Unusual Ecosystem Research Articles

The first record of pterosaurs from the Lower Cretaceous Hutubei Formation (lower Tugulu Group) of the southern Junggar Basin (NW China) – A glimpse into an unusual ecosystem

The Lower Cretaceous Hutubei Formation of the southern Junggar Basin (northwestern China) is characterised by a very low faunal diversity, yielding almost exclusively the sinemydid turtle Wuguia. Here we describe the first pterosaur remains from the Hutubei Formation comprising a complete right ulna and the distal part of a left wing metacarpal. The ulna shares a synapomorphy with the Dsungaripteridae and is morphologically similar to that of the dsungaripterid Dsungaripterus. The wing metacarpal also shares a synapomorphy with the Dsungaripteridae and the more inclusive clade Dsungaripteroidea, and is morphologically nearly indistinguishable from those of the dsungaripterids Dsungaripterus, Lonchognathosaurus and Noripterus. We therefore assign both specimens to the Dsungaripteridae. They represent one of the oldest records of dsungaripterids from the Tugulu Group and one of the few occurrences of pterosaurs from the southern Junggar Basin. Additionally, they shed light on the community structure of a highly unusual ecosystem preserved in the Lower Cretaceous Hutubei Formation, an ecosystem that appears to have persisted for several millions of years in the southern Junggar Basin.

A comparative GC-MS analysis of bioactive secondary metabolites produced by halotolerant Bacillus spp. isolated from the Great Sebkha of Oran.

The reemergence of infectious diseases and resistant pathogens represents a serious problem for human life. Hence, the screening for new or alternative antimicrobial compounds is still urgent. Unusual ecosystems such as saline habitats are considered promising environments for the purposes of isolating bacterial strains able to produce potent natural products. The aim of this study is the identification of bioactive compounds biosynthesized by three halotolerant strains isolated from the Sebkha of Oran (Algeria) using gas chromatography coupled to mass spectrometry. Primary screening investigation of antimicrobial activities were performed against reference bacterial and fungal strains and revealed a broad-spectrum activity. Secondary metabolite extraction was carried out using ethyl acetate and chloroform. Crude extracts were tested for bioactivity using the disc diffusion method and subjected to GC-MS analysis. The extracts showed an important inhibitory effect against all tested strains. Fifty-six compounds were identified; they include tert-butyl phenol compounds, fatty acid methyl esters due to the methylation procedure, hydrocarbons, aldehydes, benzoquinones, pyrrols, and terpenes. Literature reports such compounds to have wide biological and pharmaceutical applications. The molecular identification of the three isolates was achieved using the 16S-23S rRNA gene intergenic spacer region (ITS) and 16S rRNA sequencing. Partial 16S rRNA gene sequencing showed very high similarity with many species of Bacillus. This study provided insights on the potential of halotolerant Bacillus as drug research target for bioactive metabolites. The findings suggest that the Great Sebkha of Oran is a valuable source of strains exhibiting variety of beneficial attributes that can be utilized in the development of biological antibiotics.

First Records of Late Triassic Conodont Fauna and δ13Ccarb from the Dengdengqiao Section, Dangchang County, Gansu Province, Northwestern China

Based on a study of 49 conodont and 57 geochemical samples from the Upper Triassic, carbonate-dominated Dengdengqiao Formation, Qinling Basin, China, the Carnian conodonts and carbon isotope records are first reported. Two genera and four species have been identified amongst 87 conodont elements: Mosherella praebudaensis, Mo. longnanensis sp. nov., Mo. sp., and “Misikella” longidentata. The presence of Mo. praebudaensis indicates that the lower part (bed 2) of the formation is attributable to the Julian (lower Carnian) substage. A radiolarian fauna identified in a previous study belongs to the upper Carnian, but the sampling horizon is unclear. The δ13Ccarb curve shows a ∼1.8‰ negative excursion beginning from upper part of bed 3, but its stratigraphic location is uncertain. The Dengdengqiao Formation is clearly at least partly of Carnian age but could include younger strata. The abundant calcareous algae at the section is probably due to some transport rather than preserved in site. The unusual ecosystem with rare marine organisms may reflect long-term stressful and unfavorable conditions at Dengdengqiao.

Diverse subterranean fungi of an underground iron ore mine.

Mines and caves are unusual ecosystems containing unique fungi and are greatly understudied compared to other environments. The Soudan Mine in Tower, MN, an iron ore mine that closed in 1963 after operating for 80 years, was sampled to explore fungal diversity and to investigate taxa that tolerate heavy metals for potential bioprocessing technologies or as sources of bioactive molecules for drug discovery and possible biocontrol for white-nose syndrome (WNS) of bats. The mine is 714 m deep, has 18 levels and contains large quantities of wooden timbers, in contrast to many other oligotrophic subterranean environments. Fungi were cultured from samples and the ITS region was sequenced for identification and phylogenetic analysis. Results show Ascomycota are the dominant fungi followed by Basidiomycota and Mucoromycota. Out of 164 identified taxa, 108 belong to the Ascomycota and 26 and 31 to Basidiomycota and Mucoromycota, respectively. There are also 46 taxa that do not match (<97% BLAST GenBank identity) sequenced fungal species. Examples of the most commonly isolated Ascomycota include Scytalidium sp., Mariannaea comptospora, Hypocrea pachybasidioides, Oidiodendron griseum and Pochonia bulbillosa; Basidiomycota include Postia sp., Sistotrema brinkmannii, Calocera sp., Amylocorticiellum sp.; Mucoromycota include Mortierella parvispora, M. gamsii, M. hyaline, M. basiparvispora and Mortierella sp. Unusual growth forms were also found including large quantities of black rhizomorphs of Armillaria sinapina and white mycelial cords of Postia sp. mycelium, as well as Pseudogymnoascus species growing over large areas of mine walls and ceiling. The mine environment is a relatively extreme environment for fungi, with the presence of high levels of heavy metals, complete darkness and poor nutrient availability. Several genera are similar to those isolated in other extreme environments but phylogenetic analyses show differences in species between these environments. Results indicate this subterranean environment hosts a wide diversity of fungi, many of them not found in above ground environments.

The genome of a subterrestrial nematode reveals adaptations to heat

The nematode Halicephalobus mephisto was originally discovered inhabiting a deep terrestrial aquifer 1.3 km underground. H. mephisto can thrive under conditions of abiotic stress including heat and minimal oxygen, where it feeds on a community of both chemolithotrophic and heterotrophic prokaryotes in an unusual ecosystem isolated from the surface biosphere. Here we report the comprehensive genome and transcriptome of this organism, identifying a signature of adaptation: an expanded repertoire of 70 kilodalton heat-shock proteins (Hsp70) and avrRpt2 induced gene 1 (AIG1) proteins. The expanded Hsp70 genes are transcriptionally induced upon growth under heat stress, and we find that positive selection is detectable in several members of this family. We further show that AIG1 may have been acquired by horizontal gene transfer (HGT) from a rhizobial fungus. Over one-third of the genes of H. mephisto are novel, highlighting the divergence of this nematode from other sequenced organisms. This work sheds light on the genomic basis of heat tolerance in a complete subterrestrial eukaryotic genome.

Biogeography of soil bacterial populations in the Jutulsessen and Ahlmannryggen of Western Dronning Maud Land, Antarctica

Soils of continental Antarctic nunataks represent unusual ecosystems with concomitant unique bacterial community profiles which have not been assessed for the vast majority of Antarctic nunataks. This study focussed on the previously uncharacterised inland nunataks of the Jutulsessen and Ahlmannryggen ranges in Dronning Maud Land. As with many oligotrophic soils in Antarctica, bacteria from the phyla Acidobacteria, Actinobacteria and Proteobacteria were prevalent. High relative abundances of Bacteroidetes and Chloroflexi were also observed in these soils. Potential phototrophic capabilities of these bacterial populations were indicated by the presence of genes involved in the Calvin–Benson reductive pentose phosphate cycle as well as that of aerobic phototrophic bacteriochlorophyll. Clear spatial patterns of bacterial biodiversity between nunataks in this study were observed, particularly between the Jutulsessen and Ahlmannryggen nunataks which are geographically separated by the Jutulstraumen glacier. Not unexpectedly, the bacterial community profiles found in these nunataks were distinct from those found in alternate biogeographic regions (e.g. Dry Valleys, Peninsula and Larsemann Hills). Despite belonging to the same bioregion (i.e. Dronning Maud Land), however, the clear differentiation of bacterial communities between the Jutulsessen/Ahlmannryggen and that of Sor Rondane suggests that, based on bacterial phylogeography, the Dronning Maud Land bioregion can be divided into sub-bioregions.

Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.)

BackgroundArugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been also associated with high-profile outbreaks causing severe food-borne human diseases. A multiphasic approach integrating data from metagenomics, amplicon sequencing, and arugula-derived bacterial cultures was employed to understand the specificity of the indigenous microbiome and resistome of the edible plant parts.ResultsOur results indicate that arugula is colonized by a diverse, plant habitat-specific microbiota. The indigenous phyllosphere bacterial community was shown to be dominated by Enterobacteriaceae, which are well-equipped with various antibiotic resistances. Unexpectedly, the prevalence of specific resistance mechanisms targeting therapeutic antibiotics (fluoroquinolone, chloramphenicol, phenicol, macrolide, aminocoumarin) was only surpassed by efflux pump assignments.ConclusionsEnterobacteria, being core microbiome members of arugula, have a substantial implication in the overall resistome. Detailed insights into the natural occurrence of antibiotic resistances in arugula-associated microorganisms showed that the plant is a hotspot for distinctive defense mechanisms. The specific functioning of microorganisms in this unusual ecosystem provides a unique model to study antibiotic resistances in an ecological context.

Hemolymph of Baikal endemic crustacean Eulimnogammarus verrucosus as a source for novel natural products

Event Abstract Back to Event Hemolymph of Baikal endemic crustacean Eulimnogammarus verrucosus as a source for novel natural products Denis Axenov-Gribanov1, 2*, Eugenii Protasov1, Polina Drozdova1, Kseniya Vereshchagina1, Yuliya Lubyaga1, Zhanna Shatilina1 and Maxim Timofeyev1 1 Irkutsk State University, Russia 2 Baikal Research Center, Russia Background Antibiotic resistance and targeted therapy are one of the most important and worldwide issues. Extreme and unusual ecosystems such as Lake Baikal and its inhabitant are considered as potential tools for the discovery of novel natural products with biological activities. The aim of this study was to assess the possibility to use Baikal endemic amphipods as a source for screening of novel natural products. Methods Analysis of hemolymph from an amphipod Eulimnogammarus verrucosus by HPLC-MS was performed for the first time and allowed us to find a number of natural products with new molecular mass values for Baikal endemic macroinvertebrates. Results We identified a compound as chrysin by comparison of MS1, MS2 profiles and molecular masses of natural products registered in Dictionary of Natural Products and MZ-cloud databases. Also, we found a new compound with a mass of 493.80277 Da and a number of antimicrobial peptides circulating in the amphipod hemolymph. Conclusion Thus, we confirmed that the hemolymph of Baikal endemic crustacean E. verrucosus is a source of novel natural products and could have biotechnological value for pharmacy and biomedicine. Acknowledgements This study was carried out with partial financial support of the RSF project (18-74-00018), RFBR project (16-34-60060), projects of the Ministry of Education and Science of the Russian Federation 6.9654.2017/8.9, 6.12738.2018/12.2, 6.12736.2018/12.2, and the Lake Baikal Foundation. Keywords: Baikal, amphipods, endemics, Natural Products, Eulimnogammarus verrucosus Conference: International Conference on Drug Discovery and Translational Medicine 2018 (ICDDTM '18) “Seizing Opportunities and Addressing Challenges of Precision Medicine”, Putrajaya, Malaysia, 3 Dec - 5 Feb, 2019. Presentation Type: Poster Presentation Topic: Infectious diseases Citation: Axenov-Gribanov D, Protasov E, Drozdova P, Vereshchagina K, Lubyaga Y, Shatilina Z and Timofeyev M (2019). Hemolymph of Baikal endemic crustacean Eulimnogammarus verrucosus as a source for novel natural products. Front. Pharmacol. Conference Abstract: International Conference on Drug Discovery and Translational Medicine 2018 (ICDDTM '18) “Seizing Opportunities and Addressing Challenges of Precision Medicine”. doi: 10.3389/conf.fphar.2019.63.00041 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 30 Sep 2018; Published Online: 17 Jan 2019. * Correspondence: Mr. Denis Axenov-Gribanov, Irkutsk State University, Irkutsk, Russia, Denis.axengri@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Denis Axenov-Gribanov Eugenii Protasov Polina Drozdova Kseniya Vereshchagina Yuliya Lubyaga Zhanna Shatilina Maxim Timofeyev Google Denis Axenov-Gribanov Eugenii Protasov Polina Drozdova Kseniya Vereshchagina Yuliya Lubyaga Zhanna Shatilina Maxim Timofeyev Google Scholar Denis Axenov-Gribanov Eugenii Protasov Polina Drozdova Kseniya Vereshchagina Yuliya Lubyaga Zhanna Shatilina Maxim Timofeyev PubMed Denis Axenov-Gribanov Eugenii Protasov Polina Drozdova Kseniya Vereshchagina Yuliya Lubyaga Zhanna Shatilina Maxim Timofeyev Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia.

Extreme and unusual ecosystems such as isolated ancient caves are considered as potential tools for the discovery of novel natural products with biological activities. Actinobacteria that inhabit these unusual ecosystems are examined as a promising source for the development of new drugs. In this study we focused on the preliminary estimation of fatty acid composition and antibacterial properties of culturable actinobacteria isolated from water surface of underground lakes located in Badzheyskaya and Okhotnichya caves in Siberia. Here we present isolation of 17 strains of actinobacteria that belong to the Streptomyces, Nocardia and Nocardiopsis genera. Using assays for antibacterial and antifungal activities, we found that a number of strains belonging to the genus Streptomyces isolated from Badzheyskaya cave demonstrated inhibition activity against bacteria and fungi. It was shown that representatives of the genera Nocardia and Nocardiopsis isolated from Okhotnichya cave did not demonstrate any tested antibiotic properties. However, despite the lack of antimicrobial and fungicidal activity of Nocardia extracts, those strains are specific in terms of their fatty acid spectrum. When assessing fatty acid profile, we found that polyunsaturated fatty acids were quantitatively dominant in extracts of Nocardia sp. and Streptomyces sp. grown in different media. Saturated fatty acids were the second most abundant type in the fatty acid profile. It was due to palmitic acid. Also, a few monounsaturated fatty acids were detected. The obtained materials can become a basis for development of approaches to use bacteria isolated from caves as a biological sources of bioactive compounds to create medical and veterinary drugs.

Arboviruses also have an American dream

Some arboviruses that originated in the Old World have been introduced by humans into the American continent. The first of them was the yellow fever virus, coming from the West African coast with slaves in the 17th-19th centuries, followed by dengue viruses, which were always prevalent within the Americas. Next was theWest Nile virus, introduced in New York in 1999, that spread in only a few years over the whole continent. Then, Chikungunya virus arrived on Saint Martin Island in 2013 after its outbreak in Polynesia; it is now widespread in the Caribbean Islands and on the American continent from the United States to Brazil. Finally, Zika virus, already active in Asia and in the South Pacific region, was introduced in Brazil and spread between the southern part of United States and south Brazil. These unexpected emergences are the consequence of the generalization of transoceanic trading; so, it is humans who are truly responsible for such transportation of viruses from the African and Asian continents. The mechanisms of virus establishment in unusual ecosystems have to be analyzed in order to understand the conditions for the circulation of the viruses, which supposes an adaptation to new hosts and vectors that are sometimes local species (like Culex vectors of West Nile virus) but mainly previously introduced mosquitoes (like Aedes aegypti and/or Aedes albopictus). Over time, all these vectors developed a strong anthropophily and, most of them, a remarkable adaptation to urban environment; hence, these arboviruses can disseminate both in rural and urban context. This type of arboviral emergences will certainly continue in the following years and we must imperatively develop preventive strategies by detecting virus mutations with capacity for emergence, enhancing the sensibility and rapidity of epidemiological surveillance, and becoming ready to face such events that cause a truly international health crisis.

Deception Island, Antarctica, harbors a diverse assemblage of wood decay fungi

Very little is known about fungal diversity in Antarctica as compared to other biomes and how these important organisms function in this unusual ecosystem. Perhaps one of the most unusual ecosystems is that of Deception Island; an active volcanic island part of the South Shetland Islands of the Antarctic Peninsula. Here we describe the fungal diversity associated with historic wood from structures on the island, which reveals a diverse fungal assemblage of known wood decay fungi as well as the discovery of undescribed species. The major group of wood decay fungi identified were species of Cadophora and as shown in previous studies in other geographic regions of Antarctica, they caused a soft-rot type of decay in the introduced woods. Additionally, unlike other areas of Antarctica that have been studied, filamentous basidiomycetes (Hypochniciellum spp. and Pholiota spp.) were also identified that have different modes of degradation including brown and white rot. Matches of fungal sequences to known species in temperate regions likely introduced on building materials indicates human influences and volcanic activity have greatly impacted fungal diversity. Lahars (mudslides from volcanic activity) have partially buried many of the structures and the buried environment as well as the moist, warm soils provided conditions conducive for fungal growth that are not found in other regions of Antarctica. The diverse assemblage of decay fungi and different forms of wood decomposition add to the difficulty of conserving wooden structures at these important polar heritage sites.

A mixed Ediacaran-metazoan assemblage from the Zaris Sub-basin, Namibia

It has been proposed that the terminal Neoproterozoic Ediacara biota were driven to extinction by the evolution of metazoan groups capable of engineering their environments (the ‘biotic replacement’ model). However, evidence for an overlapping ecological association between metazoans and soft-bodied Ediacaran organisms is limited. Here, we describe new fossil localities from southern Namibia that preserve soft-bodied Ediacara biota, enigmatic tubular organisms thought to represent metazoans, and vertically-oriented metazoan trace fossils. Although the precise identity of the tracemakers remains elusive, the structures bear several striking similarities with the Cambrian-Recent ichnogenus Conichnus. These new data support inference of stratigraphic and ecological overlap between two very different eukaryotic clades, and indicate the existence of unusual ecosystems comprising both Ediacara biota and metazoans immediately prior to the Cambrian explosion.

Species Diversity and Succession of Dung Beetles (Coleoptera: Geotrupidae and Scarabaeidae) Attracted to Horse Dung on Assateague Island

Abstract Barrier islands represent unusual and fragile ecosystems, influenced by multiple physical stressors and populated by organisms that are resource and habitat specialists. Dung beetles (Coleoptera) provide essential ecosystem services through the removal of dung from the environment. Their role in the unique environment of a barrier island dominated by a large non-native grazing species has not been widely investigated. Using linear transects of pitfall traps baited with human dung, we examined the species diversity of dung beetles found in three habitats (marsh, dunes, and forest) of Assateague Island, a barrier island off the coast of Maryland and Virginia, USA. Fifteen species (13,626 individuals) were collected. Estimates of species richness suggest there may be an additional 3–6 species on the island that were not sampled in this study. Heterotrophic succession of dung beetles attracted to horse dung was also examined and compared between Assateague Island and mainland horse farms. Observation...

Inter‐annual site fidelity and breeding origins of Gray‐cheeked Thrushes in white sand forests of the Peruvian Amazon

White sand terra firme forests are unusual ecosystems scattered across Amazonia, covering just 3% of the basin. These forests differ from surrounding forests in their scleromorphic vegetation, low nutrient content, and propensity to harbor endemics. We report the capture of 62 Gray-cheeked Thrushes (Catharus minimus) during a study of the understory avifauna of Amazonian white sand forests near Iquitos, Peru, conducted from 20 June to 8 December 2010–2012. We captured and banded Gray-cheeked Thrushes in white sand (N = 57) and adjacent weathered clay (N = 5) terra firme forests. Sampling for three consecutive days at 19 different sites each year, the inter-annual site fidelity rate of Gray-cheeked Thrushes was 4.8% (N = 3). One bird banded in 2010 was recaptured in 2012. Of the 62 birds, 19.3% (N = 12) were recaptured on subsequent days. All recaptures were in white sand forests. The 19.3% recapture rate of Gray-cheeked Thrushes from sites re-sampled no more than 2 d in a given year suggests the presence of settled and perhaps territorial birds. Using rectrices from 12 Gray-cheeked Thrushes, stable-hydrogen isotope analyses (δ2H) suggest that the geographic breeding or natal origin of all sampled birds was likely northwestern North America. Our results suggest that Gray-cheeked Thrushes exhibit site fidelity and may concentrate in white sand forests—an uncommon and scattered ecosystem type in western Amazonia. However, annual tracking of individual Gray-cheeked Thrushes is needed to fully assess regional patterns of settlement and movement, and the connectivity between breeding and wintering areas.

Whole-stream metabolism in nutrient-poor calcareous streams on Öland, Sweden

We studied whole-stream metabolism in three headwater non-forested stream reaches on the island of Oland, Sweden in order to characterize the metabolism of this unusual ecosystem and to compare it with other stream ecosystems in NW Europe. Gross primary production (GPP) was generally low (<4 g O2 m−2 d−1) with the lowest GPP recorded in the most upstream, shallow reach draining the thin soils of the limestone Alvar plains. Here, completely flooded terrestrial plants could account for the whole primary production at baseflow. Ecosystem respiration (ER) increased several fold with agricultural impact, resulting in heterotrophic stream conditions downstream and higher light requirements for photosynthesis to outweigh respiration. A strong relationship between daily GPP and ER was found at the two most nutrient-poor sites. Temperature corrected instantaneous ER rate was highest in the beginning of the night, but decreased at the end of the night at the same reaches, indicating that dark respiration depleted photosynthetic products and became limited by organic substrates. The broad-scale comparison of open NW European streams showed a 1:1 relationship, indicating a tight link between daily GPP and ER during summer (April–August) but not during winter. This study has extended the range of GPP and ER measurements to include nutrient-poor NW European streams, thereby increasing the knowledge on stream metabolism in this, otherwise, highly agricultural impacted region. It also documented a strong relationship between GPP and ER in streams, ranging from extremely nutrient poor to moderately nutrient rich conditions during spring and summer.

Fungal jarosite biomineralization in Río Tinto

Río Tinto is an extreme environment located at the core of the Iberian Pyrite Belt (IPB). It is an unusual ecosystem due to its size, constant acidic pH, high concentration of heavy metals and a high level of microbial diversity, mainly eukaryotic. Recently it was described the biomineralization of jarosite by Purpureocillium lilacinum, an acidic filamentous fungi isolated from the banks of the Tinto basin. In this study we further investigate the specificity of jarosite biomineralization by this fungi and its importance in the generation of jarosite in the Río Tinto basin. Our results clearly show that the ratio of the redox pairs and the Fe3+ concentration is important to achieve a specific biomineralization of jarosite. The amount of nucleation sites also seems to be critical, although the presence of nucleation sites by itself is not sufficient to precipitate jarosite. There is a good correlation between the sampling sites along the river in which hydronium-jarosite has been identified and the presence of P. lilacinum.

Archaeal diversity: temporal variation in the arsenic-rich creek sediments of Carnoulès Mine, France

The Carnoulès mine is an extreme environment located in the South of France. It is an unusual ecosystem due to its acidic pH (2-3), high concentration of heavy metals, iron, and sulfate, but mainly due to its very high concentration of arsenic (up to 10 g L⁻¹ in the tailing stock pore water, and 100-350 mg L⁻¹ in Reigous Creek, which collects the acid mine drainage). Here, we present a survey of the archaeal community in the sediment and its temporal variation using a culture-independent approach by cloning of 16S rRNA encoding genes. The taxonomic affiliation of Archaea showed a low degree of biodiversity with two different phyla: Euryarchaeota and Thaumarchaeota. The archaeal community varied in composition and richness throughout the sampling campaigns. Many sequences were phylogenetically related to the order Thermoplasmatales represented by aerobic or facultatively anaerobic, thermoacidophilic autotrophic or heterotrophic organisms like the organotrophic genus Thermogymnomonas. Some members of Thermoplasmatales can also derive energy from sulfur/iron oxidation or reduction. We also found microorganisms affiliated with methanogenic Archaea (Methanomassiliicoccus luminyensis), which are involved in the carbon cycle. Some sequences affiliated with ammonia oxidizers, involved in the first and rate-limiting step in nitrification, a key process in the nitrogen cycle were also observed, including Candidatus Nitrososphaera viennensis and Candidatus nitrosopumilus sp. These results suggest that Archaea may be important players in the Reigous sediments through their participation in the biochemical cycles of elements, including those of carbon and nitrogen.

Integrated forecasts of fall Chinook salmon returns to the Pacific northwest

Forecasts of returns are used to determine appropriate levels for ocean and in-river harvests of northeast Pacific fall Chinook salmon (Oncorhynchus tshawytscha). The current preseason forecasts are made by February, six months before fish arrive at natal rivers. As such, they do not capture ecosystem changes that occur after February. We incorporated catch and effort data from the Alaska summer commercial fishery to detect unusual ecosystem variability in fish return years and to update forecasts during the ocean fishery season. In addition, the traditional model using the ordinary regression unnecessarily has an intercept term, which often leads to unusual over-forecasts. Further there are concerns about autocorrelation in Chinook salmon returns. Finally the current practice does not provide information about the uncertainty inherent in the forecasts. To address these issues, we developed new forecast models and compared them with the traditional method. The models considered are: I, traditional preseason forecasts; II, autoregressive preseason forecasts without intercept term; III, ocean fishery real-time forecasts; IV, integrated forecasts from models I and III; and V, integrated forecasts from models II and III. We validated our models, using data from three Columbia River stocks [Upriver Bright (URB), Lower River Wild (LRW), and Mid-Columbia Bright (MCB)], and from two Canadian stocks [Fraser River Lates (FRL) and West Coast Vancouver Island (WCVI)]. Based on hindcasts of URB, LRW, FRL, and WCVI returns in 1992–2008 and of MCB returns in 1998–2008, model V was superior to the other models in bias and forecast coverage.

Microbial diversity in anaerobic sediments at Rio Tinto, a naturally acidic environment with a high heavy metal content.

The Tinto River is an extreme environment located at the core of the Iberian Pyritic Belt (IPB). It is an unusual ecosystem due to its size (100 km long), constant acidic pH (mean pH, 2.3), and high concentration of heavy metals, iron, and sulfate in its waters, characteristics that make the Tinto River Basin comparable to acidic mine drainage (AMD) systems. In this paper we present an extensive survey of the Tinto River sediment microbiota using two culture-independent approaches: denaturing gradient gel electrophoresis and cloning of 16S rRNA genes. The taxonomic affiliation of the Bacteria showed a high degree of biodiversity, falling into 5 different phyla: Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Actinobacteria; meanwhile, all the Archaea were affiliated with the order Thermoplasmatales. Microorganisms involved in the iron (Acidithiobacillus ferrooxidans, Sulfobacillus spp., Ferroplasma spp., etc.), sulfur (Desulfurella spp., Desulfosporosinus spp., Thermodesulfobium spp., etc.), and carbon (Acidiphilium spp., Bacillus spp., Clostridium spp., Acidobacterium spp., etc.) cycles were identified, and their distribution was correlated with physicochemical parameters of the sediments. Ferric iron was the main electron acceptor for the oxidation of organic matter in the most acid and oxidizing layers, so acidophilic facultative Fe(III)-reducing bacteria appeared widely in the clone libraries. With increasing pH, the solubility of iron decreases and sulfate-reducing bacteria become dominant, with the ecological role of methanogens being insignificant. Considering the identified microorganisms-which, according to the rarefaction curves and Good's coverage values, cover almost all of the diversity-and their corresponding metabolism, we suggest a model of the iron, sulfur, and organic matter cycles in AMD-related sediments.

Loss of biodiversity and ecosystem functioning in Indo-Malayan peat swamp forests

The tropical peat swamp forests of Indonesia and Malaysia are unusual ecosystems that are rich in endemic species of flora, fauna and microbes despite their extreme acidic, anaerobic, nutrient poor conditions. They are an important refuge for many endangered species including orang utans. Ecosystem functioning is unusual: microbial decomposition is inhibited because the leaves are sclerophyllous and toxic to deter herbivory in the nutrient poor environment, yet bacteria are abundant and active in the surface layers of the peat, where they respire DOC leached from newly fallen leaves. The bacteria are subsequently consumed by aquatic invertebrates that are eaten by fish, and bacterially respired CO2 is assimilated by algae, so bacteria are thus vital to carbon and nutrient cycling. Peat swamp forests are highly sensitive to the impacts of logging, drainage and fire, due to the interdependence of the vegetation with the peat substrate, which relies on the maintenance of adequate water, canopy cover and leaf litter inputs. Even minor disturbances can increase the likelihood of fire, which is the major cause of CO2 emissions from regional peat swamp forests and which impact ecosystems worldwide by contributing to climate change. Indo-Malayan peat swamps affect the hydrology of surrounding ecosystems due to their large water storage capacity which slows the passage of floodwaters in wet seasons and maintains stream base flows during dry seasons. These forests are of global importance yet they are inadequately protected and vanishing rapidly, particularly due to agricultural conversion to oil palm, logging, drainage and annual fires.