Marine sponges are important components of coral-reef ecosystems because of their role in filtering thousands of litres of seawater a day, retaining the nutrients that fuel the reefs high productivity. Sponges play host to millions of microbial symbionts that are thought to contribute to the health of the sponge through the provision of nutrients and removal of waste products like ammonia. In this study, ACE researchers Pam Engelberts, Steven Robbins, and Nicole Webster present an analysis of 259 symbiont genomes from the sponge Ircinia ramosa, making it one of the first studies to investigate an entire sponge microbiome. By identifying important metabolic pathways, such as carbon fixation or the removal of waste ammonia from the sponge, within the microbial genomes we were able to identify specific taxa that are potentially critical for sponge health.
Anaerobic oxidation of methane (AOM) is a key microbiological process mitigating the release of methane into the atmosphere. AOM coupled to the reduction of manganese oxides was first reported over a decade ago yet the microorganisms responsible and the key mechanisms they employ for this process had not been conclusively demonstrated. In a newly published study by ACE researchers Andy Leu, Simon McIlroy and Gene Tyson, meta-omic studies on a long term enrichment of two novel members of the Methanoperedenaceae revealed the expression of key genes involved in methane oxidation and several shared multi-heme c-type cytochromes (MHCs) that were differentially expressed between these two microorganisms, supporting the use of two different dissimilatory manganese reduction pathways during AOM coupled Mn(IV) reduction. The study expands the known electron acceptors anaerobic methanotrophic (ANME) archaea and importantly demonstrates their role in linking the global carbon and manganese cycles. This has significance to climate change modelling, given it is estimated that 19Tg of manganese is deposited in continental margins each year making it an important global sink for this potent greenhouse gas.
The gut microbiome plays a significant role in the development of graft vs host disease following stem cell transplant. However, it is unknown whether the pre-transplant or post-transplant bacterial community is more influential in disease progression. Using a mouse model, we demonstrate that when both the pre- and post-transplant gut microbiome is modified, the development of disease in wild-type mice is greatly accelerated. An altered post-transplant microbiome also accelerates disease, however to a lesser degree. In contrast, changing the pre-transplant microbiome alone does not accelerate disease. These findings suggest post-transplant manipulation of the gut microbiome, such as via faecal microbiota transplantation, may provide the greatest clinical benefit.
ACE researchers Steven Robbins, Lauren Messer, Caitlin Singleton, Aileen Geers, and Alex Baker authored a new publication in Nature Microbiology, entitled “A genomic view of the reef-building coral Porites lutea and its microbial symbionts.” By sequencing the genomes of the coral Porites lutea, its algal symbiont, and 52 bacterial and archaeal genomes, we could look at the whole library of genes each organism has to work with to see how their metabolisms interlink. This is very exciting in a number of ways. Researchers have studied the symbiosis between corals and their algal symbionts (Symbiodinium) for many years, but the role of the bacteria and archaea in coral health is just now being recognized. This is the first bacterial/archaeal community from corals to be sequenced and the first time we’re getting to look under the hood to see what these microbes do. It’s also the first time each member of the coral community (i.e. the coral, algae, and bacteria/archaea) have been looked at as a unit, which we think will be integral if we are to properly understand coral biology.
Our method for experimental testing of a phage host-range without the need for culturing the host has been just published in Nature Microbiology. It involves fluorescent staining of anonymous phages collected from an environment which are combined with anonymous environmental bacteria, and the subset of bacteria tagged by fluorescent viruses is collected by fluorescence activated cells sorting and analysed on single-cell level. This "viral tagging" method has been demonstrated on human gut microbiome to explore possible interactions between phages and their hosts coming from different human volunteers which can have implications for faecal microbiota transplant therapy. The resulting host-phage network revealed hosts for hundreds of previously unknown viruses and it showed that the phages are mostly species-specific (and not strain-specific as previously though), and only a smaller number of phages have a wider host-range. In addition, we found out that the phages in the human gut have possibly low burst sizes and that the prophage induction in the gut is common, thus the phages do not perturb the human gut microbiome composition heavily on a daily basis.
ACE members Soo Jen Low, Mária Džunková, Pierre-Alain Chaumeil, Donovan Parks and Philip Hugenholtz published "Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales" in Nature Microbiology.
We have an exciting PhD opportunity (stipend included) available at ACE starting in July working on non-photosynthetic Cyanobacteria using metagenomics, culturing and cryo-EM with Dr. Rochelle Soo and Prof. Phil Hugenholtz. For more details contact Dr Rochelle Soo – firstname.lastname@example.org. Please include a copy of your CV and academic transcript.
ACE members Paul Evans, Joel Boyd, Andy Leu, Ben Woodcroft, Donovan Parks, Philip Hugenholtz and Gene Tyson published "An evolving view of methane metabolism in the Archaea" in Nature Reviews Microbiology.