Structure and functioning of two pelagic communities in the North Chilean Patagonian coastal system

The size composition of primary producers is important for how energy is channeled through a food web and on to the higher trophic levels and eventually to fisheries. To evaluate this, we studied the productive patterns for large (micro) versus small (nano) phytoplankton in two south marine Patagonian ecosystems: The Inner Sea of Chiloe—ISCh and, Moraleda Channel—MCh. We built Ecopath models (EwE), and evaluated the hypothesis that the overall primary productivity—rather than the ratio of large to small primary producers—constitutes an adequate proxy for predicting the amount of secondary and tertiary production and biomass (up to the fisheries). The EwE model included four small-scale fisheries and 36 functional groups. The functioning of both ecosystems was similar but the ecosystem parameters (biomass, energy transfer efficiencies from primary producers, secondary, and tertiary production) were twice as much in the basin with more microphytoplankton biomass. Overall, the hypothesis was rejected, albeit it was possible to highlight the importance of the quality and size spectrum of plankton on the structure of marine ecosystem, and to demonstrate the key role of the microbial loop over traditional food web in the functioning of the carbon biological pump in Patagonia ecosystems.     

Phylogeography of a Patagonian lizard and frog: Congruent signature of southern glacial refuges

Pleistocene glaciations produced significant increases in continental ice cover in polar and mid‐latitude temperate areas, sea‐level declines and shifts and reshuffling of biomes, all of which promote either isolation, coalescence or fragmentation in the distribution of land biota. If populations of several taxa have been co‐distributed for a prolonged time, and if the periods between perturbation or vicariance processes have been more or less stable, it is expected that divergence patterns of closely related and ecologically similar species will be congruent because of their similar biological and demographic characteristics. Based on this premise, we analysed the phylogeographic structure (cytochrome b) of Liolaemus pictus and Batrachyla leptopus, two widely co‐distributed lizard and frog species, respectively, in the Chiloé Archipelago of southern Chile, to decipher their genetic structure in response to a common climatic and environmental history. Haplotype network analysis and Bayesian inference suggest an evolutionary pattern of genetic diversity for the two species that is consistent with the Quaternary glacial history of southern Chile, and suggests a complex phylogeographic history in the Liolaemus and Batrachyla species. High‐divergence levels among haplotypes in some island populations of the archipelago also suggest genetic connectivity between putative refuges from Chiloé Island and the mainland along the exposed continental shelf during sea level minima associated with the most recent Quaternary glaciations. Our results are consistent with our hypothesis that two species have responded to parallel historical events in which the historical process during the last glacial maximum (approximately 41°S) has been sufficient to influence their phylogeographic structure.     

Trophic status of Iowa Lakes in relation to origin and glacial geology

Natural and artificial lakes in the most recently glaciated portions of Iowa have significantly greater total ion concentrations than those in other areas of the state. A similar distribution was found for total nitrogen concentrations. Lake origin seems of greater importance than location in determining trophic state. As a group, the artificial lakes have lower concentrations of total phosphorus, total chlorophyll, and greater Secchi disk transparency than do the natural lakes. This seems related to differences in the dynamics of the phosphorus cycles in these lake types.     

Climate-induced changes to the ancestral population size of two Patagonian galaxiids: the influence of glacial cycling

Patagonia is one of the few areas in the Southern Hemisphere to have been directly influenced by Quaternary glaciers. In this study, we evaluate the influence that Quaternary glacial ice had on the genetic diversity of two congeneric fish species, the diadromous Galaxias maculatus and the nondiadromous Galaxias platei, using multilocus estimates of effective population size through time. Mid-Quaternary glaciations had far-reaching consequences for both species. Galaxias maculatus and G. platei each experienced severe genetic bottlenecks during the period when Patagonia ice sheet advance reached its maximum positions c. 1.1-0.6 Ma. Concordant drops in effective size during this time suggest that range sizes were under similar constraints. It is therefore unlikely that coastal (brackish/marine) environments served as a significant refuge for G. maculatus during glacial periods. An earlier onset of population declines for G. platei suggests that this species was vulnerable to modest glacial advances. Declines in effective sizes were continuous for both species and lasted into the late-Pleistocene. However, G. maculatus exhibited a strong population recovery during the late-Quaternary (c. 400,000 bp). Unusually long and warm interglacials associated with the late-Quaternary may have helped to facilitate a strong population rebound in this primarily coastal species.     

Metabolic conversion of IQ and MeIQ to bacterial mutagens

The metabolic conversion of 2-amino-3-methyl- and 2-amino-3,4-dimethyl-imidazo[4,5-f]quinoline (IQ and MeIQ respectively) to bacterial mutagens was studied using a bacterial mutation assay. Studies were performed using S9 fractions derived from either corn oil (uninduced) or Aroclor-1254-treated Sprague-Dawley rats. Aroclor 1254 treatment lowered the S9 protein concentration required for optimum levels of mutagenesis, enhanced the numbers of mutants observed and altered the effects of metabolic inhibitors and cofactors added to the assay. Studies with uninduced preparations revealed that IQ and MeIQ exhibited similar responses to the effects of metabolic inhibitors and cofactors involved in detoxication reactions. Both IQ and MeIQ activation appeared to be inhibited by the biogenic amines tryptamine and tyramine and inactivated by conjugation with either acetyl coenzyme A or glutathione.     

Composition, diversity, and origin of the bacterial community in grass carp intestine

Gut microbiota has become an integral component of the host, and received increasing attention. However, for many domestic animals, information on the microbiota is insufficient and more effort should be exerted to manage the gastrointestinal bacterial community. Understanding the factors that influence the composition of microbial community in the host alimentary canal is essential to manage or improve the microbial community composition. In the present study, 16S rRNA gene sequence-based comparisons of the bacterial communities in the grass carp (Ctenopharyngodon idellus) intestinal contents and fish culture-associated environments are performed. The results show that the fish intestinal microbiota harbors many cellulose-decomposing bacteria, including sequences related to Anoxybacillus, Leuconostoc, Clostridium, Actinomyces, and Citrobacter. The most abundant bacterial operational taxonomic units (OTUs) in the grass carp intestinal content are those related to feed digestion. In addition, the potential pathogens and probiotics are important members of the intestinal microbiota. Further analyses show that grass carp intestine holds a core microbiota composed of Proteobacteria, Firmicutes, and Actinobacteria. The comparison analyses reveal that the bacterial community in the intestinal contents is most similar to those from the culture water and sediment. However, feed also plays significant influence on the composition of gut microbiota.     

The contribution of nitrogen fixation to sugarcane (Saccharum officinarum L.), and the identification and characterization of part of the associated diazotrophic bacterial community

Background and aims

Rhizospheric, epiphytic and endophytic bacteria are associated with several non-legumes, colonizing their surface and inner tissues. Many of these bacteria are beneficial to their hosts, and are collectively termed plant growth-promoting rhizobacteria (PGPR). Recent interest has focused particularly upon PGPR that are endophytic (i.e. PGPE), and which have been reported to be associated with important crops such as rice, wheat and sugarcane. Different mechanisms are involved in bacteria-induced plant growth promotion (PGP), including biological nitrogen fixation (BNF), mineral solubilization, production of phytohormones and pathogen biocontrol. In Uruguay, sugarcane (Saccharum officinarum L.) is considered a strategic multipurpose crop, used for bioenergy, feed, sugar and bioethanol production. The aim of this work was to estimate the BNF contribution to Uruguayan sugarcane cultivars, as well as to identify and characterize the (culturable) putatively endophytic diazotrophic bacteria associated with these varieties.

Methods and results

Results using the ¹⁵N-dilution technique have shown that these sugarcane varieties obtain significant inputs of N from BNF (34.8–58.8% Ndfa). In parallel, a collection of 598 isolates of potentially endophytic diazotrophs was obtained from surface-sterilized stems using standard isolation techniques, and nifH ⁺ isolates from these were the subject of further studies. The bacteria were shown to belong to several genera, including Pseudomonas, Stenotrophomonas, Xanthomonas, Acinetobacter, Rhanella, Enterobacter, Pantoea, Shinella, Agrobacterium and Achromobacter. Additionally, some PGP features were studied in 35 selected isolates. The data obtained in this study represent the initial steps in a program aimed at determining the mechanisms of PGP of non-legume crops in Uruguay (such as sugarcane) with potentially beneficial plant-associated bacteria.     

Alteration textures in terrestrial volcanic glass and the associated bacterial community

Alteration textures were examined in subglacial (hyaloclastite) deposits at Valafell, Southern Iceland. Pitted and 'elongate' alteration features are observed in the glass similar to granular and tubular features reported previously in deep-ocean basaltic glasses, but elongate features generally did not have a length to width ratio greater than five. Elongate features were found in only 7% of surfaces. Crystalline basalt clasts, which are incorporated into the hyaloclastite, did not display elongate structures. Pitted alteration features were poorly defined in crystalline basalt, comprising only 4% of the surface compared to 47% in the case of basaltic glass. Examination of silica-rich glass (obsidian) and rhyolite similarly showed poorly defined pitted textures that comprised less than 15% of the surface and no elongate features were observed. These data highlight the differences in alteration textures between terrestrial basaltic glass and previously studied deep-ocean and subsurface basaltic glass, and the important role of mineralogy in controlling the type and abundance of alteration features. The hyaloclastite contains a diverse and abundant bacterial population, as determined by 16S rDNA analysis, which could be involved in weathering the glass. Despite the presence of phototrophs, we show that they were not involved in the production of most alteration textures in the basaltic glass materials we examined.     

Impacts of cultivation of marine diatoms on the associated bacterial community

The composition of bacterial communities associated with four diatom species was monitored during isolation and cultivation of algal cells. Strong shifts in the associated communities, linked with an increase in the numbers of phylotypes belonging to members of the Gammaproteobacteria, were observed during cultivation.     

Characterization of bacterial community associated to biofilms of corroded oil pipelines from the southeast of Mexico

Microbial communities associated to biofilms promote corrosion of oil pipelines. The community structure of bacteria in the biofilm formed in oil pipelines is the basic knowledge to understand the complexity and mechanisms of metal corrosion. To assess bacterial diversity, biofilm samples were obtained from X52 steel coupons corroded after 40 days of exposure to normal operation and flow conditions. The biofilm samples were directly used to extract metagenomic DNA, which was used as template to amplify 16S ribosomal gene by PCR. The PCR products of 16S ribosomal gene were also employed as template for sulfate-reducing bacteria (SRB) specific nested-PCR and both PCR products were utilized for the construction of gene libraries. The V3 region of the 16S rRNA gene was also amplified to analyse the bacterial diversity by analysis of denaturing gradient gel electrophoresis (DGGE). Ribosomal library and DGGE profiles exhibited limited bacterial diversity, basically including Citrobacter spp., Enterobacter spp. and Halanaerobium spp. while Desulfovibrio alaskensis and a novel clade within the genus Desulfonatronovibrio were detected from the nested PCR library. The biofilm samples were also taken for the isolation of SRB. Desulfovibrio alaskensis and Desulfovibrio capillatus, as well as some strains related to Citrobacter were isolated. SRB consists in a very small proportion of the community and Desulfovibrio spp. were the relatively abundant groups among the SRB. This is the first study directly exploring bacterial diversity in corrosive biofilms associated to steel pipelines subjected to normal operation conditions.     

Physiological and molecular techniques for the study of bacterial community development in sausage fermentation

The development of the microbial community involved in the production process of Italian dry sausage was investigated using physiological analysis and molecular techniques for strain typing and taxonomical identification. A cycle of sausage production was followed collecting samples during the 2 months of ripening process. Microbiological analysis allowed the identification of the main bacterial groups responsible for the fermentation process as lactobacilli and coagulase-negative staphylococci. The use of a polymerase chain reaction-based technique of strain typing, RAPD fingerprinting, demonstrated that the environmental parameters interact to select a limited number of strains that dominate the fermentation process. The staphylococcal populations were characterized for their physiological properties and the two dominant strains were identified as Staphylococcus xylosus and Staph. sciuri. The use of 16S rDNA sequencing allowed the definition of the taxonomical position of the two dominant strains of lactic acid bacteria, as belonging to Lactobacillus sake and Lact. plantarum.     

Staphylococcal resistance to antimicrobial peptides of mammalian and bacterial origin

Antimicrobial host defense peptides, such as defensins, protegrins, and platelet microbicidal proteins are deployed by mammalian skin, epithelia, phagocytes, and platelets in response to Staphylococcus aureus infection. In addition, staphylococcal products with similar structures and activities, called bacteriocins, inhibit competing microorganisms. Staphylococci have developed resistance mechanisms, which are either highly specific for certain host defense peptides or bacteriocins or which broadly protect against a range of cationic antimicrobial peptides. Experimental infection models can be used to study the molecular mechanisms of antimicrobial peptides, the peptide resistance strategies of S. aureus, and the therapeutic potential of peptides in staphylococcal diseases.     

Biodegradation of Leonardite by an Alkali-producing bacterial community and characterization of the degraded products

In this study, three bacterial communities were obtained from 12 Leonardite samples with the aim of identifying a clean, effective, and economic technique for the dissolution of Leonardite, a type of low-grade coal, in the production of humic acid (HA). The biodegradation ability and characteristics of the degraded products of the most effective bacterial community (MCSL-2), which degraded 50% of the Leonardite within 21 days, were further investigated. Analyses of elemental composition, ¹³C NMR, and Fourier transform infrared revealed that the contents of C, O, and aliphatic carbon were similar in biodegraded humic acid (bHA) and chemically (alkali) extracted humic acid (cHA). However, the N and carboxyl carbon contents of bHA was higher than that of cHA. Furthermore, a positive correlation was identified between the degradation efficiency and the increasing pH of the culture medium, while increases of manganese peroxidase and esterase activities were also observed. These data demonstrated that both alkali production and enzyme reactions were involved in Leonardite solubilization by MCSL-2, although the former mechanism predominated. No fungus was observed by microscopy. Only four bacterial phylotypes were recognized, and Bacillus licheniformis-related bacteria were identified as the main group in MCSL-2 by analysis of amplified 16S rRNA genes, thus demonstrating that Leonardite degradation ability has a limited distribution in bacteria. Hormone-like bioactivities of bHA were also detected. In this study, a bacterial community capable of Leonardite degradation was identified and the products characterized. These data implicate the use of such bacteria for the exploitation of Leonardite as a biofertilizer.     

淹水培养过程中水稻土细菌丰度与群落结构变化

水稻土是非常复杂又典型的生态系统, 分析淹水培养过程中水稻土细菌的丰度和群落结构变化规律, 可以客观反映水稻土中细菌群落结构信息, 为深入探讨水稻土细菌微生物对稻田的影响和在生态系统中的作用(营养元素转换、重金属还原与抑制甲烷生成过程等)提供实验基础与理论依据。作者采用淹水非种植水稻土微环境模式系统, 提取水稻土淹水培养1 h和1、5、10、20、30、40、60 d后的微生物总DNA, 利用Real-time PCR和PCR-DGGE (denaturing gradient gel electrophoresis)技术检测了淹水培养过程中细菌丰度与群落结构的变化。结果表明: 淹水水稻土中细菌的丰度在1 d时最大, 并在40 d到达第二个峰值, 说明淹水过程改变了细菌的丰度。基于16S rRNA基因V3区的DGGE图谱分析显示, 淹水过程中细菌的群落结构发生了演替性变化: r-策略生存的细菌仅存在于淹水初期; k-策略生存的细菌存在于淹水后期; r-和k-策略共生存的细菌存在于整个淹水过程中, 淹水后期k-策略的细菌占据优势。淹水培养过程中优势种群多样性指数大体呈现先上升后减小的趋势。主成分分析(PCA)将淹水处理过程分成几类不同的生境, 反映出中、后期细菌群落结构较为稳定; 测序结果表明, 32个优势条带所代表的细菌分别属于厚壁菌门、绿弯菌门、拟杆菌门、变形菌门和酸杆菌门, 且与来自不同地域的水稻土、其他类型土壤、活性污泥以及湖泊沉积物等生态系统的细菌关系密切。     

Comparative and functional leaf anatomy of selected Alstroemeriaceae of mainly Chilean origin

The resupinate leaves of 16 species of Alstroemeriaceae were examined using light- and scanning electron microscopy. The leaf anatomy is described for all of the species, that of the petiole and stem for selected species. The mesophyll consists of chlorenchyma and includes idioblasts that contain raphides. Dorsiventral, isolateral or isobilateral leaf types were observed. Petioles are always isolateral. Two epidermal types are commonly observed: type I contains jigsaw puzzle-like intercostal cells and longitudinally elongated cells above the veins; type II contains only longitudinally elongated cells, usually longer, above the veins. Some species have an epidermis which differs from the main types. All species show adaptation to resupination by having an inverted anatomy. Due to the twist of the leaves, adaxial indicates the lower surface and abaxial the upper. Stomata are found on both surfaces. Palisade cells, when they occur, are always on the abaxial surface. Most species are mesomorphic in spite of the dry environments in which they grow; a few show xeromorphic features. The leaves are compared and discussed with relation to ecological conditions.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 261−272.     

Adaptation of the bacterial community to mercury contamination

The utilisation of 31 sole carbon sources by bacterial communities of soil in the presence of increasing concentrations of Hg(II) was measured by a colour development assay. The assay was performed on Biolog microtitre plates (Ecoplates) in the presence of Hg(II) and compared to Hg(II)-free Ecoplates. Furthermore, community tolerance to Hg(II) was measured by colour development in microtitre plates supplemented with LB broth and by enumeration of colony-forming units on LB agar plates. Both microtitre plates supplemented with LB and LB agar plates contained increasing concentrations of Hg(II). The difference in substrate utilisation profile, as shown by growth on 31 different carbon substrates in the Ecoplates, suggested an adaptation of the soil community that correlated with the metal exposure level in the soil. Similarly, growth on microtitre plates supplemented with LB and plate-spreading data showed an increased community tolerance with increasing levels of mercury in the soil. Both the multi-function microtitre plate assay (Ecoplate) and the LB broth microtitre plate assay are suitable for evaluating the adaptation of the bacterial community in soil to a heavy metal pollutant.     

Phylogenetic characterization of the blue filamentous bacterial community from an Icelandic geothermal spring

Molecular phylogenetic analysis of a blue filamentous community from an alkaline thermal spring (79-83 degrees C) in Iceland revealed that the blue filaments were affiliated with the Aquificales. The dominant sequence type, pIce1, was most closely related to a sequence (SRI-48) found in a white filamentous community from a separate Icelandic thermal spring and the pink filaments (EM17) from Yellowstone National Park. Fluorescent in situ hybridization with clone-specific oligonucleotide probes showed that the sample analyzed was essentially a monoculture of a single phylotype.     

Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand

New Zealand ephemeral wetlands are ecologically important, containing up to 12% of threatened native plant species and frequently exhibiting conspicuous cyanobacterial growth. In such environments, cyanobacteria and associated heterotrophs can influence primary production and nutrient cycling. Wetland communities, including bacteria, can be altered by increased nitrate and phosphate due to agricultural practices. We have characterized cyanobacteria from the Wairepo Kettleholes Conservation Area and their associated bacteria. Use of 16S rRNA amplicon sequencing identified several operational taxonomic units (OTUs) representing filamentous heterocystous and non‐heterocystous cyanobacterial taxa. One Nostoc OTU that formed macroscopic colonies dominated the cyanobacterial community. A diverse bacterial community was associated with the Nostoc colonies, including a core microbiome of 39 OTUs. Identity of the core microbiome associated with macroscopic Nostoc colonies was not changed by the addition of nutrients. One OTU was highly represented in all Nostoc colonies (27.6%–42.6% of reads) and phylogenetic analyses identified this OTU as belonging to the genus Sphingomonas. Scanning electron microscopy showed the absence of heterotrophic bacteria within the Nostoc colony but revealed a diverse community associated with the colonies on the external surface.     

Physiological and molecular characterization of a microbial community established in unsaturated, petroleum-contaminated soil

The microbial communities established in soil samples from an unsaturated, petroleum-contaminated zone and from an adjacent uncontaminated site were characterized by physiological and molecular approaches. Possible electron acceptors such as sulfate and nitrate had been completely depleted in these soil samples. Slurries of these soil samples were incubated in bottles in the presence of hydrocarbon indicators (benzene, toluene, xylene and decane), and the degradation of these compounds was examined. Supplementation with electron acceptors stimulated hydrocarbon degradation, although the stimulatory effect was small in the contaminated soil. The initial degradation rates in the contaminated soil under fermentative/methanogenic conditions were comparable to those under aerobic conditions. The microbial populations in the original soil samples were analysed by cloning and sequencing of polymerase chain reaction (PCR)-amplified bacterial and archaeal 16S rRNA gene fragments, showing that the sequences retrieved from these soils were substantially different. For instance, Epsilonproteobacteria, Gammaproteobacteria, Crenarchaeota and Methanosarcinales could only be detected at significant levels in the contaminated soil. Denaturing gradient gel electrophoresis (DGGE) analyses of 16S rRNA gene fragments amplified by PCR from the incubated soil-slurry samples showed that supplementation of the electron acceptors resulted in a shift in the major populations, while the DGGE profiles after incubating the contaminated soil under the fermentative/methanogenic conditions were not substantially changed. These results suggest that petroleum contamination of the unsaturated zone resulted in the establishment of a fermentative/methanogenic community with substantial hydrocarbon-degrading potential.