Rice yield formation under high day and night temperatures—A prerequisite to ensure future food security

Increasing temperatures resulting from climate change dramatically impact rice crop production in Asia. Depending on the specific stage of rice development, heat stress reduces tiller/panicle number, decreases grain number per plant and lower grain weight, thus negatively impacting yield formation. Hence improving rice crop tolerance to heat stress in terms of sustaining yield stability under high day temperature (HDT), high night temperature (HNT), or combined high day and night temperature (HDNT) will bolster future food security. In this review article, we highlight the phenological alterations caused by heat and the underlying molecular-physiological and genetic mechanisms operating under different types of heat conditions (HDT, HNT, and HDNT) to understand heat tolerance. Based on our synthesis of HDT, HNT, and HDNT effects on rice yield components, we outline future breeding strategies to contribute to sustained food security under climate change.     

The role of soil bacterial community during winter fallow period in the incidence of tobacco bacterial wilt disease

Applied Microbiology and Biotechnology - Bacterial wilt, caused by Ralstonia solanacearum, occurs occasionally during tobacco planting and potentially brings huge economic losses in affected areas....     

Insights into the fluoride-resistant regulation mechanism of <Emphasis Type="Italic">Acidithiobacillus ferrooxidans</Emphasis> ATCC 23270 based on whole genome microarrays

Acidophilic microorganisms involved in uranium bioleaching are usually suppressed by dissolved fluoride ions, eventually leading to reduced leaching efficiency. However, little is known about the regulation mechanisms of microbial resistance to fluoride. In this study, the resistance of Acidithiobacillus ferrooxidans ATCC 23270 to fluoride was investigated by detecting bacterial growth fluctuations and ferrous or sulfur oxidation. To explore the regulation mechanism, a whole genome microarray was used to profile the genome-wide expression. The fluoride tolerance of A. ferrooxidans cultured in the presence of FeSO₄ was better than that cultured with the S⁰ substrate. The differentially expressed gene categories closely related to fluoride tolerance included those involved in energy metabolism, cellular processes, protein synthesis, transport, the cell envelope, and binding proteins. This study highlights that the cellular ferrous oxidation ability was enhanced at the lower fluoride concentrations. An overview of the cellular regulation mechanisms of extremophiles to fluoride resistance is discussed.     

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms’ taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75–100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time.     

Maize growth responses to soil microbes and soil properties after fertilization with different green manures

The use of green manures in agriculture can provide nutrients, affect soil microbial communities, and be a more sustainable management practice. The activities of soil microbes can effect crop growth, but the extent of this effect on yield remains unclear. We investigated soil bacterial communities and soil properties under four different green manure fertilization regimes (Vicia villosa, common vetch, milk vetch, and radish) and determined the effects of these regimes on maize growth. Milk vetch showed the greatest potential for improving crop productivity and increased maize yield by 31.3 %. This change might be related to changes in soil microbes and soil properties. The entire soil bacterial community and physicochemical properties differed significantly among treatments, and there were significant correlations between soil bacteria, soil properties, and maize yield. In particular, abundance of the phyla Acidobacteria and Verrucomicrobia was positively correlated with maize yield, while Proteobacteria and Chloroflexi were negatively correlated with yield. These data suggest that the variation of maize yield was related to differences in soil bacteria. The results also indicate that soil pH, alkali solution nitrogen, and available potassium were the key environmental factors shaping soil bacterial communities and determining maize yields. Both soil properties and soil microbes might be useful as indicators of soil quality and potential crop yield.

     

Mapping quantitative trait loci for heat tolerance of reproductive traits in tomato (<Emphasis Type="Italic">Solanum lycopersicum</Emphasis>)

Global warming has become a worldwide concern due to its adverse effects on agricultural output. In particular, long-term mildly high temperatures interfere with sexual reproduction and thus fruit and seed set. To uncover the genetic basis of observed variation in tolerance against heat, a bi-parental F₂ mapping population from two contrasting cultivars, i.e. Nagcarlang and NCHS-1, was generated and phenotyped under continuous mild heat conditions for a number of traits underlying reproductive success, i.e. pollen viability, pollen number, style length, anther length, style protrusion, female fertility and flowering characteristics, i.e. inflorescence number and flowers per inflorescence. Quantitative trait loci (QTLs) were identified for most of these traits, including a single, highly significant one for pollen viability, which accounted for 36% of phenotypic variation in the population and modified pollen viability under high temperature with around 20%. QTLs for some traits colocalised, indicating trait dependency or pleiotropic-effect loci. We conclude that a limited set of major genes determines differences in performance of reproductive traits under continuous mild heat in tomato. The results contribute to our fundamental understanding of pollen thermotolerance and may support development of more heat-tolerant tomato varieties.     

长期连作农田土壤细菌群落结构和共现网络拓扑性质对土壤理化性质的响应

【目的】为探究长期连作土壤细菌群落结构和分子生态网络与土壤环境演化的关联性。【方法】本研究利用16S rRNA基因高通量测序技术,解析了湖南省浏阳市两块连作十二年农田(表现连作障碍的GD和健康的YA)土壤微生物群落组成结构和分子生态网络拓扑性质与土壤理化性质的关系。【结果】GD土壤总氮和有效磷含量显著高于YA,而土壤硝态氮和速效钾含量显著低于YA(P<0.05)。GD土壤细菌群落多样性高于YA,两地土壤细菌群落结构存在显著差异(P<0.01),且与土壤pH和有效磷含量相关。进一步分析表明,GD土壤细菌群落之间比YA具有更复杂的生态网络,主要体现在能量代谢、碳循环和氮循环功能模块。【结论】综上所述,连作会引起土壤细菌群落多样性、组成结构和生态网络变化,这可能与土壤理化性质恶化、土壤肥力下降密切相关,进而影响作物生长发育。     

基于空间规划情景的雄安新区生态系统休闲服务评估预测与驱动分析

雄安新区作为我国乃至世界智慧生态新型城市建设的重大探索和实践,生态和谐、绿色宜居是新区规划和建设的重要目标之一,城市生态系统为居民提供的生态休闲服务是实现该目标的重要保障与体现。随着新区的开发建设,其土地利用、空间结构、景观组分以及内部生态过程等都将发生巨大变化,这将对生态系统休闲服务供给能力的数量、质量以及可利用性产生复杂影响。从吸引力和可达性两个维度构建了新区生态系统休闲服务的评估模型,对2018年与2035年生态系统休闲服务的能力进行评估与预测,进一步利用地理探测器分析社会因子的驱动作用。研究结果表明：(1)2018年生态系统休闲服务综合指数为5.10,属于中等供给-可访问状态。其中,白洋淀湿地及周围绿带为高吸引力的集中区,可达性高的区域主要分布在雄州镇、安新镇、容城镇附近;(2)相比于2018年,2035年生态系统休闲服务综合指数增加了0.32,但区域整体仍属于中等供给-可访问状态。(3)雄安新区生态系统休闲服务的主要驱动因子从2018年的人口密度和GDP密度转变为2035年的GDP密度与第三产业占比。评估预测结果指示：在雄安新区未来生态系统休闲服务的建设中要特别考虑城镇化进程...     

Mobile genetic elements mediate the mixotrophic evolution of novel Alicyclobacillus species for acid mine drainage adaptation

Alicyclobacillus species inhabit diverse environments and have adapted to broad ranges of pH and temperature. However, their adaptive evolutions remain elusive, especially regarding the role of mobile genetic elements (MGEs). Here, we characterized the distributions and functions of MGEs in Alicyclobacillus species across five environments, including acid mine drainage (AMD), beverages, hot springs, sediments, and soils. Nine Alicyclobacillus strains were isolated from AMD and possessed larger genome sizes and more genes than those from other environments. Four AMD strains evolved to be mixotrophic and fell into distinctive clusters in phylogenetic tree. Four types of MGEs including genomic island (GI), insertion sequence (IS), prophage, and integrative and conjugative element (ICE) were widely distributed in Alicyclobacillus species. Further, AMD strains did not possess CRISPR-Cas systems, but had more GI, IS, and ICE, as well as more MGE-associated genes involved in the oxidation of iron and sulfide and the resistance of heavy metal and low temperature. These findings highlight the differences in phenotypes and genotypes between strains isolated from AMD and other environments and the important role of MGEs in rapid environment niche expansions.