This Scoop is a collection of internet publications, tweets, and newly published papers in the wide field of Microbial diversity and ecology. I try to curate these here to show relevant news items for people interested in this field.
Feel free to suggest or comment on any of my postings.
Assessing microbial diversity requires analysis of all three domains of life, including eukaryotic microbes. We examined the diversity of two ecologically important clades of microbial eukaryotes, ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), by comparing pyrosequencing to Sanger-sequenced clone libraries and microscopy. Using samples from a large temperate estuary (Long Island Sound, USA), we gained three major insights. First, richness estimates varied by up to one order of magnitude either using different criteria for pyrosequence processing or among pyrosequencing, cloning and microscopy, while taxon identification was almost always coherent. Error-correcting algorithms for pyrosequences (“denoising”) reduced discrepancies in richness but also removed known morphospecies from the data. Second, although most of the pyrosequenced Operational Taxonomic Units (OTUs) distributed within known orders and families, we found evidence of a previously uncharacterized or unknown clade even in these ciliate lineages that have a rich history of morphological description. Third, pyrosequencing allowed the detection of OTUs that were either dominant or extremely rare in different samples. Our findings confirm the potential of pyrosequencing for quantifying microbial diversity, but also highlight the importance of careful evaluation of pyrosequence processing for using this method to address ecological questions.
“This study explored the persistence and spatial distribution of a diverse Archaeal assemblage inhabiting a temperate mixed forest ecosystem. Persistence under native conditions was measured from 2001 to 2010, 2011, and ...”
Genomic %AT has been found to correlate negatively with genome size in microbes. While microbes with large genomes are often GC-rich and free-living, AT-rich bacteria tend to be host-associated with smaller genomes. With over 2000 fully sequenced microbial genomes available, we explored the relationship between genomic %AT, genome size, relative entropy (a measure of accumulated random mutations) and fraction of genome islands (GI) in microbial species with the genomes of more than 10 strains available. A negative correlation with genome size was found in 6 out of 12 phyla and a positive correlation in only 2. At the species level, we found a remarkable trend of positive correlations between genomic %AT and genome size in 8 out of 20 species, while only 4 showed a negative correlation. Estimated chromosomal fractions of GI's were found to correlate positively with genome size in the strains of 14 out of 18 species and genomic %AT in the strains of 7 species (2 correlated negatively). Although GI's may explain most of the positive correlations between genomic %AT and size observed within the strains of the microbial species, Chlamydia trachomatis seem to be an exception, therefore these findings needs to be further explored.
“Chinese researchers have now used genome sequencing to identify about 1,300 different microbial species in an exceptionally soupy smog that hit Beijing in January 2013. Reassuringly, most of the microbes they found are ...”
The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.
Via Olivier ANDRE
“Through soil metagenomics research, we can address fundamental questions about soil microbial ecology. For example, is there functional microbial redundancy in soil? Soil microbial community compositions differ in ...”
Via Andreas Sjödin
“Last Friday I added another article to my publication list. The publication was in the PLOS ONE journal and caries the title: Linking microbiology and Geology: inactive pockmarks affect sediment mi...”
“Science Codex Connectedness, human use of buildings shape indoor bacterial communities Science Codex The location, connectedness, and human use patterns in a building may influence the types of bacteria they house, according to a study published in...”
Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.
“In Pond-B, the archaeal diversity was the highest among the four, and the members of the order Sulfolobales were dominant. The Pond-D also showed relatively high diversity, and the most frequent group was uncultured ...”
“Archaea is a peer-reviewed, open access journal that publishes original research articles as well as review articles dealing with all aspects of research on the archaea, including bioinformatics, biotechnology, environmental adaptation, enzymology,...”
“The diversity indices and rarefaction analysis revealed a quite low diversity for both β-proteobacterial and archaeal amoA genes, but qPCR data showed significantly higher amoA gene copy numbers for archaea than β-proteobacteria, ...”
“Below ground activity is only just beginning to be understood in grassland systems. Below find a summary of some work to understand microbial communities in grasslands. Reconstructing the Microbial Diversity and Function ...”
“The first paper I'll tackle (Schneider et al) asks if Wolbachia strains exist as diverse quasi-species within a host and reveals that diversity using host transfer techniques. In "Uncovering Wolbachia Diversity upon Artificial Host ...”
“We've been looking for ways to analyze transcriptomes correctly, with sufficient power, not too many type I and II errors, and not much fuss. For those relatively unfamiliar with performing differential expression analyses on ...”
“For the first time ever, a team led by the University of Colorado Boulder has sequenced the internal bacterial makeup of the three major life stages of a butterfly species, a project that showed so...”
“ MOTHUR is bioinformatics package which includes functions from DOTUR, SONS, TreeClimber, S-Libshuff and Unifrac. MOTHUR aims to be a comprehensive software package that allows users to use a single piece of ...”
Via Biswapriya Biswavas Misra
Nearly all eukaryotes are host to beneficial or benign bacteria in their gut lumen, either vertically inherited, or acquired from the environment. While bacteria core to the honey bee gut are becoming evident, the influence of the hive and pollination environment on honey bee microbial health is largely unexplored. Here we compare bacteria from floral nectar in the immediate pollination environment, different segments of the honey bee (Apis mellifera) alimentary tract, and food stored in the hive (honey and packed pollen or “beebread”). We used cultivation and sequencing to explore bacterial communities in all sample types, coupled with culture-independent analysis of beebread. We compare our results from the alimentary tract with both culture-dependent and culture-independent analyses from previous studies. Culturing the foregut (crop), midgut and hindgut with standard media produced many identical or highly similar 16S rDNA sequences found with 16S rDNA clone libraries and next generation sequencing of 16S rDNA amplicons. Despite extensive culturing with identical media, our results do not support the core crop bacterial community hypothesized by recent studies. We cultured a wide variety of bacterial strains from 6 of 7 phylogenetic groups considered core to the honey bee hindgut. Our results reveal that many bacteria prevalent in beebread and the crop are also found in floral nectar, suggesting frequent horizontal transmission. From beebread we uncovered a variety of bacterial phylotypes, including many possible pathogens and food spoilage organisms, and potentially beneficial bacteria including Lactobacillus kunkeei, Acetobacteraceae and many different groups of Actinobacteria. Contributions of these bacteria to colony health may include general hygiene, fungal and pathogen inhibition and beebread preservation. Our results are important for understanding the contribution to pollinator health of both environmentally vectored and core microbiota, and the identification of factors that may affect bacterial detection and transmission, colony food storage and disease susceptibility.