The Influence of Different Land Uses on the Structure of Archaeal Communities in Amazonian Anthrosols Based on 16S rRNA and amoA Genes

Soil from the Amazonian region is usually regarded as unsuitable for agriculture because of its low organic matter content and low pH; however, this region also contains extremely rich soil, the Terra Preta Anthrosol. A diverse archaeal community usually inhabits acidic soils, such as those found in the Amazon. Therefore, we hypothesized that this community should be sensitive to changes in the environment. Here, the archaeal community composition of Terra Preta and adjacent soil was examined in four different sites in the Brazilian Amazon under different anthropic activities. The canonical correspondence analysis of terminal restriction fragment length polymorphisms has shown that the archaeal community structure was mostly influenced by soil attributes that differentiate the Terra Preta from the adjacent soil (i.e., pH, sulfur, and organic matter). Archaeal 16S rRNA gene clone libraries indicated that the two most abundant genera in both soils were Candidatus nitrosphaera and Canditatus nitrosocaldus. An ammonia monoxygenase gene (amoA) clone library analysis indicated that, within each site, there was no significant difference between the clone libraries of Terra Preta and adjacent soils. However, these clone libraries indicated there were significant differences between sites. Quantitative PCR has shown that Terra Preta soils subjected to agriculture displayed a higher number of amoA gene copy numbers than in adjacent soils. On the other hand, soils that were not subjected to agriculture did not display significant differences on amoA gene copy numbers between Terra Preta and adjacent soils. Taken together, our findings indicate that the overall archaeal community structure in these Amazonian soils is determined by the soil type and the current land use.

Changes in the genetic structure of Bacteria and microbial activity in an agricultural soil amended with tannery sludge

The application of tannery sludge to soils is a form of recycling; however, few studies have examined the impacts of this practice on soil microbial properties. We studied effects of two applications (2006 and 2007) of tannery sludge (with a low chromium content) on the structure of the bacterial community and on the microbial activity of soils. We fertilized an agricultural area in Rolandia, Parana state, Brazil with different doses of sludge based on total N content, which ranged from 0 to 1200 kg N ha(-1). Sludge remained on the soil surface for three months before being plowed. Soils were sampled seven times during the experiment. Bacterial community structure, assessed by denaturing gradient gel electrophoresis (DGGE), was modified by the application of tannery sludge. Soon after the first application, there was clear separation between the bacterial communities in different treatments, such that each dose of sludge was associated with a specific community. These differences remained until 300 days after application and also after the second sludge application, but 666 days after the beginning of the experiment no differences were found in the bacterial communities of the lowest doses and the control. The principal response curve (PRC) analysis showed that the first sludge application strongly stimulated biological activity even 300 days after application. The second application also stimulated activity, but at a lower magnitude and for a shorter time, given that 260 days after the second application there was no difference in biological activity among treatments. PRC also showed that the properties most influenced by the application of tannery sludge were enzymatic activities related to N cycling (asparaginase and urease). The redundancy analysis (RDA) showed that tannery sludge`s influence on microbial activity is mainly related to increases in inorganic N and soil pH. Results showed that changes in the structure of the bacterial community in the studied soils were directly related to changes of their biological activity. (C) 2010 Elsevier Ltd. All rights reserved.

Effects of habitat modification in mangroves on the structure of mollusc and crab assemblages

The abundance and species richness of mollusc and crab assemblages were examined in a subtropical mangrove forest in Moreton Bay, Queensland, Australia, which has been disturbed and damaged by the construction of a wooden boardwalk and a path. Sections of the forest immediately adjacent to the boardwalk and path were compared with reference areas to determine whether changes to the small-scale structural complexity within the forest affected the benthic fauna. The disturbed area was characterised by having 65-80% fewer pneumatophores, significantly fewer species and individuals of molluscs, but significantly more species and individuals of crabs than the reference areas. The abundance of mangrove pneumatophores and the attached epiphytic algae were manipulated at two sites to determine whether observed differences in these features could account for the differences in the assemblage of molluscs in the disturbed area of the forest compared with reference areas. Five experimental treatments were used: undisturbed controls, pneumatophore removals (abundance reduced by ca. 65%), epiphytic algal removals (algae removed from ca. 65% of pneumatophores), pneumatophore disturbance controls and algal disturbance controls. The experimental reduction of the abundance of mangrove pneumatophores and the associated epiphytic algae led to significant declines (by as much as 83%) in the number of molluscs utilising the substratum in the modified plots. There was no significant difference in the abundance of molluscs in the pneumatophore and algal removal plots suggesting any effect was primarily related to removal of the epiphytic algae from the surface of the pneumatophores. The responses by the biota to the changes in the physical environment demonstrate that even relatively small-scale modifications to the physical structure of subtropical mangrove forests can lead to significant effects on the diversity and abundance of macrobenthic organisms in these habitats. Such modifications have the potential to cause cascading effects at higher trophic levels with a deterioration in the value of these habitats as nursery and feeding grounds. Future efforts at conservation of these estuarine environments must focus on the prevention or reduction of modifications to the physical structure and integrity of the system, rather than just on the prevention of loss of entire patches of habitat. (C) 2000 Elsevier Science B.V. All rights reserved.

Impact of livestock on a mosquito community (Diptera: Culicidae) in a Brazilian tropical dry forest

AbstractINTRODUCTION: This study evaluated the effects of cattle removal on the Culicidae mosquito community structure in a tropical dry forest in Brazil.METHODS: Culicidae were collected during dry and wet seasons in cattle presence and absence between August 2008 and October 2010 and assessed using multivariate statistical models.RESULTS: Cattle removal did not significantly alter Culicidae species richness and abundance. However, alterations were noted in Culicidae community composition.CONCLUSIONS: This is the first study to evaluate the impact of cattle removal on Culicidae community structure in Brazil and demonstrates the importance of assessing ecological parameters such as community species composition.

Community ecology of the metazoan parasites of white croaker, Micropogonias furnieri (Osteichthyes: Sciaenidae), from the coastal zone of the State of Rio de Janeiro, Brazil

One hundred specimens of white croakers, Micropogonias furnieri (Desmarest 1823) (Osteichthyes: Sciaenidae) collected from Pedra de Guaratiba (23°01'S, 43°38'W), State of Rio de Janeiro, Brazil, from September 1997 to August 1999, were necropsied to study their parasites. The majority of the fish (95%) were parasitized by metazoan. Twenty-eight species of parasites were collected. The nematodes were the 40.5% of the total number of parasites specimens collected. Dichelyne elongatus was the most dominant species. Lobatostoma ringens, Pterinotrematoides mexicanum, Corynosoma australe, D. elongatus, and Caligus haemulonis showed a positive correlation between the host's total length and parasite prevalence and abundance. The monogenean P. mexicanum had differences in the prevalence and abundance in relation to sex of the host. The mean diversity in the infracommunities of M. furnieri was H=0.499±0.411, with correlation with the host's total length and without differences in relation to sex of the host. One pair of ectoparasites showed positive covariation, and two pairs of endoparasites showed positive association and covariation between their prevalences and abundances, respectively. Negative association or covariations were not found. The dominance of endoparasites in the croakers parasite infracommunities reinforced the differences found in sciaenids from the South American Pacific Ocean, in which the ectoparasites are dominant.

Community ecology of the metazoan parasites of pink cusk-eel, Genypterus brasiliensis (Osteichthyes: Ophidiidae), from the coastal zone of the State of Rio de Janeiro, Brazil

Fifty-five specimens of pink cusk-eel, Genypterus brasiliensis Regan, 1903 (Osteichthyes: Ophidiidae) collected from the coastal zone of the State of Rio de Janeiro, Brazil (approx. 21-23°S, 41-45°W), from September 2000 to January 2001, were necropsied to study their parasites. All fish were parasitized by one or more metazoan. Fourteen species of parasites were collected. G. brasiliensis is a new host record for nine parasite species. The larval stages of cestodes and the nematodes were the majority of the parasite specimens collected, with 38.4% and 36.5%, respectively. Cucullanus genypteri was the dominant species with highest prevalence and/or abundance. The parasites of G. brasiliensis showed the typical overdispersed pattern of distribution. Six parasite species showed correlation between the host's total body length and prevalence and abundance. Host sex did not influence prevalence and parasite abundance of any parasite species. The mean diversity in the infracommunities of G. brasiliensis was H= 0.364 ± 0.103, with correlation with the host's total length and without differences in relation to sex of the host. One pair of adult endoparasites (C. genypteri and A. brasiliensis) showed positive covariations between their abundances. Negative association or covariation was not found. Differences between the qualitative and quantitative aspects of the parasite community of G. brasiliensis from Rio de Janeiro and Argentina suggest the existence of two population stocks of pink cusk-eel in the South America Atlantic Ocean.

Understanding the concepts of community phylogenetics

Background: Community phylogenetics is an emerging field of research that has made important contributions to understanding community assembly. The rapid development of this field can be attributed to the merging of phylogenetics and community ecology research to provide improved clarity on the processes that govern community structure and composition. Question: What are the major challenges that impede the sound interpretation of the patterns and processes of phylogenetic community assembly? Methods: We use four scenarios to illustrate explicitly how the phylogenetic structure of communities can exist in stable or transient phases, based on the different combinations of phylogenetic relationships and phenotypic traits among co-occurring species. We discuss these phases by implicating a two-way process in the assembly and disintegration of the given ecological community. Conclusions: This paper synthesizes the major concepts of community phylogenetics using habitat filtering and competition processes to elucidate how the understanding of phylogenetic community structure is currently hindered by the dynamics of community assembly and disassembly.

Diversity of the bacterial community in the surface soil of a pear orchard based on 16S rRNA gene analysis

A cultivation-independent approach based on polymerase chain reaction (PCR)-amplified partial small subunit rRNA genes was used to characterize bacterial populations in the surface soil of a commercial pear orchard consisting of different pear cultivars during two consecutive growing seasons. Pyrus communis L. cvs Blanquilla, Conference, and Williams are among the most widely cultivated cultivars in Europe and account for the majority of pear production in Northeastern Spain. To assess the heterogeneity of the community structure in response to environmental variables and tree phenology, bacterial populations were examined using PCR-denaturing gradient gel electrophoresis (DGGE) followed by cluster analysis of the 16S ribosomal DNA profiles by means of the unweighted pair group method with arithmetic means. Similarity analysis of the band patterns failed to identify characteristic fingerprints associated with the pear cultivars. Both environmentally and biologically based principal-component analyses showed that the microbial communities changed significantly throughout the year depending on temperature and, to a lesser extent, on tree phenology and rainfall. Prominent DGGE bands were excised and sequenced to gain insight into the identities of the predominant bacterial populations. Most DGGE band sequences were related to bacterial phyla, such as Bacteroidetes, Cyanobacteria, Acidobacteria, Proteobacteria, Nitrospirae, and Gemmatimonadetes, previously associated with typical agronomic crop environments

The Alps Vegetation Database - a geo-referenced community-level archive of all terrestrial plants occurring in the Alps.

Mountain ranges are biodiversity hotspots worldwide and provide refuge to many organisms under contemporary climate change. Gathering field information on mountain biodiversity over time is of primary importance to understand the response of biotic communities to climate changes. For plants, several long-term observation sites and networks of mountain biodiversity are emerging worldwide to gather field data and monitor altitudinal range shifts and community composition changes under contemporary climate change. Most of these monitoring sites, however, focus on alpine ecosystems and mountain summits, such as the global observation research initiative in alpine environments (GLORIA). Here we describe the Alps Vegetation Database, a comprehensive community level archive (GIVD ID EU-00-014) which aims at compiling all available geo-referenced vegetation plots from lowland forests to alpine grasslands across the greatest mountain range in Europe: the Alps. This research initiative was funded between 2008 and 2011 by the Danish Council for Independent Research and was part of a larger project to compare cross-scale plant community structure between the Alps and the Scandes. The Alps Vegetation Database currently harbours 35,731 geo-referenced vegetation plots and 5,023 valid taxa across Mediterranean, temperate and alpine environments. The data are mainly used by the main contributors of the Alps Vegetation Database in an ecoinformatics approach to test hypotheses related to plant macroecology and biogeography, but external proposals for joint collaborations are welcome.

Ants and their effects on an insect herbivore community associated with the inflorescences of Byrsonima crassifolia (Linnaeus) H.B.K. (Malpighiaceae)

The effects of ants on the insect community on inflorescences of Byrsonima crassifolia (Malpighiaceae) were tested in an ant exclusion experiment in a cerrado vegetation in southeastern Brazil. Forty-four species of insects (23 families) and nine species of ants (6 genera and 3 subfamilies) were found on the inflorescences of B. crassifolia. The exclusion of ants, primarily Camponotus sericeiventris and Camponotus spp., reduced the treehopper population to 20% of the original abundance. Ant exclusion and time influenced the abundance of chewing (Exclusion, P<0.001; Time, P<0.002), and sucking insects (Exclusion, P<0.02; Time, P<0.01). Twice as many chewing and sucking insects were found on ant-excluded inflorescences as compared to control inflorescences (P<0.001). One and half more sucking insects were found on ant-excluded than on control inflorescences. Only time significantly influenced the richness of chewing and sucking insects associated with B. crassifolia inflorescences. Inflorescences on control branches were significantly less attacked by herbivores than inflorescences on ant-excluded branches (P<0.001). Therefore, these results suggest that the presence of ants alters the structure of insect herbivore community associated with B. crassifolia.

A 15-year post evaluation of the fire effects on ant community in an area of Amazonian forest

Fire represents an important disturbance to ant communities in areas of fire regime. Otherwise, little is known about the effects of fire on ant communities in areas of non-fire regimes, such as in the Amazonian region. We evaluated the long-term effect of fire on ant species richness in a rain forest (Bacaba Plateau) burned 15-years ago and compare our data with the data of primary unburned forest. A total of 85 ant species distributed in 21 genera and 14 tribes were collected; among them, 72 and 44 species were found on the litter and vegetation, respectively. The fire damaged forest studied supports an intermediate richness of ants when compared to a primary unburned rain forest in the same region. A comparative analysis of ant species richness showed that the Bacaba Plateau presented a different ant fauna when compared with the primary unburned forests, suggesting that fire can alter ant species composition. Although, our results cannot be conclusive on the effects of fire on ant community, they represent a pioneer data on human induced fire in tropical rain forests.

Seasonality and temporal structuration of Alticini community (Coleoptera, Chrysomelidae, Galerucinae) in the Araucaria Forest of Parana, Brazil

Seasonality was studied for Alticini trapped with malaise over a period of two years in the Vila Velha State Park, Parana, Brazil. Coleoptera, Chrysomelidae and Alticini showed seasonal distribution, with the highest abundance during spring and summer months. The abundance peaks of these groups were not synchronized. Of all environmental variables tested, photoperiod had the larger effect on the distributional patterns of Coleoptera, Chrysomelidae and Alticini. Also, Chrysomelidae and Alticini probably are related to the quality and availability of host-plants. When richness was high there was a greater similarity among seasons of different years. However, when richness was not pronounced, seasons showed more similarity within the same year than between years. The Alticini community was seasonally structured and a possible mechanism underlying this pattern is asymmetric competition. Nevertheless, it is necessary to account for indirect interactions (plant-enemy mediated) to better understand how Alticini community is structured.

Impact of Pseudomonas fluorescens strain CHA0 and a derivative with improved biocontrol activity on the culturable resident bacterial community on cucumber roots

Information on the effects of released wild-type or genetically engineered bacteria on resident bacterial communities is important to assess the potential risks associated with the introduction of these organisms into agroecosystems. The rifampicin-resistant biocontrol strain Pseudomonas fluorescens CHA0-Rif and its derivative CHA0-Rif/pME3424, which has improved biocontrol activity and enhanced production of the antibiotics 2,4-diacetylphloroglucinol (Phl) and pyoluteorin (Plt), were introduced into soil microcosms and the culturable bacterial community developing on cucumber roots was investigated 10 and 52 days later. The introduction of either of the two strains led to a transiently enhanced metabolic activity of the bacterial community on glucose dimers and polymers as measured with BIOLOG GN plates, but natural succession between the two sampling dates changed the metabolic activity of the bacterial community more than did the inoculants. The introduced strains did not significantly affect the abundance of dominant genotypic groups of culturable bacteria discriminated by restriction analysis of amplified 16S rDNA of 2500 individual isolates. About 30-50% of the resident bacteria were very sensitive to Phl and Plt, but neither the wild-type nor CHA0-Rif/pME3424 changed the proportion of sensitive and resistant bacteria in situ. In microcosms with a synthetic bacterial community, both biocontrol strains reduced the population of a strain of Pseudomonas but did not affect the abundance of four other bacterial strains including two highly antibiotic-sensitive isolates. We conclude that detectable perturbations in the metabolic activity of the resident bacterial community caused by the biocontrol strain CHA0-Rif are (i) transient, (ii) similar for the genetically improved derivative CHA0-Rif/pME3424 and (iii) less pronounced than changes in the community structure during plant growth.

Reservoir compensation releases : impact on the macroinvertebrate community of the Derwent River, Northumberland, UK-A longitudinal

River regulation for the purposes of public water supply causes the flow regime downstream of a dam to change. Traditionally, in the UK, such regulation was accompanied by requirements for reservoir releases to compensate downstream water users (e.g. industry) for the loss of natural flow (compensation flows). In this article, we compare a unique pre-impoundment macroinvertebrate data set for a regulated upland river with survey data post-impoundment. This allows a longitudinal assessment of the response of the system to regulation. The Derwent River, Northumberland, was impounded in 1966. Impacts on the hydrological regime were quantified by comparing long-term hydrographs, flow duration curves, flow ranges and flashiness indices for the pre-impoundment and post-impoundment periods. The comparison of changes in macroinvertebrate richness and diversity post-impoundment showed that the change in flow regime has had limited effect on the ecological community structure. The flow regime of the Derwent River has become less flashy with fewer extreme events, and the richness and the diversity of macroinvertebrates have, in some cases, increased and at worst have not deteriorated. We suggest that this reflects the strict compensation regime, which has guaranteed minimum flows at all times. Copyright (c) 2012 John Wiley & Sons, Ltd.

Diversity and structure of AMF communities as affected by tillage in a temperate soil.

Arbuscular mycorrhizal fungi (AMF) were studied in differently tilled soils from a long-term field experiment in Switzerland. Diversity and structure of AMF communities were surveyed either directly on spores isolated from the field soil or on spores isolated from trap cultures, planted with different host plants. Single-spore cultures were established from the AMF spores obtained from trap cultures. Identification of the AMF was made by observation of spore morphology and confirmed by sequencing of ITS rDNA. At least 17 recognised AMF species were identified in samples from field and/or trap cultures, belonging to five genera of AMF--Glomus, Gigaspora, Scutellospora, Acaulospora, and Entrophospora. Tillage had a significant influence on the sporulation of some species and non- Glomus AMF tended to be more abundant in the no-tilled soil. The community structure of AMF in the field soil was significantly affected by tillage treatment. However, no significant differences in AMF diversity were detected among different soil tillage treatments. AMF community composition in trap cultures was affected much more by the species of the trap plant than by the original tillage treatment of the field soil. The use of trap cultures for fungal diversity estimation in comparison with direct observation of field samples is discussed.