Head of the group: Dr. Laura Steindler
Marine Microbiology research group (Established 2011)
Head of the group: Dr. Laura Steindler
Lab manager: Dr. Rinat Bar-Shalom
The Lab's research focuses on the following topics:
Join us: We are recruiting M.Sc. and Ph.D. students. If you are interested please send your CV and research interests to: firstname.lastname@example.org
Our lab focuses on two main themes of marine microbiology. One relates to the adaptation of free-living heterotrophic bacteria to oligotrophic conditions, and the utilization of light energy to compensate for carbon starvation. The other focus is on adaptations of marine bacteria to life in symbiosis with invertebrate hosts, and more specifically with marine sponges.
Host-microbe interactions (symbiosis in marine sponges)
Today we look at animals as 'holobionts'. These comprise the eukaryotic host and microorganisms that are tightly associated to it. In fact it is now well accepted that animals exist only in partnership with symbionts that affect the health of such multi-organismal entities. Our laboratory investigates the interactions within holobionts using as model system marine sponges.
With sponges possibly being the earliest branching extant animal lineage, sponges are ideally evolutionary placed to inform our understanding of the early evolution of host-microbe symbioses.
We look at the molecular mechanisms involved in the establishment and maintenance of the interaction of the sponge with its microbial symbionts. One aspect is to determine how components of what could be considered an ancient innate immune system (of the sponge) may serve the sponge to differentiate between microbial symbionts and microbial food (or pathogens). Using substractive hybridization techniques we identified a sponge-gene containing a scavenger receptor cystein rich (SRCR) domain that was differentially expressed in the presence versus absence of cyanobacterial symbionts (Steindler et al, Mar Biotechnol 2007). Proteins featuring SRCR domains are either cell surface or secreted proteins and in vertebrates have functions related to host-defense during endocytosis. We hypothesized that sponge genes with SRCR domain that are differentially expressed in relation to presence/absence of microbial symbionts may have a function in the recognition of the symbiont.
Presently we are utilizing transcriptomic-based approaches to gain a more global overview of the genes that are differentially expressed in the sponge in function of the symbiotic state with cyanobacterial symbionts. Further, we seek for mechanisms of host-symbiont recognition also within the genomes of sponge symbionts. The latter are sequenced by next-generation sequencing, assembled by bioinformatic-binning methods, and then compared to available genomes of the phylogenetically clo sest free-living bacteria.
Quorum sensing in sponge holobionts
Quorum sensing (QS) is a system used by many bacteria to coordinate gene expression according to the density of their local population. It is based on the synthesis of signal molecules and on response regulator proteins that sense the concentration of the signal molecules and bind to gene-promoters to enhance or inhibit the expression of QS regulated genes. Pathogens use QS to coordinate the production of virulence factors, squid-symbionts use it to activate bioluminescence expression. Sponges harbor a remarkable diversity of microbial symbionts in an enclosed niche where signal molecules can accumulate and enable cell-cell interaction, such as QS. We have used community genome assembly and binning to investigate the uncultured majority of sponge symbionts and identify common N-acyl homoserine lactone QS systems (article in review). Our next conceptual step is to investigate the function(s) played by QS within sponge holobionts.
Sponges and biotechnology
Sponges are also a major reservoir of natural diversity, with an incredible range of different bacterial phyla that are potential source of new enzymes and small molecules of interest for the chemical industry and medicine. We use high-throughput microbial cultivation methods to try and cultivate such majority of yet-uncultured sponge symbionts. More specifically, we are adapting the successful 'dilution to extinction' technique, which has led to the cultivation of oligotrophic marine free-living bacteria such as the ubiquitous SAR11 clade, for the cultivation of sponge symbionts. Furthermore we use cosmid libraries, -omics techniques and bioinformatic analyses on DNA derived from the sponge microbiomes to search for genes responsible for the production of secondary metabolites of interest. In particular, we are interested in novel anti-microbials based on quorum-quenching mechanisms (inhibition of quorum sensing) in bacterial pathogens.
Photoheterotrophy in marine bacteria
Every drop of seawater contains about half a million bacteria, and the latter drive the cycles of energy and matter in the oceans. Despite their significance, our understanding of their physiology and their impact on marine energetic budgets is limited. Many marine heterotrophic bacteria are capable of light-mediated ATP production using proteorhodopsins (PR) proteins that, upon illumination, create a pH gradient across the cellular membrane. These organisms can therefore supplement energy obtained via consumption of exogenous carbon with PR derived ATP to meet their energetic requirements. While extensive work has examined the oceanic C cycle on the assumption that all energy must pass through photosynthetic primary production, by this mechanism solar energy can by-pass CO2 fixation. Yet few studies have tested the extent to which light-harvesting by PR can complement or substitute other energy source in pure cultures of marine bacteria, and little is known about the genetic mechanisms underlying the PR photoheterotrophic strategy. Even more limited is our understanding on the percent energetic contribution of PR directly in marine microbial consortia.
Our laboratory utilizes high-throughput microbial cultivation methods with oligtrophic seawater-based growth media and flow-cytometry to identify cells at very low cell densities (typical of those found in natural ecosystems) to isolate novel bacteria from the Eastern Mediterranean Sea. These bacterial cultures enable us to investigate the mechanisms of light-utilization in bacteria that are naturally abundant in the environment. Further we can obtain their genome sequences that serve not only to bring forward new hypotheses on cellular functions that can be tested using the microbial cultures, but also as reference genomes in environmental meta-omics studies run by our and other laboratories.
Further, we are developing physiologic methods to investigate the contribution (energetic/transport) of proteorhodopsin in natural marine microbial assemblages.
1998 BSc Tel Aviv University
2000 MSc Tel Aviv University
2005 PhD Tel Aviv University
2005-2008 ICGEB-Trieste, Italy Dr. Vittorio Venturi Lab
2008-2011 Oregon State University, OR, USA Dr. Stephen Giovannoni Lab
Chapters in books:
Ferluga S, Steindler L, Venturi V (2008) N-acyl homoserine lactone quorum sensing in gram negative rhizobacteria. In: Secondary Metabolites in Soil Ecology. Vol 14. Karlovsky, P. (Ed), Heidelberg, Germany. Springer, pp. 69-92
ISF Photoheterotrophy: Physiological and genetic characterization of how dominant heterotrophic bacteria channel light energy into the ocean.
R&D Italy-Israel A novel approach to fight antibiotic resistant pathogens: acquisition of quorum sensing inhibitors from marine sponges.
BSF Isolation of sponge-associated bacteria: a first step to reveal bacterial adaptations to life in symbiosis with a sponge.
|Dr. Laura Steindler (Head of the Lab)|
|Dr. Rinat Bar Shalom (Lab manager)||
Sponges harbor dense communities of diverse symbiotic microorganisms and there is increasing evidence that a majority of secondary metabolites found in the host extracts, originate from the symbiotic bacteria rather than by the host itself. Microbial symbionts utilize biosynthetic gene clusters for the production of secondary metabolites (e.g., PKS and NRPS). One of my goals is to determine what regulates the expression of these genes in situ within the sponge holobiont, in bacterial isolates from sponges and in heterologous systems.
|Dr. Markus Haber (post-doc)||
My current research interests are in environmental microbiology, microbial ecology and physiology. I am working on two systems:
|Dr. Kumar Saurav (post-doc)||
Anti-virulence drugs are a new type of therapeutic agent aiming at virulence factors rather than killing the pathogen, thus providing less selective pressure for evolution of resistance. One promising example of this therapeutic concept targets bacterial quorum sensing (QS), because QS controls many virulence factors responsible for bacterial infections. The general aim of my project in the lab is to isolate and purify bioactive lead molecule that interfere with QS from sponge and its associated microorganisms.
|Maya Britstein (PhD student)||
The aim of my research is to understand molecular mechanisms underlying host-microbe interactions using the facultative association with the sponge Petrosia ficiformis with the endocellular photosynthetic Candidatus Synechococcus feldmannii, as a model system.
|Ilia Burgsdorf (PhD student)||
More than 25 phyla of bacteria compose the unique microbiome of one of the oldest metazoans on Earth, sponges. Host-symbiont, symbiont-symbiont and phage-symbiont interactions within this complex holobiont (sponge-host and related microbes) are of great interest because of their long evolutionary history and genomic singularity. My study involves both bioinformatic (comparative genomics, metagenomic analyses) and molecular (genetic engineering) approaches.
Matan Lahyani (MSc student)
Isolating and culturing novel oligotrophic bacteria from the Eastern Mediterranean Sea in view of further investigation that can provide a better understanding of element cycling in the marine ecosystem. Further I am interested in cellular mechanisms involved in starvation-survival in the wide-spread marine oligotroph Candidatus Pelagibacter ubique .
Sofia Sizikov (undergraduate student, .. and soon to be MSc student)
Cyanobacterial symbionts of marine sponges have general adaptations to life inside the sponge. One of the suggested mechanisms of adaptation is the common absence of genes involved in synthesis of O-antigen in these symbionts (Burgsdorf et al., MBio 2015). In this project, I try to understand the role of O-antigen in cyanobacteria-sponge symbiosis by preventing its expression in free-living cyanobacteria.
Nitzan Barak (undergraduate student)
Assessing the presence of PKS/NRPS genes, and testing the effect of biotic and abiotic conditions on PKS expression in isolated sponge symbionts.
Dani Dubinski (MSc) Thesis: Sub-mesoscale structuring of marine microbial communities.
Maya Britstein (MSc) N-acyl homoserine lactone quorum sensing in the association between marine sponges and their symbiotic bacteria communities.
Ilia Burgsdorf (MSc) Cyanobacteria from sponge holobionts: genomic adaptations and interactions with the microbiome.
Metagenomes of the microbiomes of Theonella swinhoei (Red Sea), Petrosia ficiformis Mediterranean Sea), Ircinia variabilis (Mediterranean Sea).
Draft genomes of sponge symbionts: Candidatus Synechococcus spongiarum
For information please contact us directly
If our topics are of interest to you, go ahead and contact us to apply for a M.Sc or Ph.D. position at our lab. We address our research questions by combining diverse methodologies, including molecular biology, physiology, imaging, chemistry, next generation sequencing and bioinformatics.
If you are interested please send your CV and a description of your interests to:
Dr. Laura Steindler
Department of Marine Biology
Leon Charney School of Marine Sciences
University of Haifa,
Mt. Carmel, Haifa 3498838, Israel
School Fax: 972-4-8288267
Sdot Yam - Israel
Achziv, Israel - EMP collection together with the Ilan-Lab
Ligurian Sea – transplant experiments of P. ficiformis with Carlo Cerrano