The crisis in shifting cultivation practices and the promise of agroforestry: a review of the Panamanian experience

Deforestation is proceeding at alarming rates in the Central American Republic of Panama. This is leading to high losses of biodiversity, local wood shortages, increased erosion, and the sedimentation of water bodies. One of the principal causes of deforestation is the expansion of the agricultural frontier through extensive shifting cultivation systems. These land use systems are becoming increasingly unsustainable as populations increase and the amount of agricultural land available declines, and are often associated with low crop productivity, and reduced soil fertility. Agroforestry, or the association of trees with crops and livestock, has the potential of providing both socio-economic and ecological advantages to smallholders. While the number of agroforestry projects has increased dramatically over the past two decades in Panama, there is little information on the impacts these projects have had. This review provides a brief history of agroforestry in Panama, and outlines the current projects underway. In addition, the main factors impeding the increased adoption of agroforestry are examined, and recommendations are provided.     

Surveys reveal a complex association of phytoplasmas and viruses with the blueberry stunt disease on Canadian blueberry farms

Surveys for phytoplasmas and viruses were conducted during September 2014 and 2015 on highbush blueberry farms in the Région Montérégie, Quebec. Total DNA and RNA were extracted from blueberry bushes showing blueberry stunt (BBS) symptoms and from symptomless blueberry bushes, and utilised as templates for PCR and RT‐PCR assays, respectively. Phytoplasma DNA was amplified with universal phytoplasma primers that target the 16S rRNA, secA and secY genes from 12 out of 40 (30%) plants tested. Based on 16S rRNA, secA and secY gene sequence identity, phylogenetic clustering, actual and in silico RFLP analyses, phytoplasma strains associated with BBS disease in Quebec were identified as ‘Candidatus Phytoplasma asteris’‐related strains, closely related to the BBS Michigan phytoplasma strain (16SrI‐E). The secY gene sequence‐based single nucleotide polymorphism analysis revealed that one of the BBS phytoplasma strains associated with a leaf marginal yellowing is a secY‐I RFLP variant of the subgroup 16SrI‐E. Two viruses were detected in blueberry bushes. The Blueberry Red Ringspot Virus (BRRV) was found in a single infection in the cultivar Bluecrop with no apparent typical BRRV symptoms. The Tobacco Ringspot Virus (TRSV) was found singly infecting blueberry plants and co‐infecting a BBS phytoplasma‐infected blueberry cv. Bluecrop plant. This is the first report of TRSV in the cv. Bluecrop in Quebec. The Quebec BBS phytoplasma strain was identified in the leafhopper Graphocephala fennahi, which suggests that G. fennahi may be a potential vector for the BBS phytoplasma. The BBS disease shows a complex aetiology and epidemiology; therefore, prompt actions must be developed to support focused BBS integrated management strategies.     

Implication for DNA methylation involved in the host transfer of diamondback moth,Plutella xylostella (L.)

DNA methylation exerts extensive impacts on gene expression of various living organisms exposed to environmental variation. However, little is known whether DNA methylation is involved in the host transfer of diamondback moth, Plutella xylostella (L.), a worldwide destructive pest of crucifers. In this study, we found that P. xylostella genome exhibited a relatively low level of DNA methylation on the basis of the CpG O/E prediction and experimental validation. A significant positive linear correlation was observed between the stage‐specific expressions of PxDNMT1 and DNA methylation levels (5mC content). Particularly, high levels of DNA methylation and gene expression of PxDNMT1 were observed in eggs and mature females of P. xylostella. After host transfer of P. xylostella from Raphanus sativus to Arabidopsis thaliana, we identified some potential genomic loci that might have changed methylation levels. Using the method of fluorescence‐labeled methylation‐sensitive amplified polymorphism (F‐MSAP), we also found the corresponding genes primarily involved in neural system and signaling. The expressions of six candidate genes were verified by qRT‐PCR. One of the genes, Px009600, might be regulated by a DNA methylation‐mediated mechanism in response to host transfer. Our study provides evidence for a functional system of DNA methylation in P. xylostella and its possible role in adaptation during host transfer. Further studies should examine methylation as responsive factors to different host plants and environmental cues in insect pests.     

Irreproducibility in searches of scientific literature: A comparative analysis

1. Repeatability is the cornerstone of science, and it is particularly important for systematic reviews. However, little is known on how researchers’ choice of database, and search platform influence the repeatability of systematic reviews. Here, we aim to unveil how the computer environment and the location where the search was initiated from influence hit results.
2. We present a comparative analysis of time‐synchronized searches at different institutional locations in the world and evaluate the consistency of hits obtained within each of the search terms using different search platforms.
3. We revealed a large variation among search platforms and showed that PubMed and Scopus returned consistent results to identical search strings from different locations. Google Scholar and Web of Science''s Core Collection varied substantially both in the number of returned hits and in the list of individual articles depending on the search location and computing environment. Inconsistency in Web of Science results has most likely emerged from the different licensing packages at different institutions.
4. To maintain scientific integrity and consistency, especially in systematic reviews, action is needed from both the scientific community and scientific search platforms to increase search consistency. Researchers are encouraged to report the search location and the databases used for systematic reviews, and database providers should make search algorithms transparent and revise access rules to titles behind paywalls. Additional options for increasing the repeatability and transparency of systematic reviews are storing both search metadata and hit results in open repositories and using Application Programming Interfaces (APIs) to retrieve standardized, machine‐readable search metadata.

     

间作牧草对茶园螨类群落多样性的影响

螨类是茶园生态系统中重要且复杂的类群之一.为了了解不同植物问作后对茶园螨类群落的组成结构和多样性的影响,2006年3月至2008年4月,在武夷山市星村镇大坪洲茶园通过间作百喜草(Paspalum notatum)或圆叶决明(Cassia rotundifolia)、留养杂草和除杂草4种不同处理,对茶园茶冠层(采用盆拍法及剪枝条法)和凋落层(采用捡取凋落物法)的螨类进行系统采样、标本鉴定和统计分析.结果表明:与留养杂草对照相比,间作百喜草或圆叶决明均显著增加了茶冠层和凋落层捕食螨的物种丰富度(S)、有效多样性指数(eH')、个体数(M和绝对丰度(-/n).与留养杂草和除杂草这两种对照相比,间作百喜草或圆叶决明均显著增加了茶冠层和凋落层优势种圆果大赤螨(Anystis baccarum)的个体数(N).荼冠层植食螨和腐食螨及凋落层腐食螨的所有群落指标在不同处理茶园间均无显著差异.茶冠层和凋落层螨类群落物种丰富度(S)和个体数(N)季节性变化明显,物种组成相似性高.间作茶园和留养杂草茶园茶冠层的螨类总个体数与其对应的凋落层螨类总个体数呈显著正相关.多样化茶园有利于保护和利用捕食螨,从而对茶园有害生物进行生态控制,促进有机茶叶可持续生产.     

Practical importance for conservation of insect diversity in China

Insects are one of the most important groups in the natural world. They affect the life and welfare of humans in many different ways. While some insects are referred to as pests, others are beneficial to humans. For example, they may serve a function as pollinators of many cultivated plants, as natural enemies of harmful species, or as producers of valuable materials such as honey and silk. Several insect species, however, are not currently known as being harmful or beneficial. Nevertheless they are extremely important as essential components of both natural and modified ecosystems. In China, only 1% of insect species described are major pests. The majority of insects are either neutral or beneficial to humans. China, with its vast territory, diverse climate and ecosystems, is amongst the richest countries in insect diversity. However, as a result of the economic and population growth and development, Chinas insect diversity is now faced with habitat degradation, species extinction, and a decline in the natural enemies of harmful pests. These problems are due to the expansion of agriculture, urbanization, industrialization, pollution, mining, tourism, introduced species, hunting, and the illegal trade in endangered species. In order to exploit the beneficial components of insects as biological resources and to effectively control their harmful aspects, many national strategies, legal actions and capacity-building activities have been developed and implemented. These efforts work towards the goal of insect diversity conservation in China.     

Phenotypic plasticity inLemna minor (Lemnaceae)

Eight genotypes ofLemna minor, originating from four continents, were grown for 15 days in eight different environmental treatments. Fronds under each treatment were then transferred into each of the eight environmental conditions for 15 days. The rate of frond production (relative growth rate) and mean frond biomass were recorded for each pre- and post-transfer treatment and root length was measured for each pre-transfer treatment. For all the traits, the levels of response varied significantly between genotypes (G) and between environmental conditions (E). G × E interaction effect was significant for all traits under pre-transfer treatments and some post-transfer treatments. Both pattern and amount of plasticity were genotypically variable but the amount of variation depended on the trait. The trait representing the best estimate of fitness, growth rate, exhibited the least amount of plasticity and on average, showed the most conservative pattern of plasticity. In contrast, the trait least related to fitness, root length, was the most plastic and showed the most divergent pattern of plasticity. Under some post-transfer treatments, growth rate and mean frond biomass were affected by origin (initial treatment) effect. Pattern and amount of plasticity were also influenced by initial treatments. Since some genotypes may be more affected than others by environmental conditions, origin effect may accentuate G × E interaction and therefore, modify the pattern and amount of plasticity. Comparison between dendrograms based on genetic and phenotypic similarities suggested that there is no relationship between genetic and phenotypic divergence. This lack of relationship may be due to the fact that plasticity is not necessarily adaptive.     

DNA Sequencing Reveals the Midgut Microbiota of Diamondback Moth,Plutella xylostella (L.) and a Possible Relationship with Insecticide Resistance

Background

Insect midgut microbiota is important in host nutrition, development and immune response. Recent studies indicate possible links between insect gut microbiota and resistance to biological and chemical toxins. Studies of this phenomenon and symbionts in general have been hampered by difficulties in culture-based approach. In the present study, DNA sequencing was used to examine the midgut microbiota of diamondback moth (DBM), Plutella xylostella (L.), a destructive pest that attacks cruciferous crops worldwide. Its ability to develop resistance to many types of synthetic insecticide and even Bacillus thuringiensis toxins makes it an important species to study.

Methodology/Principal Findings

Bacteria of the DBM larval midgut in a susceptible and two insecticide (chlorpyrifos and fipronil) resistant lines were examined by Illumina sequencing sampled from an insect generation that was not exposed to insecticide. This revealed that more than 97% of the bacteria were from three orders: Enterobacteriales, Vibrionales and Lactobacillales. Both insecticide-resistant lines had more Lactobacillales and the much scarcer taxa Pseudomonadales and Xanthomonadales with fewer Enterobacteriales compared with the susceptible strain. Consistent with this, a second study observed an increase in the proportion of Lactobacillales in the midgut of DBM individuals from a generation treated with insecticides.

Conclusions/Significance

This is the first report of high-throughput DNA sequencing of the entire microbiota of DBM. It reveals differences related to inter- and intra-generational exposure to insecticides. Differences in the midgut microbiota among susceptible and insecticide-resistant lines are independent of insecticide exposure in the sampled generations. While this is consistent with the hypothesis that Lactobacillales or other scarcer taxa play a role in conferring DBM insecticide resistance, further studies are necessary to rule out other possibilities. Findings constitute the basis for future molecular work on the functions of insect midgut microbiota taxa and their possible role in conferring host resistance to toxins.