflammatory profiles. Clinical visits, blood workup, and stool samples were collected at baseline and months (M)1, 3, 6, 12. Gut microbiota was profiled using 16S rRNA targeted sequencing. Results Twenty patients were included: 10 in surgical and 10 in medical arm. Anthropometric and metabolic comparative analysis favoured RYGB over medical arm. At M12, the percentage of weight loss was 25.5 vs. 4.9% (p < 0.001) and HbA1c was 6.2 vs. 7.7% (p < 0.001) respectively. We observed a continuous increase of genus richness after RYGB up until M12. In the medical arm, genus richness ended-up being significantly lower at M12. Composition analysis indicated significant changes of the overall microbial ecosystem (permanova p = 0.004, [R2 = 0.17]) during the follow-up period after RYGB. There was a strong association between improvement of anthropometric/metabolic/inflammatory biomarkers and increase in microbial richness and Proteobacterial lineages. Conclusions This was the first RCT studying composite clinical, analytic, and microbiome changes in T2DM patients with class 1 obesity after RYGB versus standard medical therapy. The remarkable phenotypic improvement after surgery occurred concomitantly with changes in the gut microbiome, but at a lower level. Trial registration: ISRCTN53984585

Dead clades walking are a pervasive macroevolutionary pattern

D. Jablonski [Proc. Natl. Acad. Sci. U.S.A. 99, 8139–8144 (2002)] coined the term “dead clades walking” (DCWs) to describe marine fossil orders that experience significant drops in genus richness during mass extinction events and never rediversify to previous levels. This phenomenon is generally interpreted as further evidence that the macroevolutionary consequences of mass extinctions can continue well past the formal boundary. It is unclear, however, exactly how long DCWs are expected to persist after extinction events and to what degree they impact broader trends in Phanerozoic biodiversity. Here we analyze the fossil occurrences of 134 skeletonized marine invertebrate orders in the Paleobiology Database (paleobiodb.org) using a Bayesian method to identify significant change points in genus richness. Our analysis identifies 70 orders that experience major diversity losses without recovery. Most of these taxa, however, do not fit the popular conception of DCWs as clades that narrowly survive a mass extinction event and linger for only a few stages before succumbing to extinction. The median postdrop duration of these DCW orders is long (>30 Myr), suggesting that previous studies may have underestimated the long-term taxonomic impact of mass extinction events. More importantly, many drops in diversity without recovery are not associated with mass extinction events and occur during background extinction stages. The prevalence of DCW orders throughout both mass and background extinction intervals and across phyla (>50% of all marine invertebrate orders) suggests that the DCW pattern is a major component of macroevolutionary turnover.

Nematodes as bio-indicators of physical disturbance of marine sediments following polychaete bait harvesting

Sediment disturbance in marine environments is caused by activities including polychaete bait harvesting, trawling, dredging, sediment erosion and treading. These activities affect the benthic communities by changing the densities, community assemblage and diversity. The aim of this study was to evaluate the potential of nematodes as indicators of sediments disturbance following polychaete bait harvesting. The study was conducted in three sites experiencing different bait harvesting intensities in Mida Creek, Kenya. Sediment samples were collected from the mudflats during low tide, preserved in 5% formalin and transported to the laboratory for processing and identification of nematodes. The highly disturbed site recorded the lowest nematode genus richness while the less disturbed sites had the highest. Overall, the most abundant nematode genera in the non-disturbed (Dabaso) and less disturbed sites (Kirepwe) were selective deposit feeders (Spirinia and Terschellingia), while most disturbed sites (e.g. Mayonda) had predators/omnivores (Pheronus, Aporcelaimellus) and selected members of the genus Spirinia. The disturbed site was characterised by low nematode diversity (H’) and low dominance (D) while the non-disturbed and less disturbed sites had higher diversity and dominance. Clearly, nematode community assemblage, diversity and feeding guilds changed following disturbance to a low diversity that favoured higher proportions of predator/omnivore taxa.

Gut microbiota, body weight and histopathological examinations in experimental infection by methicillin-resistant Staphylococcus aureus: antibiotic versus bacteriocin

Bacteriocins have been steadily reported as potential agents that may contribute, in different ways, to overcome antimicrobial drug resistance. Here, holoxenic NMRI-F mice microbiota, their body weight recovery and histopathological alterations of organs like colon, spleen and liver were examined in mice intraperitoneally infected with 108 cfu of a clinical methicillin-resistant Staphylococcus aureus (MRSA-1), and treated with enterocin DD14 alone (165 mg/kg), erythromycin alone (100 mg/kg) or their combination. Animals that received both antimicrobials presented a better body weight recovery than other groups. Less pronounced histopathological alterations were observed in mice MRSA-infected and treated with bacteriocin than in those MRSA-infected but untreated or MRSA-infected and treated with erythromycin. Noteworthy, these alterations were absent when mice were treated with MRSA-infected and treated with both antibacterial agents. Furthermore, the genus richness was significantly lower in mice infected and treated with erythromycin, compared to mice infected and treated with both antimicrobials. The beta-diversity analysis showed that non-infected mice and those infected and treated with both antimicrobials, stand apart from the other groups as supported in a NMDS model. This in vivo study shows the relevance of bacteriocin, or bacteriocin-antibiotic formulation in protecting colonic, liver and spleen soft tissues and controlling the mouse gut microbiota, following MRSA infection.

Phanerozoic variation in dolomite abundance linked to oceanic anoxia

The abundance of dolomitic strata in the geological record contrasts with the general rarity of locations where dolomite forms today, a discrepancy that has long posed a problem for their interpretation. Recent culture experiments show that dolomite can precipitate at room temperature, raising the possibility that many ancient dolomites may be of syngenetic origin. We compiled a large geodata set of secular variations in dolomite abundance in the Phanerozoic, coupled with compilations of genus richness of marine benthic invertebrates and sulfur-isotope variations in marine carbonates. These data show that dolomite abundance is negatively correlated to genus diversity, with four dolomite peaks occurring during mass extinctions. Dolomite peaks also correspond to the rapid increase in sulfur-isotope composition (δ34S), an indicator of enhanced sulfate reduction, in anoxic oceans. These results confirm that variations in dolomite abundance during the Phanerozoic were closely linked with changes in marine benthic diversity, with both in turn related to oceanic redox conditions.

Gut Microbiota Changes After Metabolic Surgery in Adult Diabetic Patients With Mild Obesity: a Randomised Controlled Trial

Background: Roux-en-Y gastric bypass (RYGB) surgery is one of the most efficient procedures for the treatment of obesity, also improving metabolic and inflammatory status, in patients with mild obesity. The underlying mechanisms have not been fully understood, but gut microbiota is hypothesized to play a key role. Our aim was to evaluate the association between gut microbiota changes and anthropometric, metabolic and inflammatory profiles after metabolic surgery compared with medical therapy, in type 2 diabetic (T2DM) adults with mild obesity (BMI 30-35 Kg/m2).Methods: DM2 was an open-label, randomised controlled clinical trial (RCT: ISRCTN53984585) with 2 arms: (i) surgical, and (ii) medical. The main outcome was gut microbiota changes after: metabolic surgery (Roux-en-Y gastric bypass - RYGB) versus standard medical therapy. Secondary outcomes included anthropometric, metabolic and inflammatory profiles. Clinical visits, blood workup, and stool samples were collected at baseline and months (M)1, 3, 6, 12. Gut microbiota was profiled using 16S rRNA targeted sequencing.Results: Twenty patients were included: 10 in surgical and 10 in medical arm. Anthropometric and metabolic comparative analysis favoured RYGB over medical arm. At M12, the percentage of weight loss was 25.5% vs. 4.9% (p<0.001) and HbA1c was 6.2% vs. 7.7% (p<0.001) respectively.We observed a continuous increase of genus richness after RYGB up until M12. In the medical arm, genus richness ended-up being significantly lower at M12. Composition analysis indicated significant changes of the overall microbial ecosystem (permanova p=0.004, [R2=0.17]) during the follow-up period after RYGB. There was a strong association between improvement of anthropometric/metabolic/inflammatory biomarkers and increase in microbial richness and Proteobacterial lineages.Conclusions: This was the first RCT studying composite clinical, analytic, and microbiome changes in T2DM patients with class 1 obesity after RYGB versus standard medical therapy. The remarkable phenotypic improvement after surgery occurred concomitantly with changes in the gut microbiome, but at a lower level.Trial registration: ISRCTN53984585 (http://www.isrctn.com/ISRCTN53984585)