Xavier Pochon

• Associate Professor
• Senior Researcher at Cawthron Institute

Understanding the cellular symbiosis between marine holobionts and their endosymbiotic algae is crucial for predicting the resilience of coral reefs to climate change. While bleaching protocols have been widely applied to model organisms such as corals and sea anemones, their application to other symbiotic taxa remains underexplored. This study pre...

The application of environmental DNA (eDNA) and RNA (eRNA) technologies to aquatic ecosystem monitoring and management has increased rapidly in the last decade. These methods are providing many new and exciting opportunities for enhanced biodiversity assessment, ecological health evaluation, and species detection. This special issue of PeerJ Life a...

Passive environmental DNA (eDNA) samplers offer a cost-effective and scalable approach to marine biodiversity monitoring, potentially aiding detections of non-indigenous species. This study explored the efficiency of passive eDNA samplers to detect a variety of globally problematic marine invasive species in field conditions: Sabella spallanzanii ,...

Understanding biodiversity is crucial for protecting unique environments, but acquiring this knowledge is challenging in isolated areas due to limited availability of easy-to-implement biomonitoring tools. To determine optimal sampling strategies in remote regions, environmental DNA and RNA (eDNA and eRNA) sampling workflows were evaluated at 12 si...

Background Crustose Coralline Algae (CCA) play a crucial role in coral reef ecosystems, contributing significantly to reef formation and serving as substrates for coral recruitment. The microbiome associated with CCAs may promote coral recruitment, yet these microbial communities remain largely understudied. This study investigates the microbial co...

Environmental biosecurity challenges are worsening for aquatic ecosystems as climate change and increased anthropogenic pressures facilitate the spread of invasive species, thereby broadly impacting ecosystem composition, functioning, and services. Environmental DNA (eDNA) has transformed traditional biomonitoring through detection of trace DNA fra...

Predicting the response and resilience of coral reefs to climate change can only be achieved through better understanding the cellular symbiosis between coral reef holobionts and their associated endosymbiotic algae. Larger benthic foraminifera (LBF) are key calcium carbonate producers on reefs, of which two species were investigated for their suit...

Environmental DNA (eDNA) offers an efficient approach to biodiversity monitoring and biosecurity surveillance in coastal ecosystems. Understanding eDNA dynamics in tidal areas is critical for guiding sampling strategy design and interpreting molecular detection results. In a field study conducted at Ōpua, Bay of Islands, Aotearoa, New Zealand, an i...

Understanding biodiversity is crucial for protecting unique environments, but acquiring this knowledge is challenging in isolated areas due to the limited availability of easy-to-implement biomonitoring tools. To determine optimal sampling strategies in remote regions, environmental DNA and RNA (eDNA and eRNA) sampling workflows were evaluated at 1...

The global marine ecosystem is changing rapidly as the result of biogeochemical cycles and ecosystem structure being altered by industrial civilization. Invasive marine species (IMS) are one of the most damaging regional consequences of human activity, and one of the most easily attributable to specific processes. This makes IMS introduction one of...

Environmental DNA and RNA (eDNA/eRNA) can serve as molecular tools for biodiversity monitoring and biosecurity surveillance. However, uncertainties still exist regarding the persistence and dynamics of marine nucleic acids in the environment and the effects of post‐sampling storage on species detectability. To bridge these gaps, an experiment was c...

Molecular biomonitoring programs increasingly use environmental DNA (eDNA) for detecting targeted species such as marine non-indigenous species (NIS) or endangered species. However, the current molecular detection workflow is cumbersome and time-demanding, and thereby can hinder management efforts and restrict the "opportunity window" for rapid man...

New Zealand’s green-lipped mussel (Perna canaliculus) is an ecologically and economically important species. Marine heatwaves are increasing in frequency around NZ’s coastline, and these events are correlated with increased stress and mortality of some aquaculture species. This study aimed to identify general biomarkers of heat stress in P. canalic...

The combination of an efficient sampling method and high‐throughput analysis of environmental DNA (eDNA) can be a powerful approach for characterising biodiversity across aquatic ecosystems. Plankton net tows are one of the oldest, simplest, and least expensive methods for seston and eDNA collection, but require laborious filtration steps which oft...

The global marine ecosystem is changing rapidly as the result of biogeochemical cycles and ecosystem structure being altered by industrial civilization. Invasive marine species (IMS) are one of the most damaging regional consequences of human activity, and one of the most easily attributable to specific processes. This makes IMS introduction one of...

Aotearoa New Zealand’s Northern region is a major gateway for the incursion and establishment of non-indigenous species (NIS) populations due to high numbers of recreational and commercial vessels. This region also holds a unique marine ecosystem, home to many taonga (treasured) species of cultural and economic importance. Regular surveillance, era...

Molecular biosecurity surveillance programs increasingly use environmental DNA (eDNA) for detecting marine non-indigenous species (NIS). However, the current molecular detection workflow is cumbersome, prone to errors and delays, and is limited in providing knowledge about eDNA beyond the spatial and temporal extent of the sampling. These limitatio...

Almost all of Earth's oceans are now impacted by multiple anthropogenic stressors, including the spread of nonindigenous species, harmful algal blooms, and pathogens. Early detection is critical to manage these stressors effectively and to protect marine systems and the ecosystem services they provide. Molecular tools have emerged as a promising so...

Complex microbial communities colonize plastic substrates over time, strongly influencing their fate and potential impacts on marine ecosystems. Among the first colonizers, diatoms play an important role in the development of this 'plastiphere'. We investigated 936 biofouling samples and the factors influencing diatom communities associated with pl...

Molecular tools of species identification based on eNAs (environmental nucleic acids; environmental DNA [eDNA] and environmental RNA [eRNA]) have the potential to greatly transform biodiversity science. However, the ability of eNAs to obtain "real-time" biodiversity estimates may be complicated by the differential persistence and degradation dynami...

Advances in high-throughput sequencing (HTS) technologies and their increasing affordability have fueled environmental DNA (eDNA) metabarcoding data generation from freshwater, marine and terrestrial ecosystems. Research institutions worldwide progressively employ HTS for biodiversity assessments, new species discovery and ecological trend monitori...

Abstract Molecular biosecurity surveillance programs are increasingly using environmental DNA (eDNA) for the early detection and monitoring of marine non-indigenous species (NIS). However, the current molecular detection workflow is cumbersome and the various stages can introduce errors and delays, which could hamper management efforts and restrict...

Non-native fish have been shown to have deleterious impacts on freshwater ecosystems in New Zealand. Early detection is critical for their effective management. Traditional capture-based techniques may not detect newly introduced fish, especially if they are present in low abundance. Molecular techniques that target environmental DNA (eDNA) have be...

Marine nonindigenous species (NIS) are spreading at an alarming rate internationally through anthropogenic activities such as shipping and aquaculture, affecting local biodiversity and negatively impacting the ecosystem and human well-being. Countries and international organizations have recognized this global threat and have begun implementing bio...

The proliferation of marine non-indigenous species (NIS) has been classified as a major threat to local biodiversity, human health, and the economy. Early detection and monitoring of marine NIS are essential for effective biosecurity management strategies. Many countries have started implementing powerful non-invasive molecular surveillance technol...

Marine plastic debris (MPD) are a global threat to marine ecosystems. Among countless ecosystem impacts, MPD can serve as a vector for marine 'hitchhikers' by facilitating transport and subsequent spread of unwanted pests and pathogens. The transport and spread of these non-indigenous species (NIS) can have substantial impacts on native biodiversit...

Environmental DNA has increasingly been used for assessing coastal biodiversity and detecting putative marine non-indigenous species (NIS). Although eDNA has shown to be a cost-effective and sensitive tool for environmental management programmes, uncertainties around how eDNA dynamics (dispersal and distribution) within a marine environment impact...

For over a decade, Pacific oyster mortality syndrome (POMS), a polymicrobial disease, induced recurring episodes of massive mortality affecting Crassostrea gigas oysters worldwide. Recent studies evidenced a combined infection of the ostreid herpesvirus (OsHV-1 mVar) and opportunistic bacteria in affected oysters. However, the role of the oyster mi...

Environmental DNA (eDNA) analyses are powerful for describing marine biodiversity but must be optimized for their effective use in routine monitoring. To maximize eDNA detection probabilities of sparsely distributed populations, water samples are usually concentrated from larger volumes and filtered using fine-pore membranes, often a significant co...

Environmental DNA (eDNA) metabarcoding has shown great promise as an effective, non-invasive monitoring method for marine biomes. However, long filtration times and the need for state-of- the- art laboratories are restricting sample replication and in situ species detections. Methodological innovations, such as passive filtration and self-contained...

Sea surface planktonic assemblages were sampled using environmental DNA at 1.5° latitudinal increments (from 39.5-11.5°S) following the 110°E meridian in the Eastern Indian Ocean to reveal factors structuring eukaryotic diversity. Metabarcoding the v4 region of the 18S rRNA gene revealed a eukaryotic assemblage over-dominated by amplicon sequence v...

In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called marine plankton or marine microbiome, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured...

The frequency and intensity of cyanobacterial blooms is increasing worldwide. Multiple factors are implicated, most of which are anthropogenic. New Zealand provides a useful location to study the impacts of human settlement on lake ecosystems. The first humans (Polynesians) arrived about 750 years ago. Following their settlement, there were marked...

Symbiodiniaceae are a diverse group of dinoflagellates, the majority of which are free-living and/or associated with a variety of protists and other invertebrate hosts. Maintenance of isolated cultures is labour-intensive and expensive, and cryopreservation provides an excellent avenue for their long-term storage. We aimed to cryopreserve 15 cultur...

The invasive Mediterranean fanworm Sabella spallanzanii (Gmelin, 1791) is a notifiable organism under New Zealand’s Biosecurity Act and is recognized as a marine pest of particular concern, that must be reported to the Ministry for Primary Industries (MPI), New Zealand. Since its first detection in 2008, great effort and financial resources are put...

Impacts of Marine Plastic Debris (MPD) on marine ecosystems are among the most critical environmental concerns of the past three decades. Virgin plastic is often cheaper to manufacture than recycled plastics, increasing rates of plastic released into the environment and thereby impacting ecosystem health and functioning. Along with other environmen...

Background: In recent years, the aquaculture industry of Crassostrea gigas has been severely impacted by geographically widespread outbreaks of a polymicrobial disease, the Pacific Oyster Mortality Syndrome (POMS). The aetiology of these recurring summer mortality events and the disease progression have notably been recently described in France, re...

1. Growing interest and affordability of environmental DNA and RNA (eDNA and eRNA) approaches for biodiversity assessments and monitoring of complex ecosystems have led to the emergence of manifold protocols for nucleic acids (NAs) isolation and processing. Although there is no consensus on a standardized workflow, the common practice for water sam...

Fish disease surveillance methods can be complicated and time consuming, which limits their value for timely intervention strategies on aquaculture farms. Novel molecular-based assays using droplet digital Polymerase Chain Reaction (ddPCR) can produce immediate results and enable high sample throughput with the ability to multiplex several targets...

Environmental DNA (eDNA) analyses are powerful for describing marine biodiversity but must be optimized for their effective use in routine monitoring. To maximize eDNA detection probabilities of sparsely distributed populations, water samples are usually concentrated from larger volumes and filtered using fine-pore membranes, often a significant co...

Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cor...

Understanding the historical onset of cyanobacterial blooms in freshwater bodies can help identify their potential drivers. Lake sediments are historical archives, containing information on what has occurred in and around lakes over time. Paleolimnology explores these records using a variety of techniques, but choosing the most appropriate method c...

Lakes and their catchments have been subjected to centuries to millennia of exploitation by humans. Efficient monitoring methods are required to promote proactive protection and management. Traditional monitoring is time consuming and expensive, which limits the number of lakes monitored. Lake surface sediments provide a temporally integrated repre...

Contaminants are often at low concentrations in ecosystems and their effects on exposed organisms can occur over long periods of time and across multiple generations. Alterations to subcellular mechanistic pathways in response to exposure to contaminants can provide insights into mechanisms of toxicity that methods measuring higher levels of biolog...

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples....

Freshwater eels are ecologically, and culturally important worldwide. The New Zealand long-finned eel ( Anguilla dieffenbachii ) and short-finned eel ( Anguilla australis ) are apex predators, playing an important role in ecosystem functioning of rivers and lakes. Recently, there has been a national decline in their populations due to habitat destr...

The Pacific oyster Crassostrea gigas is the world's most cultivated oyster and seed supply is heavily reliant on hatchery production where recurring mass mortality events are a major constraint. Outbreaks of bacterial infection via microalgal feed are frequently implicated in these mortalities. This study assessed the effects of feeding compromised...

Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workf...

Opportunities to study community level responses to extreme natural pulse disturbances in unaltered ecosystems are rare. Lake sediment records that span thousands of years can contain well resolved sediment pulses, triggered by earthquakes. These paleo-records provide a means to study repeated pulse disturbance and processes of resistance (insensit...

The dinoflagellate family Symbiodiniaceae comprises numerous divergent genera containing species whose ecologies range from endosymbiotic to free‐living. While many associate with invertebrates including corals, sea anemones, jellyfish, giant clams, and flat worms, others occur within the cytoplasm of large protists, most notably benthic foraminife...

Characterization of microbial assemblages via environmental DNA metabarcoding is increasingly being used in routine monitoring programs due to its sensitivity and cost‐effectiveness. Several programs have been developed recently which infer functional profiles from 16S rRNA gene data using hidden‐state prediction (HSP) algorithms. These might offer...

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-sp...

he field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and depositio...

Sea cage fish farms are increasingly situated over hard and mixed substrate habitats for production and waste-dispersion reasons; yet in many cases, these installations are not being effectively managed with respect to benthic impacts due to the lack of a practical sampling method. This study presents the first set of results from a newly developed...

Following the recent leap in biotechnologies and particularly in high-throughput sequencing techniques, environmental DNA and RNA (eDNA and eRNA) are increasingly being used for biodiversity assessments and monitoring of complex ecosystems – lakes, streams and coastal waters. Growing interest and affordability of eDNA/eRNA based tools have led to t...

The Mediterranean fanworm Sabella spallanzanii was first sighted in New Zealand in 2009 (most likely introduced via hull fouling) and has spread across multiple coastal locations. The species presents significant risks to ecological, economic, and societal values, and therefore is subject to targeted surveillance in 11 major ports and marinas, that...

With an increasing demand for finfish from aquaculture, the importance of monitoring the impact of aquaculture installations on coastal ecosystems becomes more and more important. The traditional approach employs macroinvertebrates as bioindicators to assess the ecological quality (EQ) of near-field benthic ecosystem, which is costly and time consu...

Sea-based fish farms are associated with strong benthic enrichment gradients and routine monitoring is usually required by regulation. Internationally a wide range of approaches exist for measuring the degree of benthic deterioration around fish farming activities, ranging from simple visual or odour assessments to the calculation of secondary indi...

The intestinal microbiome has recently been described for a variety of fish species and has been shown to influence host biology, including physiology, health and behavior. Knowledge of the intestinal microbiome of a species and how it can favorably be modulated to enhance production in different rearing systems is therefore of benefit for farmed f...

Plankton are central to planetary ecology, generating 50% of Earth’s atmospheric oxygen and forming the largest system of interconnected life at the base of the marine food chain. Yet, current oceanographic models aimed at predicting global climate change lack high-resolution biological data, emphasizing the need for innovative approaches to collec...

The introduction and spread of marine non-indigenous species (NIS) and pathogens into new habitats are a major threat to biodiversity, ecosystem services, human health, and can have substantial economic consequences. Shipping is considered the main vector for marine biological invasions; less well understood is the increased spread of marine NIS an...

Marine sediments contain a high diversity of micro-and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective...

Globalization has increased connectivity between countries enhancing the spread of marine nonindigenous species (NIS). The establishment of marine NIS shows substantial negative effects on the structure and functioning of the natural ecosystems by competing for habitats and resources. Ports are often hubs for the spread of NIS via commercial and re...

In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called plankton, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modelled at the planeta...

In 2016, many tropical corals worldwide were exposed to anomalously high temperatures due to one of the strongest El Niño events ever recorded. Bleaching impacts were reported on 23 islands within three archipelagos of French Polynesia (Tuamotu, Society and Marquesas archipelagos). A detailed study on the effects of elevated temperatures on corals...

Incidental detection of species of concern (e.g., invasive species, pathogens, threatened and endangered species) during biodiversity assessments based on high-throughput DNA sequencing holds significant risks in the absence of rigorous, fit-for-purpose data quality and reporting standards. Molecular biodiversity data are predominantly collected fo...

Molecular-based approaches can provide timely biodiversity assessments, showing an immense potential to facilitate decision-making in marine environmental management. However, the uptake of molecular data into environmental policy remains minimal. Here, we showcase a selection of local to global scale studies applying molecular-based methodologies...

Dimethylsulfoniopropionate (DMSP) is a key compound in the marine sulfur cycle, and is produced in large quantities in coral reefs. In addition to Symbiodiniaceae, corals and associated bacteria have recently been shown to play a role in DMSP metabolism. Numerous ecological studies have focused on DMSP concentrations in corals, which led to the hyp...

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In this study, the evolution of ballast water (BW) assemblages across different trophic levels was characterized over a 21-day cross-latitudinal vessel transit using a combination of molecular methods. Triplicate ballast water (BW) samples were collected every second day and size fractionated (<2.7 µm, 10 µm, >50 µm). Measurements of adenosine trip...

A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, tec...

Giant clams are keystone species of coral reef ecosystems. Like coral, giant clams harbor a vibrant community of algae and bacteria. But unlike coral, little is known about how these microorganisms help giant clams thrive or cause them to perish. To find out, authors of a new study placed giant clams in aquariums with one or two species of coral. D...

Background: Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While the effect of environmental change on the composition of the coral microbiome has been heavily studied, we know very little abo...