Rainforest conversion to rubber plantation may not result in lower soil diversity of bacteria, fungi, and nematodes

Large areas of rainforest in Asia have been converted to plantations, with uncertain effects on soil biodiversity. Using standard metagenetic methods, we compared the soil biota of bacteria, fungi, and nematodes at three rainforest sites in Malaysia with two rubber plantation sites with similar soils and geology. We predicted the following: (1) that the rubber sites would have a lower α- and β-diversity than the rainforest sites, due to the monospecific canopy cover and intensive management with herbicides, pesticides, and fertilizers, and (2) that due to differences in the physical and biotic environment associated with cultivation, there would be distinct communities of bacteria, fungi, and nematodes. However, regarding (1), the results showed no consistent difference in α- and β-diversity of bacteria, fungi, or nematodes between rainforest and rubber plantation sites. It appears that conversion of rainforest to rubber plantations does not necessarily result in a decrease in diversity of soil biota. It may be that heterogeneity associated with the cultivation regimen compensates for loss of biotically imposed heterogeneity of the original rainforest. Regarding (2), as predicted there were statistically significant differences in community composition between rainforest and rubber plantation for bacteria, fungi, and nematodes. These differences could be related to a range of factors including light level, litter fall composition, pH, C and N, selecting a distinct set of soil taxa, and it is possible that this in itself would affect long-term soil function

Do tropical rain forest soils have greater nematode diversity than high arctic tundra? a metagenetic comparison of Malaysia and Svalbard

Aim Latitudinal differences in diversity have long fascinated ecologists. It is unclear whether small soil animals such as nematodes show latitudinal differences in diversity. Based on hypotheses concerning the basis for greater tropical diversity, and by analogy with other groups, we predicted (1) greater alpha diversity in the equatorial tropics than the High Arctic, (2) greater beta and gamma diversity in the tropics. We also predicted (3) no species overlap between the tropics and the High Arctic, and (4) lower abundance of root feeding and insect parasitic nematodes in the high Arctic. Location We sampled at three sites in equatorial rain forest in Malaysia at 2° N and three sites in High Arctic tundra in Svalbard at 79° N. Methods In Malaysia and Svalbard, three sets of 1-m2 samples were taken, in interrupted grids. Nematodes were extracted using a Baermann funnel. Bulk DNA was amplified by polymerase chain reaction for the 18S rRNA gene, followed by 454-pyrosequencing. Results Comparing operational taxonomic unit (OTU)-based nematode communities (99% sequence similarity), averaged alpha diversity per 1-m2 quadrat showed no difference between Malaysia and Svalbard. However, the classic beta diversity and gamma diversity of nematodes was higher for Malaysia. Main conclusions There was, surprisingly, no difference in the alpha diversity of nematodes between Malaysia and Svalbard. However, for beta and gamma diversity, diversity was higher in Malaysia. There was also considerable OTU overlap between the two regions, suggesting that very broad climatic niches are common in nematode ecology. Plant root feeders and insect parasites were relatively more common in Svalbard. Overall, we found a mixed and complex picture in terms of agreement with what would be predicted on the basis of ecological theory and observations on other groups. While further confirmatory studies would be beneficial, there is a need to incorporate these new findings in the formulation of hypotheses and tests for the underlying causes of latitudinal trends

pH dominates variation in tropical soil archaeal diversity and community structure

Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of pH values. DNA was PCR-amplified for the V1-V3 region of the 16S rRNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by qPCR) also decreased at higher pH. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units (OTUs), there was clear evidence of niche partitioning by pH. No individual OTU occurred across the entire range of pH values. Overall, the results of this study show that pH plays a major role in structuring tropical soil archaeal communities

Distinctive Phyllosphere bacterial communities in tropical trees.

Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1-V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leaves, clustering separately from other tree species in an ordination analysis. Bacterial communities in the phyllosphere were unique to plant leaves in that very few operational taxonomic units (0.5%) co-occurred in the surrounding soil environment. A novel and distinctive aspect of tropical phyllosphere communities is that Acidobacteria were one of the most abundant phyla across all samples (on average, 17%), a pattern not previously recognized. Sequences belonging to Acidobacteria were classified into subgroups 1-6 among known 24 subdivisions, and subgroup 1 (84%) was the most abundant group, followed by subgroup 3 (15%). The high abundance of Acidobacteria on leaves of tropical trees indicates that there is a strong relationship between host plants and Acidobacteria in tropical rain forest, which needs to be investigated further. The similarity of phyllosphere bacterial communities amongst the tree species sampled shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts

From the high Arctic to the equator: do soil metagenomes differ according to our expectations

Comparing the functional gene composition of soils at opposite extremes of environmental gradients may allow testing of hypotheses about community and ecosystem function. Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates. We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing. Based upon “classical” views of how tropical and higher latitude ecosystems differ, we made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct: the polar samples had higher relative abundance of dormancy related genes, and lower relative abundance of genes associated with respiration, and with metabolism of aromatic compounds. The network complexity of the Arctic was also lower than the tropics. However, in various other respects, the pattern was not as predicted; there were no differences in relative abundance of stress response genes or in genes associated with secondary metabolism. Conversely, CRISPR genes, phage-related genes, and virulence disease and defense genes, were unexpectedly more abundant in the Arctic, suggesting more intense biotic interaction. Also, eukaryote diversity and bacterial diversity were higher in the Arctic of Svalbard compared to tropical Brunei, which is consistent with what may expected from amplicon studies in terms of the higher pH of the Svalbard soil. Our results in some respects confirm expectations of how tropical versus polar nature may differ, and in other respects challenge them

Internet-based search of randomised trials relevant to mental health originating in the Arab world

BACKGROUND: The internet is becoming a widely used source of accessing medical research through various on-line databases. This instant access to information is of benefit to busy clinicians and service users around the world. The population of the Arab World is comparable to that of the United States, yet it is widely believed to have a greatly contrasting output of randomised controlled trials related to mental health. This study was designed to investigate the existence of such research in the Arab World and also to investigate the availability of this research on-line. METHODS: Survey of findings from three internet-based potential sources of randomised trials originating from the Arab world and relevant to mental health care. RESULTS: A manual search of an Arabic online current contents service identified 3 studies, MEDLINE, EMBASE, and PsycINFO searches identified only 1 study, and a manual search of a specifically indexed, study-based mental health database, PsiTri, revealed 27 trials. CONCLUSION: There genuinely seem to be few trials from the Arab world and accessing these on-line was problematic. Replication of some studies that guide psychiatric/psychological practice in the Arab world would seem prudent

Recent Incarceration, Substance Use, Overdose, and Service Use Among People Who Use Drugs in Rural Communities

Importance: Drug use and incarceration have a substantial impact on rural communities, but factors associated with the incarceration of rural people who use drugs (PWUD) have not been thoroughly investigated. Objective: To characterize associations between recent incarceration, overdose, and substance use disorder (SUD) treatment access among rural PWUD. Design, setting, and participants: For this cross-sectional study, the Rural Opioid Initiative research consortium conducted a survey in geographically diverse rural counties with high rates of overdose across 10 US states (Illinois, Wisconsin, North Carolina, Oregon, Kentucky, West Virginia, Ohio, Massachusetts, New Hampshire, and Vermont) between January 25, 2018, and March 17, 2020, asking PWUD about their substance use, substance use treatment, and interactions with the criminal legal system. Participants were recruited through respondent-driven sampling in 8 rural US regions. Respondents who were willing to recruit additional respondents from their personal networks were enrolled at syringe service programs, community support organizations, and through direct community outreach; these so-called seed respondents then recruited others. Of 3044 respondents, 2935 included participants who resided in rural communities and reported past-30-day injection of any drug or use of opioids nonmedically via any route. Data were analyzed from February 8, 2022, to September 15, 2023. Exposure: Recent incarceration was the exposure of interest, defined as a report of incarceration in jail or prison for at least 1 day in the past 6 months. Main outcomes and measures: The associations between PWUD who were recently incarcerated and main outcomes of treatment use and overdose were examined using logistic regression. Results: Of 2935 participants, 1662 (56.6%) were male, 2496 (85.0%) were White; the mean (SD) age was 36 (10) years; and in the past 30 days, 2507 (85.4%) reported opioid use and 1663 (56.7%) reported injecting drugs daily. A total of 1224 participants (41.7%) reported recent incarceration, with a median (IQR) incarceration of 15 (3-60) days in the past 6 months. Recent incarceration was associated with past-6-month overdose (adjusted odds ratio [AOR], 1.38; 95% CI, 1.12-1.70) and recent SUD treatment (AOR, 1.62; 95% CI, 1.36-1.93) but not recent medication for opioid use disorder (MOUD; AOR, 1.03; 95% CI, 0.82-1.28) or currently carrying naloxone (AOR, 1.02; 95% CI, 0.86-1.21). Conclusions and relevance: In this cross-sectional study of PWUD in rural areas, participants commonly experienced recent incarceration, which was not associated with MOUD, an effective and lifesaving treatment. The criminal legal system should implement effective SUD treatment in rural areas, including MOUD and provision of naloxone, to fully align with evidence-based SUD health care policies.</p

Soil pH and biome are both key determinants of soil archaeal community structure

The mechanisms underlying community composition and diversity of soil archaea are poorly understood. We compared both total archaea and ammonia oxidizing archaea (AOA) using 16S rRNA and amoA genes pyrosequencing respectively, in two different biomes: tropics (Malaysia), and temperate (Korea and Japan). Despite differences in characteristics of these biomes, we found that at the broad taxonomic level the dominant archaeal lineages are the same, except in certain instances (16S rRNA gene: group 1.1a Thaumarchaeota; amoA gene: Nitrososphaera and Nitrosotalea lineages). However, at the OTU level, both total archaea and AOA communities showed biome-specific patterns, indicating that at lower taxonomic levels biome differences are also important. In both biomes, total archaeal diversity showed a negative correlation with pH, but a hump-shaped curve for AOA diversity, peaking at ∼pH 6.0. Within each biome, pH also emerged as the delimiting factor determining variation in community composition of both total archaea and AOA. Communities from each biome clustered separately, even at analogous pH levels. At the OTU level, certain shared OTUs did occur at approximately the same pH range in both biomes. We found that closely related OTUs of both total archaea and AOA respectively tended to co-occur, suggesting that in evolutionary terms these closely related lineages have conserved very similar ecological requirements. This predictability also strongly suggests that soil archaeal community assembly has strongly deterministic aspect. Overall, our findings emphasize that soil archaeal communities are to large extent predictable and structured by both biome and by soil chemical environment, especially pH

Marine Actinomycetes: A New Source of Compounds against the Human Malaria Parasite

Background Malaria continues to be a devastating parasitic disease that causes the death of 2 million individuals annually. The increase in multi-drug resistance together with the absence of an efficient vaccine hastens the need for speedy and comprehensive antimalarial drug discovery and development. Throughout history, traditional herbal remedies or natural products have been a reliable source of antimalarial agents, e.g. quinine and artemisinin. Today, one emerging source of small molecule drug leads is the world's oceans. Included among the source of marine natural products are marine microorganisms such as the recently described actinomycete. Members of the genus Salinispora have yielded a wealth of new secondary metabolites including salinosporamide A, a molecule currently advancing through clinical trials as an anticancer agent. Because of the biological activity of metabolites being isolated from marine microorganisms, our group became interested in exploring the potential efficacy of these compounds against the malaria parasite.[br/] Methods We screened 80 bacterial crude extracts for their activity against malaria growth. We established that the pure compound, salinosporamide A, produced by the marine actinomycete, Salinispora tropica, shows strong inhibitory activity against the erythrocytic stages of the parasite cycle. Biochemical experiments support the likely inhibition of the parasite 20S proteasome. Crystal structure modeling of salinosporamide A and the parasite catalytic 20S subunit further confirm this hypothesis. Ultimately we showed that salinosporamide A protected mice against deadly malaria infection when administered at an extremely low dosage.[br/] Conclusion These findings underline the potential of secondary metabolites, derived from marine microorganisms, to inhibit Plasmodium growth. More specifically, we highlight the effect of proteasome inhibitors such as salinosporamide A on in vitro and in vivo parasite development. Salinosporamide A (NPI-0052) now being advanced to phase I trials for the treatment of refractory multiple myeloma will need to be further explored to evaluate the safety profile for its use against malaria