Biology subjects

Blackall, L.

Publications and source records attributed to Blackall, L..

4 recordsLinked to original sources

bioRxiv2024

SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data

Determining the taxonomy and relative abundance of microorganisms in metagenomic data is a foundational problem in microbial ecology. To address the limitations of existing approaches, we developed SingleM, which estimates community composition using conserved regions within universal marker genes. SingleM accurately profiles complex communities of known microbial species, and is the only tool that detects species without genomic representation, even those representing novel phyla. Given SingleMs computational efficiency, we applied it to 248,559 publicly available metagenomes and show that the vast majority of samples from marine, freshwater, sediment and soil environments are dominated by novel species lacking genomic representation (median relative abundance 75.0%). SingleM also provides a way to identify metagenomes for the recovery of novel metagenome-assembled genomes from lineages of interest, and can incorporate user-recovered genomes into its reference database to improve profiling resolution. Quantifying the full diversity of Bacteria and Archaea in metagenomic data shows that microbial genome databases are far from saturated.

microbiology↗

bioRxiv2024

Cutting through host autofluorescence: fluorescence lifetime imaging microscopy for visualising intracellular bacteria in Symbiodiniaceae

O_LIPhotoperiodicity is key to the synchronization of life stages in Symbiodiniaceae, Breviolum minutum which harbors taxonomically diverse epi- and endosymbiotic bacteria. We examined influence of a light dark regime on the spatial association between B. minutum and bacteria. C_LIO_LIWe employed a novel approach using combination of fluorescence lifetime imaging microscopy with fluorescence in situ hybridisation approach to clearly distinguish labelled intracellular bacteria from broad spectrum (450-800 nm) background autofluorescence of B. minutum. C_LIO_LIBacteria were observed inside, tethered to and burrowing into the cell exterior, and at the furrow of dividing cells in B. minutum. Significant changes in the abundance of intracellular bacteria relative to autofluorescence in B. minutum cells were observed at initiation of light and dark conditions. C_LIO_LIWe suggest that the onset of bacterial endosymbiosis is linked to the photoperiod driven changes in B. minutum life stages. The re-organisation of thecal plates during cell division of B.minutum in dark is likely to result in internalisation of bacteria. C_LI

microbiology↗

bioRxiv2023

Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts

Corals rely on a wide range of microorganisms for their functioning, including intracellular dinoflagellates (Symbiodiniaceae) and bacteria. Marine heatwaves trigger the loss of Symbiodiniaceae from coral tissues - coral bleaching - often leading to death. While coral-bacteria interactions are widely studied, Symbiodiniaceae-bacteria interactions have remained largely uninvestigated. Here, we provide a genomic analysis of 49 bacteria, spanning 16 genera, that closely associate with six cultured Symbiodiniaceae species. We analyzed bacterial functional potential by focusing on potentially beneficial functions for the Symbiodiniaceae host, including B vitamin synthesis and antioxidant abilities, which may be crucial for Symbiodiniaceae heat tolerance and in turn coral resistance to thermal bleaching. These analyses suggest a wide potential for B vitamin synthesis and the scavenging of reactive oxygen species (through the production of carotenoids or antioxidant enzymes), and possibly the transfer of organic carbon to host cells. Single nucleotide polymorphism analysis between bacteria isolated from wild-type and heat-evolved Symbiodiniaceae cultures revealed that exposure to long-term elevated temperature has resulted in mutations in genes known to be involved in host-symbiont interactions, such as secretion systems. Climate change may therefore modify how Symbiodiniaceae and bacteria interact. This study provides an overview of the possible roles of Symbiodiniaceae-associated bacteria in Symbiodiniaceae functioning and heat tolerance, reinforcing the need for further studies of such interactions to fully understand coral biology and climate resilience. ImportanceSymbiotic microorganisms are crucial for the survival of corals and their resistance to coral bleaching in the face of climate change. However, the impact of microbe-microbe interactions on coral functioning is mostly unknown, but could be essential factors for coral adaption to future climates. Here, we investigated interactions between cultured dinoflagellates of the Symbiodiniaceae family, essential photosymbionts of corals, and associated bacteria. By assessing the genomic potential of 49 bacteria, we found that they are likely beneficial for Symbiodiniaceae, through the production of B vitamins and antioxidants. Additionally, bacterial genes involved in host-symbiont interactions, such as secretion systems, accumulated mutations following long-term exposure to heat, suggesting symbiotic interactions may change under climate change. This highlights the importance of microbe-microbe interactions in coral functioning.

microbiology↗

bioRxiv2019

Presence of orange tubercles does not always indicate accelerated low water corrosion

The rapid degradation of marine infrastructure at the low tide level due to accelerated low water corrosion (ALWC) is a problem encountered worldwide. Despite this, there is limited understanding of the microbial communities involved in this process. We obtained samples of the orange-coloured tubercles commonly associated with ALWC from two different types of steel sheet piling, located adjacent to each other but with different levels of localised corrosion, at a seaside harbour. The microbial communities from the outer and inner layers of the orange tubercles, and from adjacent seawater, were studied by pure culture isolation and metabarcoding of the 16S rRNA genes. A collection of 119 bacterial isolates was obtained from one orange tubercle sample, using a range of media with anaerobic and aerobic conditions. The metabarcoding results showed that sulfur and iron oxidisers were more abundant on the outer section of the orange tubercles compared to the inner layers, where Deltaproteobacteria (which includes many sulfate reducers) were more abundant. The microbial communities varied significantly between the inner and outer layers of the orange tubercles and also with the seawater, but overall did not differ significantly between the two steel sheet types. Metallurgical analysis found differences in composition, grain size, ferrite-pearlite ratio and the extent of inclusions present between the two steel types investigated. IMPORTANCEThe presence of orange tubercles on marine steel pilings is often used as an indication that accelerated low water corrosion is taking place. We studied the microbial communities in attached orange tubercles on two closely located sheet pilings that were of different steel types. The attached orange tubercles were visually similar, but the extent of underlying corrosion on the different steel surfaces were substantially different. No clear difference was found between the microbial communities present on the two different types of sheet piling. However, there were clear differences in the microbial communities in the corrosion layers of tubercles, which were also different to the microbes present in adjacent seawater. The overall results suggest that the presence of orange tubercles, a single measurement of water quality, or the detection of certain general types of microbes (e.g. sulfate reducing bacteria) should not be taken alone as definitive indications of accelerated corrosion.

microbiology↗