Transitory Microbial Habitat in the Hyperarid Atacama Desert

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: a physico-chemical characterization of the soil habitability after an exceptional rain event, identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today's extreme hyperaridity. [Abstract copyright: Copyright © 2018 the Author(s). Published by PNAS.

Fungal Planet description sheets: 1383–1435

Novel species of fungi described in this study include those from various countries as follows: Australia, Agaricus albofoetidus, Agaricus aureoelephanti and Agaricus parviumbrus on soil, Fusarium ramsdenii from stem cankers of Araucaria cunninghamii, Keissleriella sporoboli from stem of Sporobolus natalensis, Leptosphaerulina queenslandica and Pestalotiopsis chiaroscuro from leaves of Sporobolus natalensis, Serendipita petricolae as endophyte from roots of Eriochilus petricola, Stagonospora tauntonensis from stem of Sporobolus natalensis, Teratosphaeria carnegiei from leaves of Eucalyptus grandis × E. camaldulensis and Wongia ficherai from roots of Eragrostis curvula. Canada, Lulworthia fundyensis from intertidal wood and Newbrunswickomyces abietophilus (incl. Newbrunswickomyces gen. nov.)on buds of Abies balsamea. Czech Republic, Geosmithia funiculosa from a bark beetle gallery on Ulmus minor and Neoherpotrichiella juglandicola (incl. Neoherpotrichiella gen. nov.)from wood of Juglans regia. France, Aspergillus rouenensis and Neoacrodontium gallica (incl. Neoacrodontium gen. nov.)from bore dust of Xestobium rufovillosum feeding on Quercus wood, Endoradiciella communis (incl. Endoradiciella gen. nov.)endophyticin roots of Microthlaspi perfoliatum and Entoloma simulans on soil. India, Amanita konajensis on soil and Keithomyces indicus from soil. Israel, Microascus rothbergiorum from Stylophora pistillata. Italy, Calonarius ligusticus on soil. Netherlands , Appendopyricularia juncicola (incl. Appendopyricularia gen. nov.), Eriospora juncicola and Tetraploa juncicola on dead culms of Juncus effusus, Gonatophragmium physciae on Physcia caesia and Paracosmospora physciae (incl. Paracosmospora gen. nov.)on Physcia tenella, Myrmecridium phragmitigenum on dead culm of Phragmites australis, Neochalara lolae on stems of Pteridium aquilinum, Niesslia nieuwwulvenica on dead culm of undetermined Poaceae, Nothodevriesia narthecii (incl. Nothodevriesia gen. nov.) on dead leaves of Narthecium ossifragum and Parastenospora pini (incl. Parastenospora gen. nov.)on dead twigs of Pinus sylvestris. Norway, Verticillium bjoernoeyanum from sand grains attached to a piece of driftwood on a sandy beach. Portugal, Collybiopsis cimrmanii on the base of living Quercus ilex and amongst dead leaves of Laurus and herbs. South Africa , Paraproliferophorum hyphaenes (incl. Paraproliferophorum gen. nov.) on living leaves of Hyphaene sp. and Saccothecium widdringtoniae on twigs of Widdringtonia wallichii. Spain, Cortinarius dryosalor on soil, Cyphellophora endoradicis endophytic in roots of Microthlaspi perfoliatum, Geoglossum laurisilvae on soil, Leptographium gemmatum from fluvial sediments, Physalacria auricularioides from a dead twig of Castanea sativa , Terfezia bertae and Tuber davidlopezii in soil. Sweden, Alpova larskersii, Inocybe alpestris and Inocybe boreogodeyi on soil. Thailand, Russula banwatchanensis, Russula purpureoviridis and Russula lilacina on soil. Ukraine, Nectriella adonidis on over wintered stems of Adonis vernalis. USA, Microcyclus jacquiniae from living leaves of Jacquinia keyensis and Penicillium neoherquei from a minute mushroom sporocarp. Morphological and culture characteristics are supported by DNA barcodes

Fungal Planet description sheets: 1383-1435

Novel species of fungi described in this study include those from various countries as follows: Australia, Agaricus albofoetidus, Agaricus aureoelephanti and Agaricus parviumbrus on soil, Fusarium ramsdenii from stem cankers of Araucaria cunninghamii, Keissleriella sporoboli from stem of Sporobolus natalensis, Leptosphaerulina queenslandica and Pestalotiopsis chiaroscuro from leaves of Sporobolus natalensis, Serendipita petricolae as endophyte from roots of Eriochilus petricola, Stagonospora tauntonensis from stem of Sporobolus natalensis, Teratosphaeria carnegiei from leaves of Eucalyptus grandis x E. camaldulensis and Wongia ficherai from roots of Eragrostis curvula. Canada, Lulworthia fundyensis from intertidal wood and Newbrunswickomyces abietophilus (incl. Newbrunswickomyces gen. nov.)on buds of Abies balsamea. Czech Republic, Geosmithia funiculosa from a bark beetle gallery on Ulmus minor and Neoherpotrichiella juglandicola (incl. Neoherpotrichiella gen. nov.)from wood of Juglans regia. France, Aspergillus rouenensis and Neoacrodontium gallica (incl. Neoacrodontium gen. nov.)from bore dust of Xestobium rufovillosum feeding on Quercus wood, Endoradiciella communis (incl. Endoradiciella gen. nov.)endophyticin roots of Microthlaspi perfoliatum and Entoloma simulans on soil. India, Amanita konajensis on soil and Keithomyces indicus from soil. Israel, Microascus rothbergiorum from Stylophora pistillata. Italy, Calonarius ligusticus on soil. Netherlands , Appendopyricularia juncicola (incl. Appendopyricularia gen. nov.), Eriospora juncicola and Tetraploa juncicola on dead culms of Juncus effusus, Gonatophragmium physciae on Physcia caesia and Paracosmospora physciae (incl. Paracosmospora gen. nov.)on Physcia tenella, Myrmecridium phragmitigenum on dead culm of Phragmites australis, Neochalara lolae on stems of Pteridium aquilinum, Niesslia nieuwwulvenica on dead culm of undetermined Poaceae, Nothodevriesia narthecii (incl. Nothodevriesia gen. nov.) on dead leaves of Narthecium ossifragum and Parastenospora pini (incl. Parastenospora gen. nov.)on dead twigs of Pinus sylvestris. Norway, Verticillium bjoernoeyanum from sand grains attached to a piece of driftwood on a sandy beach. Portugal, Collybiopsis cimrmanii on the base of living Quercus ilex and amongst dead leaves of Laurus and herbs. South Africa , Paraproliferophorum hyphaenes (incl. Paraproliferophorum gen. nov.) on living leaves of Hyphaene sp. and Saccothecium widdringtoniae on twigs of Widdringtonia wallichii. Spain, Cortinarius dryosalor on soil, Cyphellophora endoradicis endophytic in roots of Microthlaspi perfoliatum, Geoglossum laurisilvae on soil, Leptographium gemmatum from fluvial sediments, Physalacria auricularioides from a dead twig of Castanea sativa , Terfezia bertae and Tuber davidlopezii in soil. Sweden, Alpova larskersii, Inocybe alpestris and Inocybe boreogodeyi on soil. Thailand, Russula banwatchanensis, Russula purpureoviridis and Russula lilacina on soil. Ukraine, Nectriella adonidis on over wintered stems of Adonis vernalis. USA, Microcyclus jacquiniae from living leaves of Jacquinia keyensis and Penicillium neoherquei from a minute mushroom sporocarp. Morphological and culture characteristics are supported by DNA barcodes

Microbial communities in different Antarctic mineral deposits characterised by denaturing gradient gel electrophoresis (DGGE)

Livingston Island, located at the tip of the Antarctic Peninsula (Fig. 1),is characterised by an oceanic polar climate with temperatures above0°C for 4 months per year and a mean annual precipitation between 400and 500 mm. Under these conditions a soil formation can be observedand lichens, mosses and some higher plants are able to grow in thisenvironment. Since cultivation-independent methods have become animportant tool to investigate environmental microbes, it is possible toanalyze complex microbial networks in the face of diversity, abundance,ecology and their reaction on climate change. Here, we investigated thebacterial community structure of different soil and sediment habitatslocated on Livingston Island by polymerase chain reaction (PCR) usinga specific primer set followed by denaturing gradient gelelectrophoresis (DGGE) to get a first insight in the diversity of bacteriaexisting under these conditions. The aim of these studies is to identifythe main microbial players in nutrient turnover and to get an idea of thefunctioning of microbes within periglacial ecosystems

Biodiversity of methanogenic archaea in permafrost affected soils of the Lena Delta, Siberia

Hydromorphic arctic tundra soils are a very important source of atmospheric methane (CH4) which is according to CO2 the most climate relevant greenhouse gas.Wet tundra environments are generally a net carbon sink since the predominant environmental conditions reduce decomposition of organic matter and support a carbon accumulation. More than 14 % of the global terrestrial carbon is stored in soils and sediments of Arctic permafrost environments.Most of the climate models predict a global warming for the next century, which will be shown in deeper and longer thaw processes in the active layer of permafrost soils in the High Arctic and probably of a higher rate of degradation of organic matter and emission of methane and carbon dioxide.The microbial methane production (methanogenesis) is one of the most prominent microbiological processes during the anaerobic decomposition of organic matter. A group of strictly anaerobic organisms called methanogenic archaea is responsible for methanogenesis. The methanogenic archaea use the metabolism end products of bacteria involved in the anaerobic foodchain, which transform complex organic molecules into simple compounds like H2, CO2, acetate, formiate.After its production methane is partly oxidized either in the aerobic top layer of permafrost soils or in the aerobic rhizosphere by highly specialized Proteobacteria, belonging to the group of methanotrophic bacteria. They are using CH4 as the sole carbon source, while energy is gained by the oxidation of CH4 to CO2.In this study the community structure of methanogenic archaea was analyzed by polymerase chain reaction (PCR) using a nested primer approach with two different internal primer sets following denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene fragments. These modern molecular ecological methods allow to study the microbial community including uncultivable microorganisms.To investigate the archaeal community structure samples from three geomorphological different sites were taken:(i) a low centre polygon, (ii) a floodplain (both sites are located on Samoylov Island, Lena Delta) and (iii) a thermoerosion valley (Cape Mammontovy Klyk, ca. 400 km northwest of Samoylov). DNA was extracted directly from soils or from enrichment cultures. Samples for enrichment were taken from two different depths and were incubated under different conditions concerning temperature, salt content and substrates.The comparsion of the three different habitats showed clear differences between the composition of the methanogenic Archaea in the different environments. Both places on Samoylov showed a higher diversity than samples from Mammontovy Klyk. Results also indicate that there is a shift in the community structure from the top to the bottom of the active layer.The DGGE method is a very useful tool to get a fast overview about the composition of microbial communities in complex habitats. It can be also used to controll the enrichment and isolation of pure bacterial cultures.But nevertheless for detailed information about the methanogenic diversity the construction of a clone libary should be the next aim

Microbial communities from terrestrial mineral soils from Livingston Island, maritime Antarctica

Livingston Island (South Shetland Islands) is characterised by a maritime polar climate with temperatures above 0°C for 4 months and a mean annual precipitation of 450 mm. Nine vertical profiles were investigated regarding to their geochemical and geophysical properties and their microbial community structures. Two of the sites were covered by mosses and showed initial soil formation and humus accumulation. Total carbon and total nitrogen contents were low except for the upper layers of the moss covered sites. Denaturing gradient gel electrophoresis (DGGE) fingerprints from amplified 16S rRNA gene fragments showed large varieties in the vertical profiles and between the different sites. Most of the sequences obtained from re-amplified DGGE bands belong to the Bacteriodetes and Acidobacteria phyla. We also found sequences affiliated to methanotrophic bacteria (Methylobacter, Methylocapsa, Methylocystis) as well as to microorganisms involved in the nitrogen cycle (Nitrospira, Nitrospina). Furthermore, it was possible to isolate pure cultures, which belong mainly to Arthrobacter and Pseudomonas but also members of Frigoribacterium, Devosia, Leifsonia, Subtercola and Mucilaginibacter could be isolated. Although nutrient content is low a distinct diversity of microorganisms can be found in these extreme habitats dominated by so far unknown species

Biodiversität methanogener Archaeen in arktischen Böden des Lena-Delta / Sibirien

In der vorliegenden Arbeit wurde die Biodiversität methanogener Archaeen in arktischen Böden des Lena-Deltas / Sibirien unter Verwendung klassischer mikrobiologischer und molekularbiologischer Methoden untersucht. Dazu wurden die Aktivitätspotentiale der Methan bildenden Mikroorganismen in Abhängigkeit von verschiedenen Substraten und Temperaturen untersucht. Mit Hilfe der Denaturierenden Gradienten Gelelektrophorese (DGGE) und anschließender Sequenzierung einzelner DNA-Banden konnten dabei Unterschiede in der Populationszusammensetzung der methanbildenden Gemeinschaft im Tiefenprofil von Permafrostböden aufgezeigt und erklärt werden. Es ist bekannt, dass die Methanogenese in arktischen Böden von vielen verschiedenen klimatischen und bodenspezifischen Faktoren abhängig ist. Vor allem der Gehalt an organischer Substanz hatte einen großen Einfluss auf die Methanbildung. So förderte die Zugabe von Substrat die Methanbildung meist erheblich. Dabei war mit H2/CO2 der höchste Anstieg zu verzeichnen. Eine Ausnahme war hier die obersten 5 cm des Profils einer Überschwemmungsebene auf der Insel Samoylov. Hier war Methanol das bevorzugte Substrat. Die Erhöhung der Temperatur hatte ebenfalls einen positiven Einfluss auf die Methanbildungsrate. Es ließ sich allerdings kein einheitliches Muster in der Methanbildungsaktivität der methanogenen Archaeen für die unterschiedlichen Bodentypen nachweisen. Für alle Profile gemeinsam war, dass eine zum Teil sehr hohe Methanbildungsrate von bis zu 270 nmol CH4 h-1 g-1 mit H2/CO2 als Substrat für die obersten 10 cm festzustellen war. Mit zunehmender Tiefe änderte sich das Bild. Während die Aktivität im Polygonzentrum des Standortes Kap Mamontovy Klyk stark abnahm, gab es ein zweites Aktivitätsmaximum in der Überschwemmungsebene der Insel Samoylov in der Zone der stärksten Durchwurzelung. Das untersuchte Polygonzentrum der Insel Samoylov zeigte ebenfalls ein zweites Aktivitätsmaximum, allerdings lag dieses in der Zone dicht über dem Permafrost. Nach Analyse der Aktivitätstests, die bei verschiedenen Temperaturen und mit unterschiedlichen Substraten durchgeführt wurden, konnte bereits die Schlussfolgerung gezogen werden, dass sich die Gemeinschaft der methanogenen Archaeen in den verschiedenen Bodenhorizonten voneinander unterscheidet. Es wurde außerdem angenommen, dass die Diversität mit der Tiefe abnimmt, hervorgerufen durch die abnehmende Temperatur und den sinkenden Gehalt an organischem Kohlenstoff. Dies wurde durch die Ergebnsisse der Denaturierenden Gradienten-Gelelektrophorese (DGGE) nur teilweise bestätigt. Die Diversität nahm mit zunehmender Tiefe in der Auftauschicht erst zu und erreichte ihre größte Vielfalt in der Mitte der untersuchten Bodenprofile, um dann stark abzunehmen. Eine Ausnahme bildete die Überschwemmungsebene. Hier war die Diversität der methanogenen Mikroorganismen über das gesamte Profil etwa gleichbleibend. In allen der untersuchten arktischen Böden konnten Vertreter der Ordnung Methanomicrobiales und der Gattung Methanosarcina nachgewiesen werden. Desweiteren wurden auch Vertreter der Familie Methanosaetaceae gefunden, allerdings nur für die Überschwemmungsebene und das Polygonzentrum der Insel Samoylov. Die aus den Ergebnissen gezogenen Schlüsse lassen die Annahme zu, dass es in diesen Habitaten psychrophile bzw. psychrotolerante methanogene Mikroorganismen gibt, die optimal an die dort herrschenden, extremen klimatischen Bedingungen angepasst sind. Dies wird durch die Tatsache gestützt, dass es bereits einige psychrophile bzw. psychrotolerante Isolate von methanogenen Archaeen gibt