Sub-lithic photosynthesis in hot desert habitats

In hyper-arid soil environments, photosynthetic microorganisms are largely restricted to hypolithic (sub-lithic) habitats: i.e., on the ventral surfaces of translucent pebbles in desert pavements. Here, we combined fluorometric, spectroscopic, biochemical and metagenomic approaches to investigate in situ the light transmission properties of quartz stones in the Namib Desert, and assess the photosynthetic activity of the underlying hypolithic cyanobacterial biofilms. Quartz pebbles greatly reduced the total photon flux to the ventral surface biofilms and filtered out primarily the short wavelength portion of the solar spectrum. Chlorophylls d and f were not detected in biofilm pigment extracts; however, hypolithic cyanobacterial communities showed some evidence of adaptation to sub-lithic conditions, including the prevalence of genes encoding Helical Carotenoid Proteins, which are associated with desiccation stress. Under water-saturated conditions, hypolithic communities showed no evidence of light stress, even when the quartz stones were exposed to full midday sunlight. This initial study creates a foundation for future in-situ and laboratory exploration of various adaptation mechanisms employed by photosynthetic organisms forming hypolithic microbial communities.     

Soil fungal diversity and assembly along a xeric stress gradient in the central Namib Desert

The Namib Desert of south-western Africa is one of the oldest deserts in the world and possesses unique geographical, biological and climatic features. While research through the last decade has generated a comprehensive survey of the prokaryotic communities in Namib Desert soils, little is yet known about the diversity and function of edaphic fungal communities, and even less of their responses to aridity. In this study, we have characterized soil fungal community diversity across the longitudinal xeric gradient across the Namib desert (for convenience, divided into the western fog zone, the central low-rainfall zone and the eastern high-rainfall zone), using internal transcribed sequence (ITS) metabarcoding. Ascomycota, Basidiomycota and Chytridiomycota consistently dominated the Namib Desert edaphic fungal communities and a core mycobiome composed of only 15 taxa, dominated by members of the class Dothideomycetes (Ascomycota), was identified. However, fungal community structures were significantly different in the fog, low-rainfall and high-rainfall zones. Furthermore, Namib Desert gravel plain fungal community assembly was driven by both deterministic and stochastic processes; the latter dominating in the all three xeric zones. We also present data that suggest that the inland limit of fog penetration represents an ecological barrier to fungal dispersal across the Namib Desert.     

Hypolithic Cyanobacteria Supported Mainly by Fog in the Coastal Range of the Atacama Desert

The Atacama Desert is one of the driest places on Earth, with an arid core highly adverse to the development of hypolithic cyanobacteria. Previous work has shown that when rain levels fall below ~1 mm per year, colonization of suitable quartz stones falls to virtually zero. Here, we report that along the coast in these arid regions, complex associations of cyanobacteria, archaea, and heterotrophic bacteria inhabit the undersides of translucent quartz stones. Colonization rates in these areas, which receive virtually no rain but mainly fog, are significantly higher than those reported inland in the hyperarid zone at the same latitude. Here, hypolithic colonization rates can be up to 80%, with all quartz rocks over 20 g being colonized. This finding strongly suggests that hypolithic microbial communities thriving in the seaward face of the Coastal Range can survive with fog as the main regular source of moisture. A model is advanced where the development of the hypolithic communities under quartz stones relies on a positive feedback between fog availability and the higher thermal conductivity of the quartz rocks, which results in lower daytime temperatures at the quartz–soil interface microenvironment.     

Niche-Partitioning of Edaphic Microbial Communities in the Namib Desert Gravel Plain Fairy Circles

Endemic to the Namib Desert, Fairy Circles (FCs) are vegetation-free circular patterns surrounded and delineated by grass species. Since first reported the 1970''s, many theories have been proposed to explain their appearance, but none provide a fully satisfactory explanation of their origin(s) and/or causative agent(s). In this study, we have evaluated an early hypothesis stating that edaphic microorganisms could be involved in their formation and/or maintenance. Surface soils (0–5cm) from three different zones (FC center, FC margin and external, grass-covered soils) of five independent FCs were collected in April 2013 in the Namib Desert gravel plains. T-RFLP fingerprinting of the bacterial (16S rRNA gene) and fungal (ITS region) communities, in parallel with two-way crossed ANOSIM, showed that FC communities were significantly different to those of external control vegetated soil and that each FC was also characterized by significantly different communities. Intra-FC communities (margin and centre) presented higher variability than the controls. Together, these results provide clear evidence that edaphic microorganisms are involved in the Namib Desert FC phenomenon. However, we are, as yet, unable to confirm whether bacteria and/or fungi communities are responsible for the appearance and development of FCs or are a general consequence of the presence of the grass-free circles.     

Social dominance and feeding patterns of spotted hyaenas

In some parts of East Africa, spotted hyaenas (Crocuta crocuta) live in large groups and at high population densities, and scramble competition among clan members during feeding at large carcasses is reported. By contrast, spotted hyaenas in the Namib Desert of southwestern Africa live in small groups and at low densities. When assembled at carcasses, Namib Desert spotted hyaenas show linear dominance hierarchies. Adult females outrank adult males and usually feed one at a time or with their dependent offspring. Feeding rates at small carcasses in the Namib Desert are approximately equal to those reported in East Africa, but at large carcasses Namib Desert spotted hyaenas show linear dominance hierarchies. Adult females outrank adult males and usually feed one at a time or with their dependent offspring. Feeding rates at small carcasses in the Namib Desert are approximately equal to those reported in East Africa, but at large carcasses Namib Desert spotted hyaenas feed significantly more slowly. Thus lower-ranking individuals eventually gain access to large carcasses but are excluded from smaller ones. We relate these patterns of food consumption to possible evolutionary pathways to social hunting by spotted hyaenas.     

Plant communities of a Central Namib inselberg landscape

Abstract. Three granite inselbergs and six dolerite dykes and their surroundings were investigated in the Central Namib, at the interface between the Namib Desert and Nama Karoo biomes. The main objectives of this study included a phytoso‐ciological interpretation of the described plant communities, explanation of the correlation of the communities with environmental variables and quantification of the relative contribution of different types of variables to structuring plant communities. Nine grassland and shrubland plant communities were recognized, largely organized according to general habitat, elevation, size of inselberg and geology. Soil properties, often thought to play an important role in arid environments, showed no clear patterns in the level of analyses used in this study. Other environmental parameters of importance in arid mountain habitats, such as slope aspect and angle, also played a minor role. The main implications of the study are: 1. Central Namib inselbergs, particularly granite domes, harbour diverse plant communities, often with species from neighbouring higher rainfall areas, and are thus of high conservation value. 2. The poor contribution of environmental variables in this study, which are conventionally used in field studies of plant community – environment relationships, may demand a critical review of additional parameters to be included when analysing plant community – environment relations in arid environments. In particular between‐season variation, phytogeographic aspects and the heterogeneity of microhabitats, often contained within a plant community, need to be taken into account.     

Nematode communities indicate diverse soil functioning across a fog gradient in the Namib Desert gravel plains

Soil nematodes are fundamentally aquatic animals, requiring water to move, feed, and reproduce. Nonetheless, they are ubiquitous in desert soils because they can enter an anhydrobiotic state that allows them to persist when water is biologically unavailable. In the hyper‐arid Namib Desert of Namibia, rain is rare, but fog routinely moves inland from the coast and supports plant and animal life. Very little is understood about how this fog may affect soil organisms. We investigated the role of fog moisture in the ecology of free‐living, soil nematodes across an 87‐km fog gradient in the gravel plains of the Namib Desert. We found that nematodes emerged from anhydrobiosis and became active during a fog event, suggesting that they can utilize fog moisture to survive. Nematode abundance did not differ significantly across the fog gradient and was similar under shrubs and in interplant spaces. Interplant soils harbor biological soil crusts that may sustain nematode communities. As fog declined along the gradient, nematode diversity increased in interplant soils. In areas where fog is rare, sporadic rainfall events can stimulate the germination and growth of desert ephemerals that may have a lasting effect on nematode diversity. In a 30‐day incubation experiment, nematode abundance increased when soils were amended with water and organic matter. However, these responses were not evident in field samples, which show no correlations among nematode abundance, location in the fog gradient, and soil organic matter content. Soil nematodes are found throughout the Namib Desert gravel plains under a variety of conditions. Although shown to be moisture‐ and organic matter‐limited and able to use moisture from the fog for activity, variation in fog frequency and soil organic matter across this unique ecosystem may be biologically irrelevant to soil nematodes in situ.     

Hypolithic microbial communities: between a rock and a hard place

Drylands are the largest terrestrial biome on Earth and a ubiquitous feature is desert pavement terrain, comprising rocks embedded in the mineral soil surface. Quartz and other translucent rocks are common and microbial communities termed hypoliths develop as biofilms on their ventral surfaces. In extreme deserts these represent major concentrations of biomass, and are emerging as key to geobiological processes and soil stabilization. These highly specialized communities are dominated by cyanobacteria that support diverse heterotrophic assemblages. Here we identify global-scale trends in the ecology of hypoliths that are strongly related to climate, particularly with regard to shifts in cyanobacterial assemblages. A synthesis of available data revealed a linear trend for colonization with regard to climate, and we suggest potential application for hypoliths as 'biomarkers' of aridity on a landscape scale. The potential to exploit the soil-stabilizing properties of hypolithic colonization in environmental engineering on dryland soils is also discussed.     

Microclimate and limits to photosynthesis in a diverse community of hypolithic cyanobacteria in northern Australia

Hypolithic microbes, primarily cyanobacteria, inhabit the highly specialized microhabitats under translucent rocks in extreme environments. Here we report findings from hypolithic cyanobacteria found under three types of translucent rocks (quartz, prehnite, agate) in a semiarid region of tropical Australia. We investigated the photosynthetic responses of the cyanobacterial communities to light, temperature and moisture in the laboratory, and we measured the microclimatic variables of temperature and soil moisture under rocks in the field over an annual cycle. We also used molecular techniques to explore the diversity of hypolithic cyanobacteria in this community and their phylogenetic relationships within the context of hypolithic cyanobacteria from other continents. Based on the laboratory experiments, photosynthetic activity required a minimum soil moisture of 15% (by mass). Peak photosynthetic activity occurred between approximately 8°C and 42°C, though some photosynthesis occurred between ?1°C and 51°C. Maximum photosynthesis rates also occurred at light levels of approximately 150–550 μmol m^?2 s^?1. We used the field microclimatic data in conjunction with these measurements of photosynthetic efficiency to estimate the amount of time the hypolithic cyanobacteria could be photosynthetically active in the field. Based on these data, we estimated that conditions were appropriate for photosynthetic activity for approximately 942 h (～75 days) during the year. The hypolithic cyanobacteria community under quartz, prehnite and agate rocks was quite diverse both within and between rock types. We identified 115 operational taxonomic units (OTUs), with each rock hosting 8–24 OTUs. A third of the cyanobacteria OTUs from northern Australia grouped with Chroococcidiopsis, a genus that has been identified from hypolithic and endolithic communities from the Gobi, Mojave, Atacama and Antarctic deserts. Several OTUs identified from northern Australia have not been reported to be associated with hypolithic communities previously.     

Namib Desert edaphic bacterial,fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters

Extremophiles - The central Namib Desert is hyperarid, where limited plant growth ensures that biogeochemical processes are largely driven by microbial populations. Recent research has shown that...     

Biogeographical patterns of abundant and rare bacterial biospheres in paddy soils across East Asia

Soil bacterial communities play fundamental roles in ecosystem functioning and often display a skewed distribution of abundant and rare taxa. So far, relatively little is known about the biogeographical patterns and mechanisms structuring the assembly of abundant and rare biospheres of soil bacterial communities. Here, we studied the geographical distribution of different bacterial sub-communities by examining the relative influence of environmental selection and dispersal limitation on taxa distributions in paddy soils across East Asia. Our results indicated that the geographical patterns of four different bacterial sub-communities consistently displayed significant distance–decay relationships (DDRs). In addition, we found niche breadth and dispersal rates to significantly explain differences in community assembly of abundant and rare taxa, directly affecting the strength of DDRs. While conditionally rare and abundant taxa displayed the strongest DDR due to higher environmental filtering and dispersal limitation, moderate taxa sub-communities had the weakest DDR due to greater environmental tolerance and dispersal rate. Random forest models indicated that soil pH (9.13%–49.78%) and average annual air temperature (16.59%–46.49%) were the most important predictors of the variation in the bacterial community. This study advances our understanding of the intrinsic links between fundamental ecological processes and microbial biogeographical patterns in paddy soils.     

Regional‐scale patterns of soil microbes and nematodes across grasslands on the Mongolian plateau: relationships with climate,soil, and plants

Belowground communities exert major controls over the carbon and nitrogen balances of terrestrial ecosystems by regulating decomposition and nutrient availability for plants. Yet little is known about the patterns of belowground communities and their relationships with environmental factors, particularly at the regional scale where multiple environmental gradients co‐vary. Here, we describe the patterns of belowground communities (microbes and nematodes) and their relationships with environmental factors based on two parallel studies: a field survey with two regional‐scale transects across the Mongolia plateau and a water‐addition experiment in a typical steppe. In the field survey, soils and plants were collected across two large‐scale transects (a 2000‐km east–west transect and a 900‐km south–north transect). At the regional‐scale, the variations in soil microbes (e.g. bacterial PLFA, fungal PLFA, and F/B ratio) were mainly explained by precipitation and soil factors. In contrast, the variation in soil nematodes (e.g. density of trophic groups and the bacterial‐feeding/fungal‐feeding nematode ratio) were primarily explained by precipitation. These variations of microbe or nematode variables explained by environmental factors at regional scale were derived from different vegetation types. Along the gradient from nutrient‐poor to nutrient‐rich vegetation types, the total variation in soil microbes explained by precipitation increased and that explained by plant and soil decreased, while the opposite was true for soil nematodes. Experimental water addition, which increased rainfall by 30% during the growing season, increased biomass or density of belowground communities, with the nematodes being more responsive than the microbes. The different responses of soil microbial and nematode communities to environmental gradients at the regional scale likely reflect their different adaptations to climate, soil nutrients, and plants. Our findings suggest that the soil nematode and microbial communities are strongly controlled by bottom‐up effects of precipitation alone or in combination with soil conditions.     

The influence of multi‐scale environmental variables on the distribution of terricolous lichens in a fog desert

Question: How do environmental variables in a hyper‐arid fog desert influence the distribution patterns of terricolous lichens on both macro‐ and micro‐scales? Location: Namib Desert, Namibia. Methods: Sites with varying lichen species cover were sampled for environmental variables on a macro‐scale (elevation, slope degree, aspect, proximity to river channels, and fog deposition) and on a micro‐scale (soil structure and chemistry). Macro‐scale and micro‐scale variables were analysed separately for associations with lichen species cover using constrained ordination (DCCA) and unconstrained ordination (DCA). Explanatory variables that dominated the first two axes of the constrained ordinations were tested against a lichen cover gradient. Results: Elevation and proximity to river channels were the most significant drivers of lichen species cover in the macro‐scale DCCA, but results of the DCA suggest that a considerable percentage of variation in lichen species cover is unexplained by these variables. On a micro‐scale, sediment particle size explained a majority of lichen community variations, followed by soil pH. When both macro and micro‐scale variables were tested along a lichen cover gradient, soil pH was the only variable to show a significant relationship to lichen cover. Conclusion: The findings suggest that landscape variables contribute to variations in lichen species cover, but that stronger links occur between lichen growth and small‐scale variations in soil characteristics, supporting the need for multi‐scale approaches in the management of threatened biological soil crust communities and related ecosystem functions.     

Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale

Extreme arid regions in the worlds'' major deserts are typified by quartz pavement terrain. Cryptic hypolithic communities colonize the ventral surface of quartz rocks and this habitat is characterized by a relative lack of environmental and trophic complexity. Combined with readily identifiable major environmental stressors this provides a tractable model system for determining the relative role of stochastic and deterministic drivers in community assembly. Through analyzing an original, worldwide data set of 16S rRNA-gene defined bacterial communities from the most extreme deserts on the Earth, we show that functional assemblages within the communities were subject to different assembly influences. Null models applied to the photosynthetic assemblage revealed that stochastic processes exerted most effect on the assemblage, although the level of community dissimilarity varied between continents in a manner not always consistent with neutral models. The heterotrophic assemblages displayed signatures of niche processes across four continents, whereas in other cases they conformed to neutral predictions. Importantly, for continents where neutrality was either rejected or accepted, assembly drivers differed between the two functional groups. This study demonstrates that multi-trophic microbial systems may not be fully described by a single set of niche or neutral assembly rules and that stochasticity is likely a major determinant of such systems, with significant variation in the influence of these determinants on a global scale.     

Lithic cyanobacterial communities in the polyextreme Sahara Desert: implications for the search for the limits of life

The hyperarid Sahara Desert presents extreme and persistent dry conditions with a limited number of hours during which the moisture availability, temperature and light allow phototrophic growth. Some cyanobacteria can live in these hostile conditions by seeking refuge under (hypolithic) or inside (endolithic) rocks, by colonizing porous spaces (cryptoendoliths) or fissures in stones (chasmoendoliths). Chroococcidiopsis spp. have been reported as the dominant or even the only phototrophs in these hot desert lithic communities. However, the results of this study reveal the high diversity of and variability in cyanobacteria among the sampled habitats in the Sahara Desert. The chasmoendolithic samples presented high coccoid cyanobacteria abundances, although the dominant cyanobacteria were distinct among different locations. A high predominance of a newly described cyanobacterium, Pseudoacaryochloris sahariense, was found in hard, compact, and more opaque stones with cryptoendolithic colonization. On the other hand, the hypolithic samples were dominated by filamentous, non-heterocystous cyanobacteria. Thermophysiological bioassays confirmed desiccation and extreme temperature tolerance as drivers in the cyanobacterial community composition of these lithic niches. The results of the present study provide key factors for understanding life strategies under polyextreme environmental conditions. The isolated strains, especially the newly described cyanobacterium P. sahariense, might represent suitable microorganisms in astrobiology studies aimed at investigating the limits of life.     

中国亚热带典型天然次生林土壤微生物碳源代谢功能影响因素

天然次生林地比人工林地不仅土壤肥力较高,且土壤碳代谢功能更强。然而维持天然次生林高碳代谢功能的原因尚不十分清楚。分析天然次生林中土壤微生物碳源代谢功能的影响因素对于调控土壤微生物的功能乃至天然次生林的保护具有重要意义。本文选择中国亚热带地区典型天然次生林,研究了土壤微生物碳源代谢功能与土壤化学和物理因素及植物因素的关系。结果表明,3类因素能显著解释土壤微生物碳源代谢功能54.4% 的变异。乔木层植物多样性、土壤碳氮比、pH值和含水量是导致天然次生林碳代谢功能差异的主要因素,分别显著解释了土壤微生物碳源代谢16.7%、12.4%、10.5%和10.5%的变异。天然次生林较低的土壤碳氮比、较高的土壤含水量和土壤pH值（酸性范围内）,有利于土壤微生物碳源代谢功能的提高,同时天然次生林较高的阔叶树种的比例也能增加土壤微生物碳源代谢功能。     

Abiotic drivers and plant traits explain landscape‐scale patterns in soil microbial communities

The controls on aboveground community composition and diversity have been extensively studied, but our understanding of the drivers of belowground microbial communities is relatively lacking, despite their importance for ecosystem functioning. In this study, we fitted statistical models to explain landscape‐scale variation in soil microbial community composition using data from 180 sites covering a broad range of grassland types, soil and climatic conditions in England. We found that variation in soil microbial communities was explained by abiotic factors like climate, pH and soil properties. Biotic factors, namely community‐weighted means (CWM) of plant functional traits, also explained variation in soil microbial communities. In particular, more bacterial‐dominated microbial communities were associated with exploitative plant traits versus fungal‐dominated communities with resource‐conservative traits, showing that plant functional traits and soil microbial communities are closely related at the landscape scale.     

阿拉善荒漠灌丛群落谱系结构及其影响因子

为探究阿拉善荒漠灌丛群落的构建机制,该研究选取净亲缘关系指数(NRI)作为谱系结构指数,在对阿拉善荒漠灌丛群落野外调查的基础上,以群落物种组成为基础数据,计算各样地群落的NRI,并分析NRI在经纬度梯度上的变化趋势及其与土壤因子和水热因子的关系。结果表明:(1)阿拉善荒漠灌丛群落谱系结构在阿拉善高原东南部以发散状态为主,在阿拉善高原西部和北部地区以聚集状态为主。(2)阿拉善荒漠灌丛群落的NRI随经度的升高而减小,随纬度的升高而增大。(3)阿拉善荒漠土壤质地、土壤容重、土壤pH值和土壤有机碳含量与其群落谱系结构均无显著相关性;在降水因子和温度因子中,与群落谱系结构相关系数最大的分别为年降水量和年温度变化范围(最暖月最高温与最冷月最低温的差值),其中:年降水量与NRI呈显著负相关关系,年温度变化范围与NRI呈显著正相关关系,且最暖月最高温和最冷月最低温与NRI均有显著相关性,推测年温度变化范围对阿拉善灌丛群落谱系结构的影响是通过最暖月最高温和最冷月最低温起作用的。研究发现,阿拉善高原东南部区域的荒漠灌丛群落构成主要受竞争排斥的作用,其西部和北部地区的群落构成主要受环境过滤的影响;阿拉善荒漠灌丛群落的谱系结构主要受年降水量和极端温度的影响。