Aquatic Actinomycete-Fungal Interactions and Their Effects on Organic Matter Decomposition: A Microcosm Study

The role of fungi in the decomposition of organic matter in streams has been well examined, although the role of bacterial antagonists in such processes has gained little attention. To examine bacterial-fungal interactions, experiments involving pairwise combinations of four actinomycete isolates (A1+ and A2+ could remove chitin from chitin-containing media, and A1? and A2? could not) and two fungal isolates (F+ a true fungus, F? an oomycote) were conducted. For each bacterial-fungal combination, 250-ml microcosms were sampled at 8 day intervals for 32 days. Microbial biomass and organic matter, as well as the activities of five extracellular enzymes, were measured. Each experiment consisted of a control group and four treatment groups. Controls comprised sterilized stream water and macrophytes. The first treatment was inoculated with only actinomycetes (~103 cells ml-1), the second treatment was inoculated with only fungi (~102 cells ml-1), the third group was inoculated simultaneously with actinomycetes and fungi, and the fourth group was inoculated with actinomycetes 2 days after fungal establishment. For all combinations, the lowest rates of organic matter decomposition were expected in the controls, as a result of only physical degradation. In contrast, the greatest rates of organic matter decomposition were predicted in treatments inoculated with F+ 2 days prior to A1? or A2?. Greater than 50% of the organic matter was decomposed in each of the fungal treatments. Fungal-actinomycete interactions resulted in reduced fungal biomass relative to the fungal-only treatments. However, when inoculated 2 days apart, combinations of F? and actinomycetes resulted in enhanced rates of organic matter decomposition, as well as greater levels of extracellular enzyme activities. These results demonstrate that actinomycete-fungal interactions and their colonization dynamics affect the accumulation of biomass, extracellular enzyme activities, and rates of organic matter decomposition.     

苜蓿遗传多样性的取样数目——RAPD和SSR群体标记法

紫花苜蓿为异花授粉植物,其DNA多态性研究的取样策略与遗传多样性分析直接相关.选取了4个苜蓿品种陇东(地方品种)、中兰1号(育成品种)、牧歌(Graze)和金皇后(Queen)(引进品种),设置了取样数目分别为10、20、40和60个单株进行DNA混合,利用RAPD(random amplification polymorphic DNA,随机扩增长度多态性DNA)和SSR(simple sequence repeat,简单重复序列)标记分别进行了遗传多样性分析,结果发现40和60个单株DNA混合样的聚类结果一致,表明10和20个单株组成的群体太小,随着苜蓿群体取样数目的增加,遗传多样性分析的准确性也随之增加,但是分析成本也相应提高.鉴于此,利用RAPD和SSR标记分析苜蓿遗传多样性时采用40个单株的DNA混合样是较适宜的群体大小.     

Evaluation of Genetic Diversity in Lemons and Some of Their Relatives Based on SRAP and SSR Markers

Genetic diversity was evaluated by sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers among 45 lemons (Citrus limon (L.) Burm. f.), five citrons (Citrus medica L.), four rough lemons (Citrus jambhiri Lush), and two Citrus volkameriana accessions. Twenty-one SRAP primer combinations produced a total of 141 (77%) polymorphic fragments with an average of 6.7 fragments per primer combinations whereas 13 SSR primers produced a total of 26 (76%) polymorphic fragments with an average of 2.0 per primer. The unweighted pair-group method arithmetic average analysis as assessed with combined SRAP and SSR data demonstrated that the accessions had a similarity range from 0.65 to 1.00. Rough lemons and C. volkameriana accessions were relatively closely related. In lemon group, accessions from hybrid origin were distant from the others. We also applied principal components analysis (PCA) for a better presentation of relation among the accessions studies. Using PCA, 88.7% of the total variation in the original dimensions could be represented by just the two dimensions defined by the first two PCs. Although nearly all accessions could be distinguished, there was a low level of genetic diversity detected among lemon cultivars.     

Plant Functional Diversity Can Be Independent of Species Diversity: Observations Based on the Impact of 4-Yrs of Nitrogen and Phosphorus Additions in an Alpine Meadow

Past studies have widely documented the decrease in species diversity in response to addition of nutrients, however functional diversity is often independent from species diversity. In this study, we conducted a field experiment to examine the effect of nitrogen and phosphorus fertilization ((NH₄)₂ HPO₄) at 0, 15, 30 and 60 g m^-2 yr^-1 (F0, F15, F30 and F60) after 4 years of continuous fertilization on functional diversity and species diversity, and its relationship with productivity in an alpine meadow community on the Tibetan Plateau. To this purpose, three community-weighted mean trait values (specific leaf area, SLA; mature plant height, MPH; and seed size, SS) for 30 common species in each fertilization level were determined; three components of functional diversity (functional richness, FRic; functional evenness, FEve; and Rao’s index of quadratic entropy, FRao) were quantified. Our results showed that: (i) species diversity sharply decreased, but functional diversity remained stable with fertilization; (ii) community-weighted mean traits (SLA and MPH) had a significant increase along the fertilization level; (iii) aboveground biomass was not correlated with functional diversity, but it was significantly correlated with species diversity and MPH. Our results suggest that decreases in species diversity due to fertilization do not result in corresponding changes in functional diversity. Functional identity of species may be more important than functional diversity in influencing aboveground productivity in this alpine meadow community, and our results also support the mass ratio hypothesis; that is, the traits of the dominant species influenced the community biomass production.     

高黎贡山不同土地利用方式对土壤 微生物数量和多样性的影响

测定了高黎贡山不同利用方式土壤中微生物的数量、小型真菌的多样性和属的分布,分析了上述指标在不同利用方式土壤中的分布与人为干扰和环境因素之间的相互关系。结果表明微生物数量和真菌的多样性在不同利用方式土壤中的分布是,原生林(次生林(幼杉木纯林;耕作通常使条件更有利于土壤微生物生长繁殖,成熟人工纯林和旱地的土壤微生物数量及真菌多样性均较高;在五类利用方式中,土壤微生物数量及真菌多样性以原生林最高,荒地最低。     

Respiratory Gas Bladders in Teleosts: Functional Conservatism and Morphological Diversity

SYNOPSIS. Respiratory gas bladders are found in the Osteoglossomorpha,Elopomorpha and Euteleostei and are absent in the Clupeomorpha.All teleosts with respiratory gas bladders share a common patternof air ventilation: during the transfer phase gas is transferredpassively from the gas bladder to the buccal cavity. Subsequently,gas is expelled during the active expulsion phase mediated byaction of the geniohyoideus muscle causing a positive pressurepulse in the buccal cavity. This is followed by an active intakephase by action of the sternohyoideus muscle creating a negativepressure pulse, which is succeeded by an extensive compressivephase by action of the geniohyoideus muscle forcing fresh airinto the gas bladder. Saltatory evolution of gas bladders andtheir buccal pumps seems to have proceeded by major transformationsin structural design without appreciable changes in the patternof neural control. The hypothesis of symmorphosis in gas bladderdesign is well corroborated by the independent evolution ofaccessory esophageal pumps in three unrelated lineages. Evolutionaryreversals (Primitive lung evolving into nonrespiratory hydrostaticswim bladder which subsequently reverts back to become a respiratorygas bladder) have occurred repeatedly. Such reversed shiftsare facilitated by the conserved neuromuscular pattern duringfunctional transformations. Experimental comparative evidenceis offered for the notion that evolutionary innovations mayinvolve the addition of entirely new functions (respiratory)of a structural complex (gas bladder) while the original functions(hydrostatic, hearing and sound production) are rigidly retained.The paucity in Elopomorpha and absence in Clupeomorpha of respiratorygas bladders reflect the lack of functional demands for newhabits in the environment rather than the absence of essentialpreexisting building blocks.     

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic way and in a species-neutral manner with the aim of unifying the representation of gene function across different organisms. Each contributing member of the GO Consortium independently associates GO terms to gene products from the organism(s) they are annotating. Here we introduce the Reference Genome project, which brings together those independent efforts into a unified framework based on the evolutionary relationships between genes in these different organisms. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO's logical structure and biological content.     

Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Factor Analysis

We consider the statistical analysis of population structure using genetic data. We show how the two most widely used approaches to modeling population structure, admixture-based models and principal components analysis (PCA), can be viewed within a single unifying framework of matrix factorization. Specifically, they can both be interpreted as approximating an observed genotype matrix by a product of two lower-rank matrices, but with different constraints or prior distributions on these lower-rank matrices. This opens the door to a large range of possible approaches to analyzing population structure, by considering other constraints or priors. In this paper, we introduce one such novel approach, based on sparse factor analysis (SFA). We investigate the effects of the different types of constraint in several real and simulated data sets. We find that SFA produces similar results to admixture-based models when the samples are descended from a few well-differentiated ancestral populations and can recapitulate the results of PCA when the population structure is more “continuous,” as in isolation-by-distance models.     

The Nauplius Larva of Crustaceans: Functional Diversity and the Phylotypic Stage

SYNOPSIS. The crustacean nauplius larva is a development stagecharacterized by the presence of three pairs of head appendages.All crustaceans pass through the naupliar stage whether embryonicallyor as freeliving larvae. The nauplius is thought to be the phylotypicstage and represent a fundamental developmental constraint incrustaceans. However, free-living nauplii are primitive andI present evidence that this form is functionally plastic, e.g.,locomotory modes are diverse even in closely related species.I argue that this functional plasticity allowed the persistenceof nauplii in the early evolution of crustaceans and, as a consequence,naupliar development became a deep-seated feature of crustaceans.Thus, we see nauplii as phylotypic. This suggests that, in spiteof the presence of phylotypic stages in various phyla, phylotypyitself may not represent a similar, underlying developmentalconstraint in every case.     

One-Seeded Fruits in the Core Caryophyllales: Their Origin and Structural Diversity

The core Caryophyllales consist of approximately 30 families (12 000 species) distributed worldwide. Many members evolved one-seeded or conjoined fruits, but their origin and structural diversity have not been investigated. A comparative anatomical investigation of the one-seeded fruits within the core Caryophyllales was conducted. The origin of the one-seeded fruits and the evolutionary reconstructions of some carpological characters were traced using a tree based on rbcl and matK data in order to understand the ancestral characters and their changes. The one-seeded fruit type is inferred to be an ancestral character state in core Caryophyllales, with a subsequent increase in the seed number seen in all major clades. Most representatives of the ‘Earlier Diverging’ clade are distinguished in various carpological traits. The organization of the pericarp is diverse in many groups, although fruits with a dry, many-layered pericarp, consisting of sclerenchyma as outer layers and a thin-walled parenchyma below, with seeds occupying a vertical embryo position, are likely ancestral character states in the core Caryophyllales clade. Several carpological peculiarities in fruit and seed structure were discovered in obligate one-seeded Achatocarpaceae, Chenopodiaceae, Nyctaginaceae, Seguieriaceae and Sarcobataceae. The horizontal embryo evolved in only certain groups of Chenopodiaceae. The bar-thickening of endotegmen cells appears to be an additional character typical of core Caryophyllales. The syncarpy-to-lysicarpy paradigm in Caryophyllaceae needs to be reinterpreted.     

Abundance and Diversity of Bacterial Nitrifiers and Denitrifiers and Their Functional Genes in Tannery Wastewater Treatment Plants Revealed by High-Throughput Sequencing

Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs) due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB) amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.     

Functional Genetic Variants of TNFSF15 and Their Association with Gastric Adenocarcinoma: A Case-Control Study

The purpose of this study was to identify functional genetic variants in the promoter of tumor necrosis factor superfamily member 15 (TNFSF15) and evaluate their effects on the risk of developing gastric adenocarcinoma. Forty DNA samples from healthy volunteers were sequenced to identify single nucleotide polymorphisms (SNPs) in the TNFSF15 promoter. Two TNFSF15 SNPs (−358T>C and −638A>G) were identified by direct sequencing. Next, genotypes and haplotypes of 470 gastric adenocarcinoma patients and 470 cancer-free controls were analyzed. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by logistic regression. Serologic tests for Helicobacter pylori infection were measured by enzyme-linked immuno-sorbent assay (ELISA). Subjects carrying the TNFSF15 −358CC genotype were at an elevated risk for developing gastric adenocarcinoma, compared with those with the −358TT genotype (OR 1.42, 95% CI, 1.10 to 2.03). H. pylori infection was a risk factor for developing gastric adenocarcinoma (OR 2.31, 95% CI, 1.76 to 3.04). In the H. pylori infected group, subjects with TNFSF15 −358CC genotype were at higher risks for gastric adenocarcinoma compared with those carrying −358TT genotype (OR: 2.01, 95%CI: 1.65 to 4.25), indicating that H. pylori infection further influenced gastric adenocarcinoma susceptibility. The −358 T>C polymorphism eliminates a nuclear factor Y (NF-Y) binding site and the −358C containing haplotypes showed significantly decreased luciferase expression compared with −358T containing haplotypes. Collectively these findings indicate that functional genetic variants in TNFSF15 may play a role in increasing susceptibility to gastric adenocarcinoma.