Structure of microbial communities in red ferralitic soils of Varadero National Park (Matanzas,Cuba)

Comparative study of microbial communities in red ferralitic soil, as well as tree waste and phylloplane of woody plants, of Varadero National Park (Cuba) has been performed. It is shown that the total bacterial abundance and the length of the actinomycete mycelium in the studied soil samples (A horizon) are comparable to and the length of the viable fungal mycelium is lower than the analogous parameters recorded in forest soils of the temperate zone. It is noted that the viability of bacteria is close to that in forest soils of the temperate zone. The maximum concentration of soil biota is found in the A horizon of the studied soils, in contrast to forest biogeocenoses of the temperate zone, where soil biota is concentrated in the litter. It is shown for the first time that prokaryote communities are characterized by a significant presence of filterable forms of bacteria, the content of which increases in the series: soil (A horizon) → tree waste (dry leaves) → phylloplane (green leaves).     

Structure and role of microbial communities in southern taiga soils

General regularities in the structure of the microbial communities of southern taiga soil ecosystems and taxonomic differences between the microbial communities of soils with different hydrothermal characteristics are discussed with reference to the main types of soils of the Central State Forest Biosphere Reserve.     

Structure,function and floristic relationships of plant communities in stressful habitats marginal to the Brazilian Atlantic rainforest

The Brazilian Atlantic rainforest consists of a typical tropical rainforest on mountain slopes, and stands out as a biodiversity hotspot for its high species richness and high level of species endemism. This forest is bordered by plant communities with lower species diversity, due mostly to more extreme environmental conditions than those found in the mesic rainforest. Between the mountain slopes and the sea, the coastal plains have swamp forests, dry semi-deciduous forests and open thicket vegetation on marine sand deposits. At the other extreme, on top of the mountains (>2000 m a.s.l.), the rainforest is substituted by high altitude fields and open thicket vegetation on rocky outcrops. Thus, the plant communities that are marginal to the rainforest are subjected either to flooding, drought, oceanicity or cold winter temperatures. It was found that positive interactions among plants play an important role in the structuring and functioning of a swamp forest, a coastal sandy vegetation and a cold, high altitude vegetation in the state of Rio de Janeiro. Moreover, only a few species seem to adopt this positive role and, therefore, the functioning of these entire systems may rely on them. Curiously, these nurse plants are often epiphytes in the rainforest, and at the study sites are typically terrestrial. Many exhibit crassulacean acid metabolism. Conservation initiatives must treat the Atlantic coastal vegetation as a complex rather than a rainforest alone.     

Synergistic effects of drought and deforestation on the resilience of the south-eastern Amazon rainforest

The south-eastern Amazon rainforest is subject to ongoing deforestation and is expected to become drier due to climate change. Recent analyses of the distribution of tree cover in the tropics show three modes that have been interpreted as representing alternative stable states: forest, savanna and treeless states. This situation implies that a change in environmental conditions, such as in the climate, could cause critical transitions from a forest towards a savanna ecosystem. Shifts to savanna might also occur if perturbations such as deforestation exceed a critical threshold. Recovering the forest would be difficult as the savanna will be stabilized by a feedback between tree cover and fire. Here we explore how environmental changes and perturbations affect the forest by using a simple model with alternative tree-cover states. We focus on the synergistic effects of precipitation reduction and deforestation on the probability of regime shifts in the south-eastern Amazon rainforest. The analysis indicated that in a large part of the south-eastern Amazon basin rainforest and savanna could be two alternative states, although massive forest dieback caused by mean-precipitation reduction alone is unlikely. However, combinations of deforestation and climate change triggered up to 6.6 times as many local regime shifts than the two did separately, causing large permanent forest losses in the studied region. The results emphasize the importance of reducing deforestation rates in order to prevent a climate-induced dieback of the south-eastern Amazon rainforest.     

Comparison of the ant communities of annually inundated and terra firme forests at Trombetas in the Brazilian Amazon

Summary The composition of the ant community was assessed along standardized 100 m transects in annually flooded Varzea forest and in terra firme forests on sandy soil (Flanco forest) and on claytopped mesas (Planalto forest). Standardized samples were taken by unit-time hand collecting (day and night times), sweeping, beating, baiting and by Winkler sacks. A total of 156 species, representing 49 genera were found, of which 98, 88 and 55 were respectively found in the Planalto, Flanco and Varzea forests. Species lists are presented and the ant community composition and species richness are compared between the three forests. By considering the nesting and foraging habits of the various species, the differences in overall community composition are related to the forest type and susceptibility to inundation of the three forests which were surveyed.The data confirm the view that tropical rain forests support an extremely diverse ant fauna and comparisons with other forested areas suggest that ant species richness declines in subtropical and temperate rain forests. Although alpha diversity is high, species turnover between forests is lower than expected, suggesting that ant species richness in this forested region is not as great as is implied in some published estimates of global arthropod diversity.     

Structure and function of microbial communities in soil from the southern Taiga

General regularities in the structure of the microbial communities of southern taiga soil ecosystems and taxonomic differences between the microbial communities of soils with different hydrothermal characteristics are discussed with reference to the main types of soils of the Central State Forest Biosphere Reserve.     

Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.     

Resistance and resilience of benthic biofilm communities from a temperate saltmarsh to desiccation and rewetting

Periods of desiccation and rewetting are regular, yet stressful events encountered by saltmarsh microbial communities. To examine the resistance and resilience of microbial biofilms to such stresses, sediments from saltmarsh creeks were allowed to desiccate for 23 days, followed by rewetting for 4 days, whereas control sediments were maintained under a natural tidal cycle. In the top 2 mm of the dry sediments, salinity increased steadily from 36 to 231 over 23 days, and returned to seawater salinity on rewetting. After 3 days, desiccated sediments had a lower chlorophyll a (Chl a) fluorescence signal as benthic diatoms ceased to migrate to the surface, with a recovery in cell migration and Chl a fluorescence on rewetting. Extracellular β-glucosidase and aminopeptidase activities decreased within the first week of drying, but increased sharply on rewetting. The bacterial community in the desiccating sediment changed significantly from the controls after 14 days of desiccation (salinity 144). Rewetting did not cause a return to the original community composition, but led to a further change. Pyrosequencing analysis of 16S rRNA genes amplified from the sediment revealed diverse microbial responses, for example desiccation enabled haloversatile Marinobacter species to increase their relative abundance, and thus take advantage of rewetting to grow rapidly and dominate the community. A temporal sequence of effects of desiccation and rewetting were thus observed, but the most notable feature was the overall resistance and resilience of the microbial community.     

Diversity patterns and chronobiology of hawkmoths (Lepidoptera,Sphingidae) in the Brazilian Amazon rainforest

As biodiversity loss rapidly increases through habitat degradation in the Amazon rainforest, the need to characterize and understand the species diversity becomes even more important. In this study we used empirical and published datasets to assess the diversity patterns and produce the first overview of the sphingid fauna in the Brazilian Amazon. We compared the diversity patterns in distinct areas in the biome by analyzing hawkmoth assemblages considering both species composition and abundance, and asked whether these communities are structured according to environmental factors. Additionally, we provide information of diel activity pattern of sphingids and evaluated the importance of time in sampling effort. We found that the Brazilian Amazon may harbor more than 80 % of the hawkmoth species that occur in Brazil and more than half of the species recorded in South America. Species composition and assemblage structure is determined by the quality of the habitat (disturbed or undisturbed vegetation), temperature and relative humidity. Finally, we show that the temporal activity of sphingids presents distinct patterns at different taxonomic levels, highlighting the importance of full night collections to better characterize the fauna. Our results show that habitat alteration can be an important factor affecting sphingid assemblages, illustrating the importance of Protected Areas in species maintenance.     

Structure and function of anthropogenically altered microbial communities in coastal waters

Human-based (anthropogenic) nutrient and other pollutant enrichment of the world's coastal waters is causing unprecedented changes in microbial community structure and function. Symptoms of these changes include accelerating eutrophication, the proliferation of harmful microalgal blooms, excessive oxygen consumption (hypoxia, anoxia), increasing toxicity, altered routes and fluxes of organic and inorganic matter cycling, and disruption of food webs. Biogeochemical and trophic consequences are expanding on local, regional and global scales.     

Quantification of mcrA by fluorescent PCR in methanogenic and methanotrophic microbial communities

A quantitative fluorogenic PCR method for detecting methanogenic and methanotrophic orders was established using a refined primer set for the methyl coenzyme M reductase subunit A gene (mcrA). The method developed was applied to several microbial communities in which diversity and abundance of methanogens or anaerobic methanotrophs (ANMEs) was identified by 16S rRNA gene clone analysis, and strong correlations between the copy numbers of mcrA with those of archaeal 16S rRNA genes in the communities were observed. The assay can be applied to detecting and assessing the abundance of methanogens and/or ANMEs in anoxic environments that could not be detected by 16S rRNA gene sequence analyses.     

Microbial communities of ultramafic soils in maquis and rainforest at Mont Do,New Caledonia

We analysed variation in microbial community richness and function in soils associated with a fire‐induced vegetation successional gradient from low maquis (shrubland) through tall maquis to rainforest on metal‐rich ultramafic soils at Mt Do, New Caledonia. Random amplified polymorphic DNA fingerprinting was used to determine the extent of genetic relatedness among the microbial communities and indicated that the open and tall maquis microbial communities were more similar to each other than they were to the rainforest community. Sole‐source carbon utilization indicated variation in the microbial communities, again with greater diversity in rainforest soils. Plate counts showed that both rainforest and maquis soils contained bacteria that can grow in the presence of up to 20 mmol L^?1 nickel and 10 mmol L^?1 chromium. Understanding microbial community composition and dynamics in these ultramafic soils may lead to a better understanding of the processes facilitating vegetation succession from shrubland to forest on these high‐metal substrates, and of approaches to successful revegetation following mining for metals including nickel, chromium and cobalt.     

Molecular analysis of methanogenic archaeal communities in managed and natural upland pasture soils

Grassland management influences soil archaeal communities, which appear to be dominated by nonthermophilic crenarchaeotes. To determine whether methanogenic Archaea associated with the Euryarchaeota lineage are also present in grassland soils, anaerobic microcosms containing both managed (improved) and natural (unimproved) grassland rhizosphere soils were incubated for 28 days to encourage the growth of anaerobic Archaea. The contribution of potential methanogenic organisms to the archaeal community was assessed by the molecular analysis of RNA extracted from soil, using primers targeting all Archaea and Euryarchaeota. Archaeal RT‐PCR products were obtained from all anaerobic microcosms. However, euryarchaeal RT‐PCR products (of putative methanogen origin) were obtained only from anaerobic microcosms of improved soil, their presence coinciding with detectable methane production. Sequence analysis of excised denaturing gradient gel electrophoresis (DGGE) bands revealed the presence of euryarchaeal organisms that could not be detected before anaerobic enrichment. These data indicate that nonmethanogenic Crenarchaeota dominate archaeal communities in grassland soil and suggest that management practices encourage euryarchaeal methanogenic activity.     

Structure of microbial communities of peat soils in two bogs in Siberian tundra and forest zones

The structure and functional activity of microbial complexes of a forest oligo-mesotrophic subshrub- grass-moss bog (OMB, Central Evenkiya) and a subshrub-sedge bog in the polygonal tundra (PB, Lena River Delta Samoylovsky Island) was studied. Soil of the forest bog (OMB) differed from that of the polygonal tundra bog (PB) in higher productivity (C_org, N_total, P, and K reserves), higher biomass of aerobic chemoorganotrophs (2.0 to 2.6 times), and twice the level of available organic matter. The contribution of microorganisms to the carbon pool was different, with the share of C_mic in C_org 1.4 to 2.5 times higher in PB compared to OMB. Qualitative composition of the methane cycle microorganisms in PB and OMB soils differed significantly. Methanogenic archaea (Euryarchaeota) in the shrub-sedge PB of tundra were more numerous and diverse than in the oligo-mesotrophic bog (OMB) and belonged to six families (Methanomassiliicoccaceae, Methanoregulaceae, Methanobacteriaceae, Methanomicrobiaceaee, Methanosarcinaceae, and Methanotrichaceae), while members of only four families (Methanosarcinacea, Methanobacteriaceae, Methanotrichaceae, and Methanomassiliicoccaceae) were revealed in OMB. In both bogs, methane-oxidizing bacteria belonged to Alphaproteobacteria (II) and Gammaproteobacteria (I). Methanotroph diversity was higher in OMB than in PB. Microbial communities of PB soils had higher potential activity of methanogenesis and methanotrophy compared to those of OMB. Methanogenic and methanotrophic activities in PB were 20 and 2.3 times higher, respectively, than in OMB.     

Diversity and dynamics of microbial communities in soils from agro-ecosystems

Soil microbial communities are integrally involved in biogeochemical cycles and their activities are crucial to the productivity of terrestrial ecosystems. Despite the importance of soil microorganisms, little is known about the distribution of microorganisms in the soil or the manner in which microbial community structure responds to changes in land management. We investigated the structure of microbial communities in the soil over two years in a series of replicated plots, that included, cultivated fields, fields abandoned from cultivation and fields with no history of cultivation. Microbial community structure was examined by monitoring the relative abundance of ribosomal RNA (rRNA) from seven of the most common bacterial groups in soil (the Alpha and Beta Proteobacteria, Actinobacteria, Cytophagales, Planctomycetes, Verrucomicrobia and the Acidobacteria) and the Eukarya. These data reveal that soil microbial communities are dynamic, capable of significant change at temporal scales relative to seasonal events. However, despite temporal change in microbial community structure, the rRNA relative abundance of particular microbial groups is affected by the local environment such that recognizable patterns of community structure exist in relation to field management.     

Heavy metal tolerance of Fe(III)-reducing microbial communities in contaminated creek bank soils

Fe(III)-reducing soil enrichment cultures can tolerate 100 μM Cu and Cd, 150 μM Co, 600 μM Ni, and 2,500 μM Zn. Metal-tolerant cultures were dominated by Geobacter-related Deltaproteobacteria and Gram-positive Firmicutes spp. (Clostridia and Sedimentibacter). A Cd- and Cu-tolerant Fe(III)-reducing coculture of Desulfosporosinus and Desulfitobacterium indicated the importance of the Firmicutes for Fe(III) reduction in the presence of metals.     

Differential structure and function of phosphorus-mineralizing microbial communities in organic and upper mineral soil horizons across a temperate rainforest chronosequence

Microbial community structure and function were assessed in the organic and upper mineral soil across a ~4000-year dune-based chronosequence at Big Bay, New Zealand, where total P declined and the proportional contribution of organic soil in the profile increased with time. We hypothesized that the organic and mineral soils would show divergent community evolution over time with a greater dependency on the functionality of phosphatase genes in the organic soil layer as it developed. The structure of bacterial, fungal, and phosphatase-harbouring communities was examined in both horizons across 3 dunes using amplicon sequencing, network analysis, and qPCR. The soils showed a decline in pH and total phosphorus (P) over time with an increase in phosphatase activity. The organic horizon had a wider diversity of Class A (phoN/phoC) and phoD-harbouring communities and a more complex microbiome, with hub taxa that correlated with P. Bacterial diversity declined in both horizons over time, with enrichment of Planctomycetes and Acidobacteria. More complex fungal communities were evident in the youngest dune, transitioning to a dominance of Ascomycota in both soil horizons. Higher phosphatase activity in older dunes was driven by less diverse P-mineralizing communities, especially in the organic horizon.     

A(r)Ray of hope in analysis of the function and diversity of microbial communities

The vast majority of microorganisms in the environment remain uncultured, and their existence is known only from sequences retrieved by PCR. As a consequence, our understanding of the ecological function of dominant microbial populations in the environment is limited. We will review microbial diversity studies and show that these may have moved from an extreme underestimation to a potentially severe overestimation of diversity. The latter results from a simple PCR-generated artifact: the cloning of heteroduplex molecules followed by Escherichia coli mismatch repair, which may generate an exponential increase in observed sequence diversity. However, simple modifications to current PCR amplification protocols minimize such artifactual sequences and may bring within our reach estimation of bacterial diversity in environmental samples. Such estimates may spur new culture-independent approaches based on genomic and microarray technology, allowing correlation of phylogenetic identity with the ecological function of unculturable organisms. In particular, we are developing a DNA microarray that enables identification of individual populations active in utilization of specific organic substrates. The array consists of 16S and 23S rDNA-targeted oligonucleotides and is hybridized to RNA extracted from samples incubated with (14)C-labeled organic substrates. Populations that metabolize the substrate can be identified by the radiolabel incorporated in their rRNA after only one to two cell doublings, ensuring realistic preservation of community structure. Thus, the microarray approach may provide a powerful means to link microbial community structure with in situ function of individual populations.     

Attraction of Chagas disease vectors (Triatominae) to artificial light sources in the canopy of primary Amazon rainforest

Adult triatomines occasionally fly into artificially lit premises in Amazonia. This can result in Trypanosoma cruzi transmission to humans either by direct contact or via foodstuff contamination, but the frequency of such behaviour has not been quantified. To address this issue, a light-trap was set 45 m above ground in primary rainforest near Manaus, state of Amazonas, Brazil and operated monthly for three consecutive nights over the course of one year (432 trap-hours). The most commonly caught reduviids were triatomines, including 38 Panstrongylus geniculatus, nine Panstrongylus lignarius, three Panstrongylus rufotuberculatus, five Rhodnius robustus, two Rhodnius pictipes, one Rhodnius amazonicus and 17 Eratyrus mucronatus. Males were collected more frequently than females. The only month without any catches was May. Attraction of most of the known local T. cruzi vectors to artificial light sources is common and year-round in the Amazon rainforest, implying that they may often invade premises built near forest edges and thus become involved in disease transmission. Consequently, effective Chagas disease prevention in Amazonia will require integrating entomological surveillance with the currently used epidemiological surveillance.