Publications
Selected recent publicaitons
Shark eggs contribute to the trophic ecology of a cold seeps
This recent publication by Dr. Tal Zvi-Kedem from the MRBLab reveals that collagen-rich eggs of the blackmouth catshark (Galeus melastomus) contribute to the complex food web of cold seeps in the southeastern Mediterranean. Using compound-specific isotope analyses, she shows how shark eggs provide nutrition to both opportunistic predators and chemosynthetic fauna, challenging previous assumptions that deep-sea seep ecosystems rely solely on microbial productivity. These findings uncover surprising trophic links and highlight the ecological importance of shark nurseries in nutrient-poor deep-sea environments.
Ghost shrimp burrows fuel life in the deep sea
This "Biogeosciences" study underscores the profound impact of the ghost shrimp Calliax lobata at cold seep ecotones in the Eastern Mediterranean, enhancing microbial productivity and nutrient cycling.
We found that the shrimp create unique microhabitats through high-resolution seabed mapping, sediment sampling, DNA sequencing, and microbial activity assays. These habitats support a diverse microbial community that degrades macromolecules, facilitates sulfate reduction, and promotes chemosynthesis, including Bacteroidota fermenters and the giant sulfur bacteria Thiomargarita.
These interactions extend the ecological impact of cold seeps, playing a crucial role in nitrogen fixation and carbon cycling in deep-sea ecosystems. The findings reveal that C. lobata shapes sediment structure and "gardens" its burrows to foster nutrient-rich microbial habitats, highlighting the vital role of seep ecotones in marine biogeochemistry.
Clam symbionts with a secret talent
This work led by Lina Ratinskaia uncovers that symbiotic bacteria living in the gills of Lucinoma kazani clams near Mediterranean brine pools have the genetic potential to fix nitrogen - a trait previously thought unique to shallow-water habitats. These Thiodiazotropha symbionts display remarkable metabolic versatility, powering their hosts with sulfur, methanol, and formate-based energy, and harbor complex molecular tools to interact with both their hosts and microbial rivals. This study reveals how warm, deep-sea environments may drive unexpected adaptations in microbial symbiosis.
Heavy metal nurseries: How deep-sea sharks cope with mercury-rich habitats
This research from MRBLab and IOLR's Chemistry Department investigates how deep-sea catsharks (Galeus melastomus) that use Mediterranean brine pool nurseries are exposed to toxic mercury (Hg) from naturally enriched seawater. We found high total mercury (THg) levels in adult tissues - particularly kidneys - and confirmed maternal transfer to embryos, suggesting both environmental uptake and potential biological mechanisms for coping with mercury. These findings offer the first insights into how oviparous elasmobranchs might adapt to extreme, metal-rich ecosystems.
Microbial life thrives in deep desert aquifers
Recent research by Betzabe Atencio, a PhD student in the Zuckerberg Institute for Water Research and the MRB lab, has unveiled the remarkable adaptability and productivity of microbial communities residing in ancient, deep aquifers beneath Israel's Negev Desert. These studies highlight the presence of diverse microbes that play crucial roles in biogeochemical cycles, even in extreme environments.
Betzabe discovered productive microbial communities in the Judea Group carbonate and Kurnub Group Nubian sandstone aquifers. Approximately 60% of the metagenome-assembled genomes (MAGs) from these aquifers contain genes for autotrophic pathways, such as the Calvin–Benson–Bassham cycle and the Wood–Ljungdahl pathway. This indicates a substantial capacity for carbon fixation and energy usage in these deep subsurface environments.
Complementing these findings, site-specific incubations revealed diverse biofilm communities with functional adaptations tailored to the unique conditions of each aquifer. These adaptations underscore the metabolic versatility of subsurface microbes, enabling them to use available carbon and energy sources efficiently.
These two papers shed light on the hidden microbial ecosystems in deep aquifers, emphasizing their potential role in global carbon cycling and their importance as ecological hotspots.
https://www.nature.com/articles/s41598-024-68868-9
ttps://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1533115/full
Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea
We analyzed the microbiome in deep-sea gas-rich brine pools (SE Mediterranean Sea), showing that dense and productive microbial communities occupy brine chemocline. Campylobacterota, especially a single Sulfurimonas genotype, were the key producers, Both aerobic and anaerobic microbes likely degrade macromolecules in brines. Low-abundance organisms support autotrophs, providing energy-rich H2 and vital organics.
Tar patties are hotspots of hydrocarbon turnover and nitrogen fixation during a nearshore pollution event in the oligotrophic southeastern Mediterranean Sea
We used metagenomics and more to describe life and interactions on nearshore tar pollution. Lots of diazotrophs enhanced N2 fixation. And we found tardigrades :) Can they help degrade tar?
Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels
In her second PhD paper, Tal Zvi-Kedem describes symbionts that allow chemosynthetic deep-sea mussels to use macromolecules from wood falls, etc. Could this association help Idas to colonize the deep sea? Many thanks to Manuel Kleiner and Simina Vintila from NCSU for the great collaboration!
Anthropogenic and natural disturbances along a river and its estuary alter the diversity of pathogens and antibiotic resistance mechanisms
Antibiotic resistance is a major threat to human health. We collaborated with Peleg Astrahan from the Kinneret Lake Laboratory (KLL) and the director of the Infectious Diseases department at Hillel Yaffe Medical Center Dr. Regev Cohen, uncovering AMRs along a polluted Alexander River , using metagenomics and bioinformatics.
Discovery and chemical composition of the eastmost deep-sea anoxic brine pools in the Eastern Mediterranean Sea
We discovered the eastmost brine pools in the Mediterranean Sea, 60 km offshore Israel at 1150 m water depth. These Palmahim brine pools are located directly above Messinian evaporites, which were up thrust to ~350 m below the seafloor. We found a bunch of small, anoxic, methanic and warm (21.6°C) brine pools, with salinity 1.5 times the ambient. This paper discusses their chemical properties and compares them with other deep saline basins.
Metagenomes of Red Sea subpopulations challenge the use of marker genes and morphology to assess Trichodesmium diversity
Trichodesmium is a globally-important, nitrogen-fixing, bloom-forming cyanobacterium. Coco Koedooder investigated the genotypes of the Red Sea Trichodesmium that form distinct colony morphotypes - two types of spherical "puffs" and raft-like "tufts". Puffs were shaped by Trichodesmium thiebautii and tufts by Trichodesmium erythraeum. Coco also identified genotypes of Trichodesmium that do not fix nitrogen. Previous attempts to look at the Red Sea Trichodesmium population structure using the hetR marker gene revealed a higher diversity. They found other species such as Trichodesmium aureum. Still, this metagenomics study suggests that the presence of hetR gene paralogs in Trichodesmium thiebautii genomes may account for the inflation in diversity. Great collaboration with Yeala Shaked's laboratory!
Cold seeps alter the near-bottom biogeochemistry in the ultraoligotrophic Southeastern Mediterranean Sea
Gas seeps at Palmahim Disturbance offshore Israel potentially affect the functionality of the deep oligotrophic Southeastern Mediterranean Sea. This study is truly a multidisciplinary effort, combining chemists (including the leading author Dr. Guy Sisma-Ventura), physical oceanographers, geologists and biologists. We show that gas seepage may lower the pH of water as low as 6.8 tens of meters above the seep site, and alter the N to P ratio to 30:1–53:1. Bioturbated sediments near the Palmahim Disturbance seeps catalyze rapid nutrient cycling. We show high microbial activity and changes in microbial communities near the seabed, even in seeps with low activity.
These sites export C and N into the water column, changing the deep hydrosphere.
Diversity, activity and abundance of benthic microbes in the Southeastern Mediterranean Sea
Microbes are great for biomonitoring! We sampled marine sediments from various depths (6-2000 m), offshore the Levant basin, within the framework of the National Monitoring Program of the Israeli Mediterranean Waters, in years 2018-2020. We show how the bacteria, archaea and fungi are distributed offshore, over coastal, shelf, slope and bathyal stations. One of the main findings indicates that microbial indices are affected by the downslope transport of organic matter.
The worm affair: fidelity and environmental adaptation in symbiont species that co-occur in vestimentiferan tubeworms
This paper is led by Tal Zvi Kedem. We investigate the fascinating symbiosis between deep-sea tubeworms and chemosynthetic bacteria. Two closely-related symbiont species often co-occur in one tubeworm host. We used this natural experimental system to ask how the fidelity of these associations is maintained.
We collaborated with the laboratory of Prof. Orit Sivan, using metagenomics to look for microbes that mediate iron cycling and methane oxidation in anoxic lake sediments.
We used mesocosm experiments to investigate the response of microbial communities to crude oil pollution in the Eastern Mediterranean.