Persepolis, a UNESCO World Heritage Site in south-western Iran, dates back to more than 2500 years ago, and is colonized by a great diversity of lichen-forming fungi. A survey of the lichen-forming fungi revealed a species abundant in different areas of the cultural site, which turned out to be a new species of the genus Circinaria. The new species, Circinaria persepolitana, is introduced and described on the basis of morphological and molecular data. Circinaria persepolitana is characterized by having a crustose thallus, rimose to areolate, usually with bullate areoles, with an olive green to olive-brown surface and angular to elongate areoles in the marginal zone. Phylogenetic analyses including other species of the genus showed that the new species is phylogenetically close to C. mansourii, C. ochracea and C. reptans. We propose a new combination of Circinaria reptans (Looman) Sohrabi, Owe-Larsson & Paukov. The bioweathering capacity of the new species was also analyzed by scanning electron microscopy, examining the interface between the lichen thallus and the lithic substratum to assess its potential threat to the conservation of heritage surfaces. We found this species to be a potential biodeteriogenic agent, as thalli were closely attached to the lithic substratum and biogeophysical and biogeochemical changes at the rock surface could be associated with the colonization.

Antarctic soils provide an excellent setting to test biogeographical patterns across spatial and environmental scales given their relatively simple communities and the dominance of physical factors that create strong environmental gradients. Additional urgency is given by the fact that their unique terrestrial communities are the subject of conservation efforts in a rapidly changing environment. We investigated relationships of soil community assembly and alpha and beta diversity with climatic and environmental parameters across regional and local scales in Maritime Antarctica. We sampled from a regional gradient of sites that differ in habitat severity, ranging from relatively favourable to harsher physicochemical conditions. At the regional scale, bacterial community characteristics and microarthropod abundance varied along this severity gradient, but most measures of fungal communities did not. Microarthropod and microbial communities differed in which soil and climate parameters were most influential, and the specific parameters that influenced each taxon differed across broad and fine spatial scales. This suggests that conservation efforts will need to focus on a large variety of habitat characteristics to successfully encompass diversity across taxa. Because beta diversity was the result of species turnover, conservation efforts also cannot focus on only the most biodiverse sites to effectively preserve all aspects of biodiversity.

The evolution of helminth parasites has long been seen as an interplay between host resistance to infection and the parasite's capacity to bypass such resistance. However, there has recently been an increasing appreciation of the role of symbiotic microbes in the interaction of helminth parasites and their hosts. It is now clear that helminths have a different microbiome from the organisms they parasitize, and sometimes amid large variability, components of the microbiome are shared among different life stages or among populations of the parasite. Helminths have been shown to acquire microbes from their parent generations (vertical transmission) and from their surroundings (horizontal transmission). In this latter case, natural selection has been strongly linked to the fact that helminth-associated microbiota is not simply a random assemblage of the pool of microbes available from their organismal hosts or environments. Indeed, some helminth parasites and specific microbial taxa have evolved complex ecological relationships, ranging from obligate mutualism to reproductive manipulation of the helminth by associated microbes. However, our understanding is still very elementary regarding the net effect of all microbiome components in the eco-evolution of helminths and their interaction with hosts. In this non-exhaustible review, we focus on the bacterial microbiome associated with helminths (as opposed to the microbiome of their hosts) and highlight relevant concepts and key findings in bacterial transmission, ecological associations, and taxonomic and functional diversity of the bacteriome. We integrate the microbiome dimension in a discussion of the evolution of helminth parasites and identify fundamental knowledge gaps, finally suggesting research avenues for understanding the eco-evolutionary impacts of the microbiome in host–parasite interactions in light of new technological developments.

The eastern larch beetle (Dendroctonus simplex Le Conte) is recognized as a serious destructive forest pest in the upper part of North America. Under epidemic conditions, this beetle can attack healthy trees, causing severe damages to larch stands. Dendroctonus species are considered as holobionts, as they engage in multipartite interactions with microorganisms, such as bacteria, filamentous fungi, and yeasts, which are implicated in physiological processes of the insect, such as nutrition. They also play a key role in the beetle's attack, as they are responsible for the detoxification of the subcortical environment and weaken the tree's defense mechanisms. The eastern larch beetle is associated with bacteria and fungi, but their implication in the success of the beetle remains unknown. Here, we investigated the bacterial and fungal microbiota of this beetle pest throughout its ontogeny (pioneer adults, larvae and pupae) by high-throughput sequencing. A successional microbial assemblage was identified throughout the beetle developmental stages, reflecting the beetle's requirements. These results indicate that a symbiotic association between the eastern larch beetle and some of these microorganisms takes place and that this D. simplex symbiotic complex is helping the insect to colonize its host tree and survive the conditions encountered.

Reduction of seed-bank persistence is an important goal for weed management systems. Recent interest in more biological-based weed management strategies has led to closer examination of the role of soil microorganisms. Incidences of seed decay with certain weed species occur in the laboratory; however, their persistence in soil indicates the presence of yet-unknown factors in natural systems that regulate biological mechanisms of seed antagonism by soil microorganisms. A fundamental understanding of interactions between seeds and microorganisms will have important implications for future weed management systems targeting seed banks. Laboratory studies demonstrate susceptibility to seed decay among weed species, ranging from high (velvetleaf) to very low (giant ragweed). Microscopic examinations revealed dense microbial assemblages formed whenever seeds were exposed to soil microorganisms, regardless of whether the outcome was decay. Microbial communities associated with seeds of four weed species (woolly cupgrass, jimsonweed, Pennsylvania smartweed, and velvetleaf) were distinct from one another. The influence of seeds on microbial growth is hypothesized to be due to nutritional and surface-attachment opportunities. Data from velvetleaf seeds suggests that diverse assemblages of bacteria can mediate decay, whereas fungal associations may be more limited and specific to weed species. Though microbial decay of seeds presents clear opportunities for weed biocontrol, limited success is met when introducing exogenous microorganisms to natural systems. Alternatively, a conservation approach that promotes the function of indigenous natural enemies through habitat or cultural management may be more promising. A comprehensive ecological understanding of the system is needed to identify methods that enhance the activities of microorganisms. Herein, we provide a synthesis of the relevant literature available on seed microbiology; we describe some of the major challenges and opportunities encountered when studying the in situ relationships between seeds and microorganisms, and present examples from studies by the ARS Invasive Weed Management Unit.

Comparative analysis of morphological and chemical properties of the soil chronosequence on Kastanozems soils in the steppe zone of the Russian Plain, which included paleosoils buried beneath kurgans erected ca. 2000 BC, AD 50, AD 200, and AD 1250 was performed to reconstruct the paleoenvironmental conditions in this archeologically important region. Paleoenvironmental dynamics were traced using the state of microbial communities of paleo and modern soils (including the dynamics of total and glucose-reactive biomass, and the abundance of microorganisms grown on selected media). We demonstrate that the share of the glucose-reactive microorganisms in the microbial community, the ecological–trophic structure, and oligotrophicity index might serve as indicators of the state of microbial communities and be used for paleoenvironmental reconstructions. The morphological–chemical and microbial properties confirm an arid period ca. 2000 BC, slightly wetter conditions ca. AD 50, and more humid conditions ca. AD 1250.

Fifty years after the hyporheic zone was first defined (Orghidan, 1959), there are still gaps in the knowledge regarding the role of biodiversity in hyporheic processes. First, some methodological questions remained unanswered regarding the interactions between biodiversity and physical processes, both for the study of habitat characteristics and interactions at different scales. Furthermore, many questions remain to be addressed to help inform our understanding of invertebrate community dynamics, especially regarding the trophic niches of organisms, the functional groups present within sediment, and their temporal changes. Understanding microbial community dynamics would require investigations about their relationship with the physical characteristics of the sediment, their diversity, their relationship with metabolic pathways, their interactions with invertebrates, and their response to environmental stress. Another fundamental research question is that of the importance of the hyporheic zone in the global metabolism of the river, which must be explored in relation to organic matter recycling, the effects of disturbances, and the degradation of contaminants. Finally, the application of this knowledge requires the development of methods for the estimation of hydrological exchanges, especially for the management of sediment clogging, the optimization of self-purification, and the integration of climate change in environmental policies. The development of descriptors of hyporheic zone health and of new metrology is also crucial to include specific targets in water policies for the long-term management of the system and a clear evaluation of restoration strategies.

Archaea, once thought to be only extremophiles, are now known to be abundant in most environments. They can predominate in microbial communities and be significantly involved in many global biogeochemical cycles. However, Archaea have not been reported in Antarctic sea ice. Our understanding of the ecology of Antarctic sea ice prokaryotes is still in its infancy but this information is important if we are to understand their diversity, adaptations and biogeochemical roles in Antarctic systems. We detected Archaea in sea ice at two sampling sites taken from three subsequent years using conserved 16S rRNA gene archaeal primers and PCR. Archaeal abundance was measured using quantitative PCR and community diversity was investigated by sequencing cloned 16S rRNA gene PCR products. Archaea in Antarctic sea ice were found to be in low abundance consisting of ≤ 6.6% of the prokaryotic community. The majority, 90.8% of the sequences, clustered with the recently described phylum Thaumarchaeota, one group closely clustered with the ammonia-oxidizing Candidatus Nitrosopumilus maritimus. The remainder of the clones grouped with the Euryarchaeota.

The search for evidence of past or present life on Mars will require the detection of markers that indicate the presence of life. Because deoxyribonucleic acid (DNA) is found in all known living organisms, it is considered to be a ‘biosignature’ of life. The main function of DNA is the long-term storage of genetic information, which is passed on from generation to generation as hereditary material. The Polymerase Chain Reaction (PCR) is a revolutionary technique which allows a single fragment or a small number of fragments of a DNA molecule to be amplified millions of times, making it possible to detect minimal traces of DNA. The compactness of the contemporary PCR instruments makes routine sample analysis possible with a minimum amount of laboratory space. Furthermore the technique is effective, robust and straightforward. Our goal was to establish a routine for the detection of DNA from micro-organisms using the PCR technique during the EuroGeoMars simulation campaign. This took place at the Mars Society's Mars Desert Research Station (MDRS) in Utah in February 2009 (organized with the support of the International Lunar Exploration Working Group (ILEWG), NASA Ames and the European Space Research and Technology Centre (ESTEC)). During the MDRS simulation, we showed that it is possible to establish a minimal molecular biology lab in the habitat for the immediate on-site analysis of samples by PCR after sample collection. Soil and water samples were taken at different locations and soil depths. The sample analysis was started immediately after the crew returned to the habitat laboratory. DNA was isolated from micro-organisms and used as a template for PCR analysis of the highly conserved ribosomal DNA to identify representatives of the different groups of micro-organisms (bacteria, archaea and eukarya). The PCR products were visualized by agarose gel electrophoresis and documented by transillumination and digital imaging. The microbial diversity in the collected samples was analysed with respect to sampling depth and the presence or absence of vegetation. For the first time, we have demonstrated that it is possible to perform direct on-site DNA analysis by PCR at MDRS, a simulated planetary habitat in an extreme environment that serves as a model for preparation and optimization of techniques to be used for future Mars exploration.

Bromochloromethane (BCM), a halogenated methane analogue, was evaluated for its anti-methanogenic activity in both batch and continuous fermentation systems. For batch fermentation, a roughage-based substrate was incubated with mixed rumen microflora for 24 h at two concentrations of BCM (5 and 10 μm). A 89–94 % reduction in methane was obtained in terms of volume and truly degraded substrate (TDS; P < 0·05). The partitioning factor (an index of efficiency of microbial protein production; expressed as mg TDS/ml net gas produced) increased from 3·55 to 3·73 (P < 0·05), while the acetate:propionate proportion decreased from 2·80 to 2·22 (P < 0·05). A complete inhibition of methanogens was associated with a 48 % decrease in Ruminococcus flavefaciens, a 68 % increase in Fibrobacter succinogenes and a 30 % increase in rumen fungi when quantified using qPCR. The continuous fermentation was carried out using the roughage-based substrate in four fermenters, two fermenters being control and the other two fed with BCM (5 μm) once in a day, for nine consecutive days. A persistent effect of BCM on methane reduction (85–90 %) was obtained throughout the study (P < 0·05) with no effect on gas production, SCFA production, acetate:propionate proportion, true degradability and efficiency of microbial mass synthesis (P>0·05). The complete inhibition of methane resulted in a significant decrease in R. flavefaciens and methanogens (P < 0·05) and an increase in fungal population (P < 0·05), while there was no effect on total bacterial and F. succinogenes populations (P>0·05). The batch fermentation confirms the anti-methanogenic activity of BCM, while the continuous fermentation indicates the persistency of this effect under in vitro conditions.

Bacteria in nature appear as diverse communities, which may comprise of hundreds of different species. The shared capacity of the bacterial communities to adapt in any imaginable set of conditions is remarkable. Many bacteria have growth requirements, as yet undiscovered, which are fulfilled by their natural habitats. Indeed, bacterial communities have members specialized on different functions and providing vital elements to other bacteria living in the same community. Therefore, most bacteria cannot easily be isolated from their habitats by the routine culturing methods used in most laboratories today. To overcome the difficulties in culturing of individual microbes, modern approaches analyse the structure of bacterial communities by determining the characteristic features of the microbial DNA extracted from the community samples. Using such techniques we have found that 90% of the bacteria in the chicken gastrointestinal tract represent previously unknown species. Furthermore, more than half of the 640 different species found represent previously unknown bacterial genera. Bacteria in the gastrointestinal tract derive most of their carbon and energy from dietary compounds which are either resistant to attack by digestive fluids or absorbed so slowly by the host that bacteria can successfully compete for them. The performance improvements on use of a growth promoting feed antibiotic is due to factors such as reduced competition for nutrients in the small intestine, reduced local inflammation due to control of pathogens, and reduced size of intestine. Since bacterial species differ in their substrate preferences and growth requirements, the chemical composition and structure of the digesta largely determines the species distribution of the bacterial community in the gastrointestinal tract. Consequently, it should be possible to shift the microbial community from harmful to non-harmful bacteria by changing the diet.

In this review, we discuss the potential for mycorrhizal fungi to act as a source or sink for carbon (C) under elevated CO2 and nitrogen deposition. Mycorrhizal tissue has been estimated to comprise a significant fraction of soil organic matter and below-ground biomass in a range of systems. The current body of literature indicates that in many systems exposed to elevated CO2, mycorrhizal fungi might sequester increased amounts of C in living, dead and residual hyphal biomass in the soil. Through this process, the fungi might serve as a negative feedback on the rise in atmospheric CO2 levels caused by fossil fuel burning and deforestation. By contrast, a few preliminary studies suggest that N deposition might increase turnover rates of fungal tissue and negate CO2 effects on hyphal biomass. If these latter responses are consistent among ecosystems, C storage in hyphae might decline in habitats surrounding agricultural and urban areas. When N additions occur without CO2 enrichment, effects on mycorrhizal growth are inconsistent. We note that analyses of hyphal decomposition under elevated CO2 and N additions are extremely sparse but are critical in our understanding of the impact of global change on the cycling of mycorrhizal C. Finally, shifts in the community composition of arbuscular and ectomycorrhizal fungi with increasing CO2 or N availability are frequently documented. Since mycorrhizal groups vary in growth rate and tissue quality, these changes in species assemblages could produce unforeseeable impacts on the productivity, survivorship, or decomposition of mycorrhizal biomass.