Modern bivalve shell assemblages on three atolls offshore Belize (Central America,Caribbean Sea)

The Belize atolls—Glovers Reef, Lighthouse Reef and Turneffe Islands—show differences in geomorphology, lagoonal depth, bottom sediment, growth of mangroves and sea-grass, exposure to waves and currents as well as in their sedimentation rates and their age. Bivalve shell assemblages in lagoonal areas reflect these geomorphological differences. On each atoll, 32 to 44 recent sediment samples were taken (total number of samples 111) and bivalve shells subsequently identified. The resulting database (32,122 bivalve shells in total) was analysed using Q-mode cluster analyses. Both the distribution of species characteristic of different lagoonal habitats and the distribution of bivalves with different life and feeding habits were investigated. Epifaunal suspension feeders were found particularly on hard-bottom along the reef-crests or clinging to mangrove roots. Infaunal suspension feeders show a more diverse distribution. Deeper lagoonal parts and areas with mangrove growth are often inhabited by chemosymbiont-carrying bivalves, indicating locations of reduced sediment. Deep burrowing detritus feeders are very abundant in shallow-water areas with moderate to high water agitation and were seldom found in Halimeda-rich sediments.     

Alteration of oxidative and carbohydrate metabolism under abiotic stress in two rice (Oryza sativa L.) genotypes contrasting in chilling tolerance

Abiotic stress is a major limiting factor in crop production. Physiological comparisons between contrasting abiotic stress-tolerant genotypes will improve understanding of stress-tolerant mechanisms. Rice seedlings (S3 stage) of a chilling-tolerant (CT) genotype (CT6748-8-CA-17) and a chilling-sensitive (CS) genotype (INIAP12) were subjected to abiotic stresses including chilling (13/12 degrees C), salt (100mM NaCl), and osmotic (200mM mannitol). Measures of physiological response to the stresses included changes in stress-related sugars, oxidative products and protective enzymes, parameters that could be used as possible markers for selection of improved tolerant varieties. Metabolite analyses showed that the two genotypes responded differently to different stresses. Genotype survival under chilling-stress was as expected, however, CT was more sensitive to salt stress than the CS genotype. The CT genotype was able to maintain membrane integrity better than CS, perhaps by reduction of lipid peroxidation via increased levels of antioxidant enzymes during chilling stress. This genotype accumulated sugars in response to stress, but the accumulation was usually less than in the CS genotype. Chill-stressed CT accumulated galactose and raffinose whereas these saccharides declined in CS. On the other hand, the tolerance mechanism in the more salt- and water-deficit-tolerant CS may be associated with accumulation of osmoprotectants such as glucose, trehalose and mannitol.     

Identification of disulfide reductases in Campylobacterales: a bioinformatics investigation

Disulfide reductases of host-colonising bacteria are involved in the expression of virulence factors, resistance to drugs, and elimination of toxic compounds. Large-scale genome analyses of 281 prokaryotes identified CXXC and CXXC-derived motifs in each microorganism. The total number of these motifs showed correlations with genome size and oxygen tolerance of the prokaryotes. Specific bioinformatic analyses served to identify putative disulfide reductases in the Campylobacterales Campylobacter jejuni, Helicobacter pylori, Wolinella succinogenes and Arcobacter butzleri which colonise the gastrointestinal tract of higher animals. Three filters applied to the genomes of these species yielded 35, 25, 28 and 34 genes, respectively, encoding proteins with the characteristics of disulfide reductases. Ten proteins were common to the four species, including four belonging to the thioredoxin system. The presence of thioredoxin reductase activities was detected in the four bacterial species by observing dithiobis-2-nitrobenzoic acid reduction with β-nicotinamide adenine dinucleotide phosphate as cofactor. Phylogenetic analyses of the thioredoxin reductases TrxB₁ and TrxB₂ of the four Campylobacterales were performed. Their TrxB₁ proteins were more closely related to those of Firmicutes than to the corresponding proteins of other Proteobacteria. The Campylobacterales TrxB₂ proteins were closer to glutathione reductases of other organisms than to their respective TrxB₁ proteins. The phylogenetic features of the Campylobacterales thioredoxin reductases suggested a special role for these enzymes in the physiology of these bacteria. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Ground‐nesting by the chimpanzees of the Nimba Mountains,Guinea: environmentally or socially determined?

The chimpanzees (Pan troglodytes verus) of the Nimba Mountains, Guinea, West Africa, commonly make both elaborate ("night") and simple ("day") nests on the ground. In this study we investigated which factors might influence ground-nesting in this population, and tested two ecological hypotheses: 1) climatic conditions, such as high wind speeds at high altitudes, may deter chimpanzees from nesting in trees; and 2) a lack of appropriate arboreal nesting opportunities may drive the chimpanzees to nest on the ground. In addition to testing these two hypotheses, we explored whether ground-nesting is a sex-linked behavior. Data were collected monthly between August 2003 and May 2004 along transects and ad libitum. To identify the sex of ground-nesting individuals, we used DNA extracted from hair samples. The results showed that the occurrence and distribution of ground nests were not affected by climatic conditions or a lack of appropriate nest trees. Support was found for the notion that ground-nesting is a sex-linked behavior, as males were responsible for building all of the elaborate ground nests and most of the simple ground nests sampled. Elaborate ground nests occurred mostly in nest groups associated with tree nests, whereas simple ground nests usually occurred without tree nests in their vicinity. These results suggest that ground-nesting may be socially, rather than ecologically, determined.     

Transport capabilities of eleven gram-positive bacteria: Comparative genomic analyses

The genomes of eleven Gram-positive bacteria that are important for human health and the food industry, nine low G + C lactic acid bacteria and two high G + C Gram-positive organisms, were analyzed for their complement of genes encoding transport proteins. Thirteen to 18% of their genes encode transport proteins, larger percentages than observed for most other bacteria. All of these bacteria possess channel proteins, some of which probably function to relieve osmotic stress. Amino acid uptake systems predominate over sugar and peptide cation symporters, and of the sugar uptake porters, those specific for oligosaccharides and glycosides often outnumber those for free sugars. About 10% of the total transport proteins are constituents of putative multidrug efflux pumps with Major Facilitator Superfamily (MFS)-type pumps (55%) being more prevalent than ATP-binding cassette (ABC)-type pumps (33%), which, however, usually greatly outnumber all other types. An exception to this generalization is Streptococcus thermophilus with 54% of its drug efflux pumps belonging to the ABC superfamily and 23% belonging each to the Multidrug/Oligosaccharide/Polysaccharide (MOP) superfamily and the MFS. These bacteria also display peptide efflux pumps that may function in intercellular signalling, and macromolecular efflux pumps, many of predictable specificities. Most of the bacteria analyzed have no pmf-coupled or transmembrane flow electron carriers. The one exception is Brevibacterium linens, which in addition to these carriers, also has transporters of several families not represented in the other ten bacteria examined. Comparisons with the genomes of organisms from other bacterial kingdoms revealed that lactic acid bacteria possess distinctive proportions of recognized transporter types (e.g., more porters specific for glycosides than reducing sugars). Some homologues of transporters identified had previously been identified only in Gram-negative bacteria or in eukaryotes. Our studies reveal unique characteristics of the lactic acid bacteria such as the universal presence of genes encoding mechanosensitive channels, competence systems and large numbers of sugar transporters of the phosphotransferase system. The analyses lead to important physiological predictions regarding the preferred signalling and metabolic activities of these industrially important bacteria.     

Inducing whole-assemblage change by experimental manipulation of habitat structure

1. Habitat structure long has been identified as a primary factor influencing local assemblage composition. Most evidence has been in the form of correlations of species occurrence and assemblage composition over a range of habitats, with experimental verification of relationships being relatively uncommon because of the difficulties of enacting precise manipulations of habitat structure. 2. Fallen timber (also known as coarse or large woody debris) is one of the few habitat-structural elements in forests and woodlands that can be manipulated with relatively high precision. We report on manipulations of wood-loads on 30 experimental 1-ha plots in floodplain forests of northern Victoria, Australia, over 4 years (one pre- and three post-manipulation). 3. We show that very high wood-loads (80 Mg ha(-1)) and intermediate wood-loads derived from tree crowns (40 Mg ha(-1)) increase species richness (all species and ground-foraging species) and numbers of birds (all species and ground-foraging species) relative to the control plots. 4. Three bird species consistently increased most following manipulations: white-plumed honeyeater Lichenostomus penicillatus (Gould 1837) (fam. Meliphagidae), brown treecreeper Climacteris picumnus (Temm. & Laug. 1824) (fam. Climacteridae) and yellow rosella Platycercus elegans flaveolus (Gould 1837) (fam. Psittacidae). The honeyeater is not considered as a ground or fallen timber dependent species, while the treecreeper and rosella both are regarded as being dependent on ground-layer structure. 5. Fallen timber management needs to be considered in a landscape and temporal context for improving conservation of avian biodiversity.     

From the Apennines to the Alps: colonization genetics of the naturally expanding Italian wolf (Canis lupus) population

Wolves in Italy strongly declined in the past and were confined south of the Alps since the turn of the last century, reduced in the 1970s to approximately 100 individuals surviving in two fragmented subpopulations in the central-southern Apennines. The Italian wolves are presently expanding in the Apennines, and started to recolonize the western Alps in Italy, France and Switzerland about 16 years ago. In this study, we used a population genetic approach to elucidate some aspects of the wolf recolonization process. DNA extracted from 3068 tissue and scat samples collected in the Apennines (the source populations) and in the Alps (the colony), were genotyped at 12 microsatellite loci aiming to assess (i) the strength of the bottleneck and founder effects during the onset of colonization; (ii) the rates of gene flow between source and colony; and (iii) the minimum number of colonizers that are needed to explain the genetic variability observed in the colony. We identified a total of 435 distinct wolf genotypes, which showed that wolves in the Alps: (i) have significantly lower genetic diversity (heterozygosity, allelic richness, number of private alleles) than wolves in the Apennines; (ii) are genetically distinct using pairwise F(ST) values, population assignment test and Bayesian clustering; (iii) are not in genetic equilibrium (significant bottleneck test). Spatial autocorrelations are significant among samples separated up to c. 230 km, roughly correspondent to the apparent gap in permanent wolf presence between the Alps and north Apennines. The estimated number of first-generation migrants indicates that migration has been unidirectional and male-biased, from the Apennines to the Alps, and that wolves in southern Italy did not contribute to the Alpine population. These results suggest that: (i) the Alps were colonized by a few long-range migrating wolves originating in the north Apennine subpopulation; (ii) during the colonization process there has been a moderate bottleneck; and (iii) gene flow between sources and colonies was moderate (corresponding to 1.25-2.50 wolves per generation), despite high potential for dispersal. Bottleneck simulations showed that a total of c. 8-16 effective founders are needed to explain the genetic diversity observed in the Alps. Levels of genetic diversity in the expanding Alpine wolf population, and the permanence of genetic structuring, will depend on the future rates of gene flow among distinct wolf subpopulation fragments.     

Nuclear Magnetic Resonance Spectroscopic Studies on the Microbial Degradation of Mononitrophenol Isomers

The biochemical pathways followed by a mixed bacterial culture and one of its constituent strains, Sarcina maxima, MTCC 5216 (hitherto unreported) during the degradation of mononitrophenol isomers was studied using extensive nuclear magnetic resonance (NMR) spectroscopy (One- and Two-Dimensional Heteronuclear Multiple Quantum Coherence Transfer-2D HMQCT NMR). NMR investigations revealed that o-nitrophenol (ONP) could be degraded by the consortium to metabolites such as catechol, cis, cis-muconic acid, γ-hydroxymuconic semialdehyde, maleylacetate and β-ketoadipate. The spectra of ONP reaction mixture degraded by S.␣maxima showed that formation of maleylacetate from γ-hydroxymuconic semialdehyde should go through a new metabolite γ-hydroxymaleylacetate, hitherto unreported. The consortium could breakdown m-nitrophenol (MNP) to 4-aminocatechol indicating that it came from 3-hydroxyaminophenol. However, S. maxima MTCC 5216, could convert MNP to hitherto unreported 2-nitrohydroquinone and the subsequent 2-hydroxylaminohydroquinone to 1,2,4-benzenetriol along with γ-hydroxymuconic semialdehyde, muconolactone and maleylacetate. The pathway followed by the consortium during p-nitrophenol (PNP) degradation was by the formation of 4-nitrocatechol, maleylacetate and β-ketoadipate. PNP reaction mixture of S.␣maxima, MTCC 5216 on the other hand, showed that the pathway could proceed through the formation of p-hydroquinone as the initial metabolite. The present study conclusively established the nitrophenol-degrading ability of both the consortium and S. maxima MTCC 5216, including exhibiting slight deviations from the pathways followed by the other reported microorganisms.     

在系统发育分析中编码空位

空位包含了可用于系统发育分析的进化信息.为了准确地计算系统发育关系,空位包含的信息应该予以考虑.本文讨论了7种最常用的空位编码方法,并举例说明这些方法的编码原理.另外,本文还介绍了一些经验用以帮助研究者在使用现有的系统发育软件时选择空位编码方法.但是,所有的空位编码方法都有其优点和缺点,需要提出新的空位编码方法才能使空位信息在系统发育分析中得以充分地应用.     

First detection and molecular characterization of grapevine phytoplasmas in Kosovo

A search for phytoplasma-associated diseases was conducted for the first time in the main grapevine-growing localities of the Dukagjini plain in Kosovo. A total of 144 samples were collected from grapevine cultivars displaying leaf yellowing, reddening, discolouration and irregular wood ripening, and analysed using nested and quantitative PCR assays. These assays showed that 35.4% of samples belonging to eight cultivars were positive to the presence of phytoplasmas in the 16SrXII group. The 16S rDNA phytoplasma sequences obtained from 15 samples shared identity greater than 99.5% with ‘Candidatus Phytoplasma solani’. Sequence analysis of the tuf gene showed that the strains found in Kosovar grapevines are in the tuf-type b1 group, sharing 99.6% to 99.8% identity with ‘Ca. P. solani'-related strains associated with the “bois noir” grapevine disease in many European countries; the secY gene sequences, on the other hand, shared 100% identity with ‘Ca. P. solani' strains from Bosnia and Herzegovina, Serbia, Croatia and Turkey. This study constitutes the first report on the presence and molecular characterization of phytoplasmas in Kosovar vineyards. Based on these results, it is recommended that testing for phytoplasma be included in the certification program for grapevine in Kosovo.