Alessandro N. Garritano

Research

Life runs on a small set of elements, and none of them stays in living matter for long. Carbon, nitrogen and phosphorus pass from rock, air and water into cells and back out again, and microbes carry out most of the steps in between. I study those steps in soils and in the microbiomes of marine hosts, asking how microbes obtain the elements and what their metabolism means for the host and the ecosystem around them.

How do soils hold on to carbon, nitrogen and phosphorus when supply comes in pulses?

The textbook soil microbe keeps a fixed ratio of carbon to nitrogen to phosphorus in its biomass, growing only as fast as the scarcest element allows. Real soil microbes are more flexible than that. When carbon arrives in a pulse they build reserves such as the polyester PHB and storage lipids, so the carbon to phosphorus ratio of the community can rise sharply, and when phosphorus is short they replace the phospholipids in their membranes with lipids that contain none. That flexibility should let a community take up a pulse of carbon and nutrients faster than it could grow on it, and so keep in the soil what would otherwise be lost. At the University of Sydney I test this in incubations that feed soil ¹³C labelled substrate in pulses or at a constant rate and follow the label into biomass, storage compounds and respired CO₂, with heavy water (²H₂O) added alongside so that the lipids of growing cells tell me which microbes a pulse favours.

Soil carbon, nitrogen and phosphorus under pulsed or constant supply Two supply regimes, pulsed and constant, feed labelled carbon into a soil profile with roots, aggregates and microbial cells. Carbon dioxide leaves as respiration while biomass and storage compounds retain carbon, nitrogen and phosphorus. Pulsed supply Constant supply ¹³C labelled substrate CO₂ respired cells with storage granules Biomass and storage compounds retain carbon, nitrogen and phosphorus
Labelled carbon added to soil as pulses or as a constant supply, then followed into microbial biomass, storage compounds and respired CO₂.

How do we get from raw reads to answers?

Since joining the University of Sydney in 2025 I have written the pipelines my students and collaborators needed, then released them so other groups can use them. HiFiTaxa and AmplinkOne are postdoctoral work. Research groups in Australia, Denmark, Saudi Arabia, Brazil and Sweden use pipelines I wrote. Each one is built to run the same way on a laptop and on a cluster, with the reference databases versioned so a result can be reproduced a year later.

Illustration of a laptop showing sequence reads, a tree and a bar chart, beside soil and water samples in tubes
From samples to sequences to tables and figures, in one command.

  • HiFiTaxa

    Under review Preprint on bioRxiv, under review at ISME Communications

    A Nextflow pipeline that takes raw PacBio HiFi reads for the full length 16S rRNA gene or the fungal ITS region to taxonomy in a single command. It builds versioned references from current GTDB and UNITE releases and runs BLCA, naive Bayes, Emu and EMITS classifiers so their calls can be compared on the same samples. Benchmarked on mock communities and on holdout tests in the preprint.

    GitHubPreprint

  • AmplinkOne

    Under review Under review at ISME Communications

    A reproducible and modular R workflow that carries marker gene amplicon data through the downstream analysis, from ASV and taxonomy tables to community statistics and publication figures. Written with colleagues at the University of Sydney. The manuscript is under review and the code will be released with it.

PhD UNSW Sydney, 2020 to 2025

How does life run without light?

Deep sea sponges live where no light reaches and little food arrives. In my PhD, I investigated how their microbial symbionts make this possible. The answer, across four papers, is a community built around ammonia oxidising archaea that turn host ammonia into energy and fixed carbon, alongside heterotrophs that break down carbon too tough for most organisms, with viruses and metabolite exchange tying the partners together.

A deep sea sponge holobiont running on ammonia and recalcitrant carbon A glass sponge at 830 metres with ammonia oxidising archaea, heterotrophic bacteria and a phage inside. Host ammonia and dissolved carbon dioxide feed the archaea, marine snow polysaccharides feed the bacteria, and fumarate and vitamin B12 are exchanged between partners. 830 m, no light Host ammonia (NH₃) Dissolved CO₂ Ammonia oxidation and carbon fixation by ammonia oxidising archaea Marine snow polysaccharides Fumarate and vitamin B12 exchanged between archaeon, bacterium and phage Heterotrophic bacteria degrade recalcitrant carbon
Inside a deep sea sponge, archaea oxidise host ammonia and fix carbon while bacteria break down recalcitrant carbon from marine snow. Metabolites and a phage link the partners.

  • Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge

    Published N. Garritano A et al. Microbiome 14, 153 (2026)

    Metagenomics, metatranscriptomics and isotope labelling of the deep sea sponge Calyx sp. Heterotrophs break down tough algal polysaccharides from marine snow while two ammonia oxidising archaea fix carbon worth about a fifth of the sponge’s body carbon a year. The community is mixotrophic.

    PaperThe Conversation

  • Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage

    Published N. Garritano A et al. The ISME Journal 18, wrae197 (2024)

    The glass sponge Aphrocallistes beatrix hosts one archaeon and one bacterium, the simplest sponge holobiont reported. The archaeon runs on sponge ammonia and feeds the bacterium fumarate, and a virus that lyses the archaeon supplies the vitamin B12 the bacterium cannot make. Covered by BBC News.

    Paper

  • Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae

    Published N. Garritano A et al. The ISME Journal 17, 1517–1519 (2023)

    In three deep sea sponge genera, ammonia oxidising archaea make up at least three quarters of the microbial community, so these holobionts can fix carbon in the dark. Each sponge species carries its own archaeal lineage, which points to vertical transmission. Cited in an international patent application.

    Paper

  • Symbiotic Ammonia Oxidation in the Marine Environment

    Published Thomas T, N. Garritano A. Annual Review of Marine Science 18, 409–427 (2026)

    An invited review of ammonia oxidation by microbes living in or on marine animals, from sponges and corals to bivalves and crustaceans. It covers the dominance of Nitrosopumilaceae, the variation in rates between hosts, genomic adaptation to life in a host and the open questions.

    Paper

Who are the symbionts and how are they related?

Deep sea expeditions off Brazil, where I was the only member of my group on board, started collaborations that continue today. These papers describe the symbiont lineages that recur across corals, crinoids and sponges, the names and genomes that pin down who they are, and the data released so that others can use them.

Illustration of a deep sea coral, a crinoid and a sponge on rock, each above a circle of its microbial symbionts
Corals, crinoids and sponges from the deep South Atlantic and the symbiont lineages that recur across them.

  • Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling

    Published Modolon F, N. Garritano A et al. Microbiome 13, 234 (2025)

    Deep sea corals and the crinoids that live on them share the same Endozoicomonadaceae and Nitrosopumilaceae symbionts. A new dominant species, Endozoicomonas promiscua, can reduce nitrate to ammonia, a possible feed for the archaea and a nitrogen cycling link across hosts.

    Paper

  • The novel, wide-spread sponge-associated phylum Spongivicinota shows metabolic complementarity to its sister-phylum Latescibacterota

    Published Allen MA, N. Garritano A et al. ISME Communications 6, ycag317 (2026)

    Seventeen genomes from deep sea sponges define Spongivicinota, a proposed phylum for a widespread clade known until now by placeholder names. Its members live mostly in sponges and corals beside their sister phylum Latescibacterota and specialise in degrading complex peptides.

    Paper

  • Resolving the evolutionary duality of marine symbionts: redefining the genus Endozoicomonas and proposing Neoendozoicomonas gen. nov.

    Published Modolon F, N. Garritano A et al. ISME Communications 6, ycag123 (2026)

    Phylogenomics across 63 genomes redraws the genera of the Endozoicomonadaceae, symbionts of corals, sponges, molluscs and fishes. Core proteome identity resolved genera best and splits Endozoicomonas into Endozoicomonas sensu stricto and the new genus Neoendozoicomonas.

    Paper

  • Metagenome-assembled genomes and viral sequences from deep-sea sponges

    In press Allen MA, N. Garritano A et al. Scientific Data, in press (2026). No DOI yet

    A data descriptor for the metagenome assembled genomes and viral sequences recovered from deep sea sponges during the PhD, released so that other groups can build on them.

How do microbiomes differ between hosts and places?

Not every microbiome is specific to its host, and not every host keeps the microbes it is given. These collaborative papers compare communities between coral species on the same seafloor, follow coral probiotics into sponges, isolate the bacteria living against algal cells inside coral tissue, and watch bacteria change their behaviour with the microalga they grow on.

Illustration of deep sea corals, sponges and single celled algae on a rocky sea floor, each with a magnified patch showing the microbes living in its tissue
Each host carries its own microbes. Corals, sponges and microalgae on the sea floor, each with a magnified view of the community living in its tissue, down to the bacteria packed around the algal cells inside the coral on the left.

  • Contrasting microbiomes in deep-sea scleractinian and octocoral species from the South Atlantic Ocean

    Published Hill LJ, Damasceno T, N. Garritano A et al. Sustainable Microbiology 3, qvag048 (2026)

    Amplicon sequencing of stony corals and octocorals from 710 metres in the Campos Basin shows each species carrying a community distinct from the water and sediment around it. The octocoral Candidella imbricata had the most specialised microbiome, dominated by Endozoicomonadaceae.

    Paper

  • Not only for corals: exploring the uptake of beneficial microorganisms for corals by sponges

    Published Ribeiro B, N. Garritano A et al. npj Biofilms and Microbiomes 10, 125 (2024)

    A four week field trial gave coral probiotics to two sponge species. Related strains were enriched in Stylissa carteri, both microbiomes shifted, and the sponges stayed healthy and kept pumping, so treating nearby corals is unlikely to harm them.

    Paper

  • Bacteria associated with the in hospite Symbiodiniaceae’s phycosphere

    Published Hill LJ, Messias CSMA, Vilela CLS, N. Garritano A et al. iScience 27, 109531 (2024)

    A Percoll gradient enriches intact Symbiodiniaceae cells and their attached bacteria from Pocillopora damicornis tissue. Halieaceae, Flavobacteriaceae and Alcanivoraceae associate with the algal cells inside the host, opening the phycosphere within coral tissue to study.

    Paper

  • Dual transcriptomics reveal commensal interactions between microalgae and phycosphere bacteria

    Under review Roager L, Schostag M, N. Garritano A, Gram L, Egan S. bioRxiv (2026). Under review

    Dual transcriptomics of two phycosphere bacteria grown with three microalgae. The bacterial transcriptomes changed with the host, and in co culture with the diatom Conticribra weissflogii a Maribacter sp. switched on polysaccharide degradation genes and grew on laminarin alone.

    Paper

Where is carbon fixed across the tree of life?

Carbon fixation is the entry point of carbon into living matter, yet its distribution across bacteria and archaea had not been mapped at scale. I built hidden Markov models for the key enzymes of the six known pathways and screened 52,515 metagenome assembled genomes with them, then used the same models to find the pathways in the sponge symbionts above. The models are public as HMM_CFP on GitHub, and I am extending the approach with random forest classifiers trained on genome annotations.

Illustration of a circular tree of life with the molecules of the carbon fixation pathways at its centre, a sun and photosynthetic cells at the bottom left and bacteria with hydrogen, ammonia and minerals at the bottom right
Carbon fixation across the tree of life. The bacterial and archaeal tree with the key molecules of the fixation pathways at its centre, and below it the two kinds of energy that drive them, sunlight on the left and the chemical energy of hydrogen, ammonia and minerals on the right.

  • Carbon fixation pathways across the bacterial and archaeal tree of life

    Published N. Garritano A, Song W, Thomas T. PNAS Nexus 1, pgac226 (2022)

    Hidden Markov models screened 52,515 genomes and found carbon fixation pathways in 1,007 of them, including the reverse TCA cycle in phyla where it had not been recognised and a cycle thought to be archaeal in bacteria. Carbon fixation is far more widespread than the textbook picture.

    Paper Code

Master’s Federal University of Rio de Janeiro, 2015 to 2017

Can waste become fuel?

My master’s research used mixed microbial consortia to ferment palm oil mill effluent, the wastewater of palm oil extraction, into hydrogen and then methane, with decentralised energy for remote parts of Brazil as the aim. It is where I learned gas chromatography and how to follow carbon and energy through a microbial community, skills I still use on soils today.

Illustration of palm fruit and a flask of effluent feeding two sealed fermentation jars, one producing hydrogen and the next methane
Palm oil mill effluent fermented in two stages, hydrogen first and then methane from what is left.

  • Palm oil mill effluent (POME) as raw material for biohydrogen and methane production via dark fermentation

    Published N. Garritano A, Faber MO, De Sá LRV, Ferreira-Leitão VS. Renewable and Sustainable Energy Reviews 92, 676–684 (2018)

    A review of palm oil mill effluent as a feedstock for hydrogen and methane by dark fermentation, bringing together the microbiology, the process conditions and the reported yields, and the two stage approach that recovers methane from the spent medium.

    Paper

  • Efficient biohydrogen production via dark fermentation from hydrolized palm oil mill effluent by non-commercial enzyme preparation

    Published N. Garritano A, De Sá LRV, Aguieiras ÉCG, Freire DMG, Ferreira-Leitão VS. International Journal of Hydrogen Energy 42, 29166–29174 (2017)

    Hydrolysing the effluent with an enzyme preparation made in the laboratory from Ricinus communis, in place of a commercial enzyme, raised the hydrogen yield from dark fermentation of this wastewater.

    Paper