Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain ...a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Antarctic biodiversity is much more extensive, ecologically diverse and biogeographically structured than previously thought. Understanding of how this diversity is distributed in marine and ...terrestrial systems, the mechanisms underlying its spatial variation, and the significance of the microbiota is growing rapidly. Broadly recognizable drivers of diversity variation include energy availability and historical refugia. The impacts of local human activities and global environmental change nonetheless pose challenges to the current and future understanding of Antarctic biodiversity. Life in the Antarctic and the Southern Ocean is surprisingly rich, and as much at risk from environmental change as it is elsewhere.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SBMB, SIK, UILJ, UKNU, UL, UM, UPUK
The arid soils of the Antarctic Dry Valleys constitute some of the oldest, coldest, driest and most oligotrophic soils on Earth. Early studies suggested that the Dry Valley soils contained, at best, ...very low levels of viable microbiota. However, recent applications of molecular methods have revealed a dramatically contrasting picture - a very wide diversity of microbial taxa, many of which are uncultured and taxonomically unique, and a community that seems to be structured solely by abiotic processes. Here we review our understanding of these extreme Antarctic terrestrial microbial communities, with particular emphasis on the factors that are involved in their development, distribution and maintenance in these cold desert environments.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Geothermal springs are model ecosystems to investigate microbial biogeography as they represent discrete, relatively homogenous habitats, are distributed across multiple geographical scales, span ...broad geochemical gradients, and have reduced metazoan interactions. Here, we report the largest known consolidated study of geothermal ecosystems to determine factors that influence biogeographical patterns. We measured bacterial and archaeal community composition, 46 physicochemical parameters, and metadata from 925 geothermal springs across New Zealand (13.9-100.6 °C and pH < 1-9.7). We determined that diversity is primarily influenced by pH at temperatures <70 °C; with temperature only having a significant effect for values >70 °C. Further, community dissimilarity increases with geographic distance, with niche selection driving assembly at a localised scale. Surprisingly, two genera (Venenivibrio and Acidithiobacillus) dominated in both average relative abundance (11.2% and 11.1%, respectively) and prevalence (74.2% and 62.9%, respectively). These findings provide an unprecedented insight into ecological behaviour in geothermal springs, and a foundation to improve the characterisation of microbial biogeographical processes.
Bacterial diversity from McMurdo Dry Valleys in Antarctica, the coldest desert on earth, has become more easily assessed with the development of High Throughput Sequencing (HTS) techniques. However, ...some of the diversity remains inaccessible by the power of sequencing. In this study, we combine cultivation and HTS techniques to survey actinobacteria and cyanobacteria diversity along different soil and endolithic micro-environments of Victoria Valley in McMurdo Dry Valleys. Our results demonstrate that the Dry Valleys actinobacteria and cyanobacteria distribution is driven by environmental forces, in particular the effect of water availability and endolithic environments clearly conditioned the distribution of those communities. Data derived from HTS show that the percentage of cyanobacteria decreases from about 20% in the sample closest to the water source to negligible values on the last three samples of the transect with less water availability. Inversely, actinobacteria relative abundance increases from about 20% in wet soils to over 50% in the driest samples. Over 30% of the total HTS data set was composed of actinobacterial strains, mainly distributed by 5 families:
,
,
,
, and
. However, the 11 actinobacterial strains isolated in this study, belonged to
and
families that were underrepresented in the HTS data set. A total of 10 cyanobacterial strains from the order Synechococcales were also isolated, distributed by 4 different genera (
,
,
, and
-like). In agreement with the cultivation results,
was identified as dominant genus in the HTS data set.
-like cyanobacteria were found exclusively in the endolithic sample and represented 44% of the total 16S rRNA sequences, although despite our efforts we were not able to properly isolate any strain from this
-related group. The importance of combining cultivation and sequencing techniques is highlighted, as we have shown that culture-dependent methods employed in this study were able to retrieve actinobacteria and cyanobacteria taxa that were not detected in HTS data set, suggesting that the combination of both strategies can be usefull to recover both abundant and rare members of the communities.
Dispersal is a critical yet poorly understood factor underlying macroecological patterns in microbial communities
. Airborne microbial transport is assumed to occupy a central role in determining ...dispersal outcomes
, and extra-range dispersal has important implications for predicting ecosystem resilience and response to environmental change
. One of the most pertinent biomes in this regard is Antarctica, given its geographic isolation and vulnerability to climate change and human disturbance
. Here, we report microbial diversity in near-ground and high-altitude air above the largest ice-free Antarctic habitat, as well as that of underlying soil microbial communities. We found that persistent local airborne inputs were unable to fully explain Antarctic soil community assembly. Comparison with airborne microbial diversity from high-altitude and non-polar sources suggests that strong selection occurs during long-range atmospheric transport. The influence of selection during airborne transit and at sink locations varied between microbial phyla. Overall, the communities from this isolated Antarctic ecosystem displayed limited connectivity to the non-polar microbial pool, and alternative sources of recruitment are necessary to fully explain extant soil diversity. Our findings provide critical insights into the role of airborne transport limitation in determining microbial biogeographic patterns.
Lecideoid lichens as dominant vegetation-forming organisms in the climatically harsh areas of the southern part of continental Antarctica show clear preferences in relation to environmental ...conditions (i.e. macroclimate). 306 lichen samples were included in the study, collected along the Ross Sea coast (78°S-85.5°S) at six climatically different sites. The species compositions as well as the associations of their two dominant symbiotic partners (myco- and photobiont) were set in context with environmental conditions along the latitudinal gradient. Diversity values were nonlinear with respect to latitude, with the highest alpha diversity in the milder areas of the McMurdo Dry Valleys (78°S) and the most southern areas (Durham Point, 85.5°S; Garden Spur, 84.5°S), and lowest in the especially arid and cold Darwin Area (~ 79.8°S). Furthermore, the specificity of mycobiont species towards their photobionts decreased under more severe climate conditions. The generalist lichen species Lecanora fuscobrunnea and Lecidea cancriformis were present in almost all habitats, but were dominant in climatically extreme areas. Carbonea vorticosa, Lecidella greenii and Rhizoplaca macleanii were confined to milder areas. In summary, the macroclimate is considered to be the main driver of species distribution, making certain species useful as bioindicators of climate conditions and, consequently, for assessing the consequences of climate change.
New evidence in aerobiology challenges the assumption that geographical isolation is an effective barrier to microbial transport. However, given the uncertainty with which aerobiological organisms ...are recruited into existing communities, the ultimate impact of microbial dispersal is difficult to assess. Here we use molecular genetic approaches to examine microbial communities inhabiting fumarolic soils on Mount Erebus, the southernmost geothermal site on Earth, to evaluate the ecological significance of global-scale microbial dispersal. There, hot, fumarolic soils provide an effective environmental filter to test the viability of organisms that have been distributed via aeolian transport over geological time. We find that cosmopolitan thermophiles dominate the surface, whereas endemic Archaea and members of poorly understood Bacterial candidate divisions dominate the immediate subsurface. These results imply that aeolian processes readily disperse viable organisms globally, where they are incorporated into pre-existing complex communities of endemic and cosmopolitan taxa.
The reflectance spectroscopic characteristics of cyanobacteria-dominated microbial mats in the McMurdo Dry Valleys (MDVs) were measured using a hyperspectral point spectrometer aboard an unmanned ...aerial system (remotely piloted aircraft system, unmanned aerial vehicle or drone) to determine whether mat presence, type and activity could be mapped at a spatial scale sufficient to characterize inter-annual change. Mats near Howard Glacier and Canada Glacier (ASPA 131) were mapped and mat samples were collected for DNA-based microbiome analysis. Although a broadband spectral parameter (a partial normalized difference vegetation index) identified mats, it missed mats in comparatively deep (> 10 cm) water or on bouldery surfaces where mats occupied fringing moats. A hyperspectral parameter (B6) did not have these shortcomings and recorded a larger dynamic range at both sites. When linked with colour orthomosaic data, B6 band strength is shown to be capable of characterizing the presence, type and activity of cyanobacteria-dominated mats in and around MDV streams. 16S rRNA gene polymerase chain reaction amplicon sequencing analysis of the mat samples revealed that dominant cyanobacterial taxa differed between spectrally distinguishable mats, indicating that spectral differences reflect underlying biological distinctiveness. Combined rapid-repeat hyperspectral measurements can be applied in order to monitor the distribution and activity of sentinel microbial ecosystems across the terrestrial Antarctic.
Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene ...sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2
, which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.
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