Perran L. M. Cook

• PhD
• Professor (Associate) at Monash University (Australia)

Microbialites—carbonate structures formed under the influence of microbial action —are the earliest macroscopic evidence of life. For three billion years, the microbial mat communities responsible for these structures fundamentally shaped the biogeochemical cycle of Earth. In photosynthetic microbial communities, light energy ultimately drives prim...

Cable bacteria are a unique type of filamentous microorganism, which can grow up to centimetres long and are capable of long-distance electron transport over their entire lengths. Due to their unique metabolism and conductive capacities, the study of cable bacteria has required technical innovations, both in adapting existing techniques and develop...

Methanogenesis is classically thought to be limited to strictly anoxic environments. While oxygenated oceans are a known methane source, it is argued that methanogenesis is driven by methylphosphonate-degrading bacteria or potentially is associated to zooplankton gut microbiomes rather than by methanogenic archaea. Here we show through in situ moni...

Permeable sediments, which make up almost half of the continental shelf worldwide, are potential sources of the important greenhouse gas N2O from coastal regions. Yet, the extent to which interactions between these sediments and anthropogenic pollution produce N2O is still unknown. Here we use laboratory experiments and modeling to explore the fact...

Most aerated cave ecosystems are assumed to be oligotrophic given they receive minimal inputs of light energy. Diverse microorganisms have nevertheless been detected within caves, though it remains unclear what strategies enable them to meet their energy and carbon needs. Here we determined the processes and mediators of primary production in aerat...

In marine sediments, microbial degradation of organic matter under anoxic conditions is generally thought to proceed through fermentation to volatile fatty acids (VFA), which are then oxidized to CO2 coupled to the reduction of terminal electron acceptors (e.g. nitrate, iron, manganese and sulfate). It has been suggested that, in environments with...

In marine sediments, microbial degradation of organic matter under anoxic conditions is generally thought to proceed through fermentation to volatile fatty acids (VFA), which are then oxidized to CO2 coupled to the reduction of terminal electron acceptors (e.g. nitrate, iron, manganese and sulfate). It has been suggested that, in environments with...

The Gippsland Lakes is the largest estuarine system in Australia. Over the last 2 centuries, this unique aquatic ecosystem has suffered substantial modifications mostly associated with anthropogenic impacts, including the creation in 1889 of an artificial channel to the ocean after European arrival, creating chronic salinisation in the system. Howe...

In soil ecosystems, obligately aerobic bacteria survive oxygen deprivation (hypoxia) by entering non-replicative persistent states. Little is known about how these bacteria rewire their metabolism to stay viable in these states. The model obligate aerobe Mycobacterium smegmatis maintains redox homeostasis during hypoxia by mediating fermentative hy...

Dihydrogen (H 2 ) is an important intermediate in anaerobic microbial processes, and concentrations are tightly controlled by thermodynamic limits of consumption and production. However, recent studies reported unusual H 2 accumulation in permeable marine sediments under anoxic conditions, suggesting decoupling of fermentation and sulfate reduction...

Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-o...

The effectiveness of these wetlands in removing nitrogen relies heavily on the biological processes that control its removal. Here, we used δ15N and δ18O of nitrate (NO3-) to assess the presence and the dominance of transformation processes of nitrogen in two urban water treatment wetlands in Victoria, Australia over two rainfall events. Laboratory...

Molecular hydrogen (H2) is an abundant and readily accessible energy source in marine systems, but it remains unknown whether marine microbial communities consume this gas. Here we use a suite of approaches to show that marine bacteria consume H2 to support growth. Genes for H2-uptake hydrogenases are prevalent in global ocean metagenomes, highly e...

Sustainable management of estuaries depends on understanding the synergistic effects of nutrients and hydrological factors on estuarine food webs. We examined how phytoplankton, zooplankton and selected fish larval counts (Acanthopagrus butcheri, black bream) vary in relation to groundwater inputs and environmental flow releases (EFRs) in a small,...

Eutrophication and stratification events have increased the incidences of hypoxia and anoxia in coastal environments. The depletion of oxygen in these environments can lead to a shift in biogeochemical processes such as denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The balance between denitrification and DNRA is critical b...

Nitrogen (N) is often the key nutrient limiting primary production in coastal waters. Quantifying sources and sinks of N is therefore critical to understanding the factors that underpin the productivity of coastal ecosystems. Constraining nitrogen inputs can be difficult for some terms such as N fixation and marine exchange as a consequence of unce...

Nitrogen (N) is often the key nutrient limiting primary production in coastal waters. Quantifying sources and sinks of N is therefore critical to understanding the factors that underpin the productivity of coastal ecosystems. Constraining nitrogen inputs can be difficult for some terms such as N fixation and marine exchange as a consequence of unce...

Molecular hydrogen (H2) and carbon monoxide (CO) are supersaturated in seawater relative to the atmosphere and hence are readily accessible energy sources for marine microbial communities. Yet while marine CO oxidation is well-described, it is unknown whether seawater communities consume H2. Here we integrated genome-resolved metagenomics, biogeoch...

The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide-and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communiti...

The identification of nitrogen sources and cycling processes is critical to the management of nitrogen pollution. Here, we used both stable (δ15N-NO3-, δ18O-NO3-, δ15N-NH4+) and radiogenic (222Rn) isotopes together with nitrogen concentrations to evaluate the relative importance of point (i.e. sewage) and diffuse sources (i.e. agricultural-derived...

Filamentous cable bacteria display long-range electron transport, generating electrical currents over centimeter distances through a highly ordered network of fibers embedded in their cell envelope. The conductivity of these periplasmic wires is exceptionally high for a biological material, but their chemical structure and underlying electron trans...

Ecological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in...

The permeable (sandy) sediments that dominate the world’s coastlines and continental shelves are highly exposed to nitrogen pollution, predominantly due to increased urbanisation and inefficient agricultural practices. This leads to eutrophication, accumulation of drift algae and changes in the reactions of nitrogen, including the potential to prod...

Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how so...

Nitrogen pollution in subtropical waters is rapidly increasing due to land-use change, but specific sources, transformations, and attenuation rates remain understudied compared to cooler temperate catchments. Here, we quantify high-resolution nitrate (NO3⁻-N) loads, sources and natural attenuation in a subtropical creek in Australia over contrastin...

Atmospheric trace gases such as dihydrogen (H2), carbon monoxide (CO) and methane (CH4) play important roles in microbial metabolism and biogeochemical cycles. Analysis of these gases at trace levels requires reliable storage of discrete samples of low volume. While commercial sampling vials such as Exetainers® have been tested for CH4 and other gr...

Estuaries have been identified as sources of nitrous oxide (N2O) emissions to the atmosphere but questions remain as to which production pathway(s) govern the oversaturation of N2O observed in most estuaries worldwide. Here, we use a suite of nitrate and N2O isotopes, as well as the 15N site preference signatures of N2O to assess (1) the relative i...

Ongoing land-use intensification in subtropical catchments is expected to release more inorganic nitrogen to downstream coastal waters similar to historical changes in temperate ecosystems. Here, we examined spatial and temporal drivers of stream nitrogen loads across a subtropical land-use gradient using the isotopic compositions of nitrate (NO3⁻-...

Filamentous cable bacteria display unrivalled long-range electron transport, generating electrical currents over centimeter distances through a highly ordered network of fibers embedded in their cell envelope. The conductivity of these periplasmic wires is exceptionally high for a biological material, but their chemical structure and underlying ele...

Atmospheric trace gases such as dihydrogen (H2), carbon monoxide (CO) and methane (CH4) play important roles in microbial metabolism and biogeochemical cycles. Analysis of these gases at trace levels requires reliable storage of discrete samples of low volume. While commercial sampling vials such as Exetainers® have been tested for CH4 and other gr...

The role of permeable sediments and subterranean estuaries as coastal nutrient filters is a question of key interest, particularly in areas with high nitrogen loadings. Here, we evaluated the effectiveness of a sandy subterranean estuary in cycling and removing nitrate using stable isotopes of N and O at natural (δ15N‐NO3− and δ18O‐NO3−) and enrich...

Increasing nitrogen (N) loads present a threat to estuaries, which are among the most heavily populated and perturbed parts of the world. N removal is largely mediated by the sediment microbial process of denitrification, in direct competition to dissimilatory nitrate reduction to ammonium (DNRA), which recycles nitrate to ammonium. Molecular proxi...

Due to decreases in seawater pH resulting from ocean acidification, permeable calcium carbonate reef sands are predicted to be net dissolving by 2050. However, the rate of dissolution and factors that control this rate remain poorly understood. Experiments performed in benthic chambers predict that reefs will become net dissolving when the aragonit...

Ecological theory suggests that habitat disturbance differentially influences distributions of generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resourc...

Constructed wetlands are increasingly used within urban areas to reduce pollutant runoff, including nitrogen. These environments are exposed to frequent wetting and drying events, and also increasing temperatures due to the heat island effect and seasonal variation. In this study, we have investigated the role of drying and rewetting of sediments a...

Permeable (sandy) sediments cover half of the continental margin and are major regulators of oceanic carbon cycling. The microbial communities within these highly dynamic sediments frequently shift between oxic and anoxic states, and hence are less stratified than those in cohesive (muddy) sediments. A major question is, therefore, how these commun...

Water treatment wetlands are increasingly being used to reduce pollutant loads including nitrogen (N) in urban runoff. Processes such as denitrification (DNF) and anaerobic ammonium oxidation (anammox), which remove N, and dissimilatory nitrate reduction to ammonium (DNRA), which recycles N, play an important role in controlling NOx (NO3⁻ + NO2⁻) r...

Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) are two competing nitrate reduction pathways that remove or recycle nitrogen, respectively. However, factors controlling the partitioning between these two pathways are manifold and our understanding of these factors is critical for the management of N loads in constructed...

Cable bacteria represent a newly discovered group of filamentous microorganisms, which are capable of spatially separating the oxidative and reductive half‐reactions of their sulfide‐oxidizing metabolisms over centimeter distances. We investigated three ways that cable bacteria might interact with the nitrogen (N) cycle: (1) by reducing nitrate thr...

Seagrass meadows form an ecologically important ecosystem in the coastal zone. The 15N/14N ratio of seagrass is commonly used to assess the extent to which sewage-derived nitrogen may be influencing seagrass beds. There have, however, been few studies comparing the 15N/14N ratios of seagrass beds, their associated sediments and, of critical importa...

In this paper, we investigate the period of successful spawning for black bream Acanthopagrus butcheri, an obligate estuarine species in southern Australia that typically spawn in spring and early summer. However, back‐calculated spawning dates of juveniles sampled in Gippsland Lakes, Victoria from February to May 2016 indicated that spawning was c...

Understanding the relationship between land use and the dynamics of nitrate (NO3-) is the key to constrain sources of NO3- export in order to aid effective management of waterways. In this study, isotopic compositions of NO3- (δ15N–NO3- and δ18O–NO3-) were used to elucidate the effects of land use (agriculture in particular) and rainfall on the maj...

The balance between estuarine denitrification and dissimilatory nitrate reduction to ammonium (DNRA) is critical for determining nitrogen loads received by oceans from inland waters. We aimed to determine the factors controlling the ratio between these processes and determining whether nitrogen was generally removed or recycled in estuaries. Rates...

Nitrogen is a pollutant of great concern when present in excess in surface waters. Living wall biofiltration systems that employ ornamentals and climbing plants are an emerging green technology that has recently demonstrated significant potential to reduce nitrogen concentrations from greywater before outdoor domestic re-use. However, there still e...

Seagrass meadows form an ecologically important ecosystem in the coastal zone. Excessive nitrogen inputs to the coastal zone pose a key threat to seagrass through eutrophication and associated algal overgrowth. The ¹⁵N / ¹⁴N ratio of seagrass is commonly used to assess extent to which sewage derived nitrogen may be influencing seagrass beds. There...

Changes in land use often increase nutrient loading to aquatic ecosystems, affecting primary productivity and water quality, with flow-on effects to consumers. We explored whether fish-assemblage composition, species diversity, and the representation and richness of ecological guilds were associated with catchment land use in 31 estuaries in Victor...

Stream physics set the limits A combination of physical transport processes and biologically mediated reactions in streams and their sediments removes dissolved inorganic nitrogen (DIN) from the water. Although stream chemistry and biology have been considered the dominant controls on how quickly DIN is removed, Grant et al. show that physics is wh...

Many estuaries are becoming increasingly eutrophic from human activities within their catchments. Nutrient loads often are used to assess risk of eutrophication to estuaries, but such data are expensive and time consuming to obtain. We compared the percent of fertilized land within a catchment, dissolved inorganic nitrogen loads, catchment to estua...

• Wetlands are often biogeochemical hotspots, and they can remove excess N via denitrification and assimilatory uptake. Wetlands are also susceptible to plant invasions, but the effect of invasive plants on denitrification in freshwater wetland sediments is not well‐studied. • Two distinct mechanisms suggest the potential for invasive plants to alt...

Plant species are diverse in form, function and environmental response. This provides enormous potential for designing nature-based stormwater treatment technologies, such as biofiltration systems. However, species can vary dramatically in their pollutant-removal performance, particularly for nitrogen removal. Currently, there is a lack of informat...

Bed sediment resuspension is a potential source of faecal microorganisms in the water column of estuaries. As such, it is important to identify the survival of faecal microorganisms in these bed sediments and understand how bed sediment resuspension impacts the quality of estuarine waters. This study explores the effect of bed sediment resuspension...

The balance between denitrification and nitrogen fixation is the key control of the availability of nitrogen in coastal ecosystems and thus the primary productivity of these environments. However, evaluating the importance of denitrification and nitrogen fixation over large spatial and temporal scales is problematic. In this study, a combined mass...

The effects of changes in catchment nutrient loading and composition on the phytoplankton dynamics, development of hypoxia and internal nutrient dynamics in a stratified coastal lagoon system (the Gippsland Lakes) were investigated using a 3-D coupled hydrodynamic biogeochemical water quality model. The study showed that primary production was equa...

Understanding the relationship between land use and the dynamics of nitrate (NO3−) is the key to constrain sources of NO3− export in order to aid effective management of waterways. In this study, isotopic compositions of NO3− (δ¹⁵N-NO3− and δ¹⁸O-NO3−) were used to elucidate the effects of land use (agriculture in particular) and rainfall on the maj...

Plants play a critical role in the nutrient removal performance of stormwater biofilters. However, the influence of biofilter design on plant growth and subsequent implications for treatment performance are not well understood. A 12 month, laboratory-scale biofilter column experiment was conducted to investigate the response of Carex appressa to va...

Dissolved oxygen (DO) is a key environmental variable that drives and feeds back with numerous processes. In the aquatic sediment that make up the hyporheic zone, DO may exhibit pronounced spatial gradients and complex patterns which control the distribution of a series of redox processes. Yet, little is known regarding the dynamics of hyporheic zo...

Seagrass meadows perform several important ecological roles in coastal areas. However, with multiple stressors threatening these aquatic plants, their current rate of decline is likely to increase, so understanding their ability to acclimate to a range of environments may be key to their survival. Light availability is critical for seagrass health,...

One of the goals of urban ecology is to link community structure to ecosystem function in urban habitats. Pollution-tolerant wetland invertebrates have been shown to enhance greenhouse gas (GHG) flux in controlled laboratory experiments, suggesting that they may influence urban wetland roles as sources or sinks of GHG. However, it is unclear if the...

The effects of changes in catchment nutrient loading and composition on the phytoplankton dynamics, development of hypoxia and internal nutrient dynamics in a stratified coastal lagoon system (the Gippsland Lakes) was investigated using a 3D coupled hydrodynamic biogeochemical water quality model. The study showed that primary productivity was equa...

Modeling and experimental studies demonstrate that ambient groundwater flow reduces the flux of water through the hyporheic zone, but the implications of this observation for stream N-cycling is not yet clear. Here we utilize a simple process-based model (the Pumping and Streamline Segregation or PASS model) to evaluate N-cycling over two scales of...

Phosphorus, a critical environmental pollutant, is effectively removed from stormwater by biofiltration systems, mainly via sedimentation and straining. However, the fate of dissolved inflow phosphorus concentrations in these systems is unknown. Given the growing interest in using biofiltration systems to treat other polluted waters, for example gr...

A 3-D coupled hydrodynamic-biogeochemical/ecological model was developed and validated for the coastal Gippsland Lakes system, Australia, to explore the importance of bioirrigation on sediment phosphorus dynamics and the subsequent effects on the formation of summer blooms of Nodularia spumigena. Bottom water phosphorus concentrations and sediment...

Carbonate sands form a major sediment type in coral reef environments and play a major role in organic matter recycling. It has previously been postulated that porosity of carbonate sand grains may lead to the formation of anoxic microniches that promote denitrification within these sediments. Under this conceptual model, we expect diffusion to exe...

Based on in situ microprofiles, chamber incubations and eddy covariance measurements, we investigated the benthic carbon mineralization and nutrient regeneration in a ~65-m-deep sedimentation basin of Loch Etive, UK. The sediment hosted a considerable amount of infauna that was dominated by the brittle star A. filiformis. The numerous burrows were...

Greywater is being increasingly used as an alternative water source to reduce potable water demand and to alleviate pressure on sewerage systems. This paper presents the development of a low energy and low maintenance greywater treatment technology: a living wall system, employing ornamental plants (including vines) grown in a sand filter on a side...

Permeable sediments are common across continental shelves and are critical contributors to marine biogeochemical cycling. Organic matter in permeable sediments is dominated by microalgae, which as eukaryotes have different anaerobic metabolic pathways to bacteria and archaea. Here we present analyses of flow-through reactor experiments showing that...

Many fish lay their eggs in nests, or redds, which they construct in sediment. The viability of eggs depends on many factors, particularly their oxygenation. Because dissolved oxygen is typically saturated within the stream channel, the dissolved oxygen distribution within the redd depends on whether or not hyporheic flow and transport occur within...

Urban estuaries throughout the world typically contain elevated levels of faecal contamination, the extent of which is generally assessed using faecal indicator organisms (FIO) such as Escherichia coli. This study assesses whether the bacterial FIO, E. coli is a suitable surrogate for Campylobacter spp., in estuaries. The presence and survival dyna...

Rates of denitrification (isotope pairing) and nitrogen fixation (acetylene reduction) were simultaneously measured in three temperate, intertidal Zostera muelleri meadows and adjacent non-vegetated tidal flats within Western Port, Australia. Net daily nitrogen fluxes ranged from −276 (net denitrification) to 520 μmol N/m2 d (net nitrogen fixation)...

Blooms of noxious N2 fixing cyanobacteria such as Nodularia spumigena are a recurring problem in some estuaries; however, the historic occurrence of such blooms in unclear in many cases. Here we report the results of a palaeoecological study on a temperate Australian lagoon system (the Gippsland Lakes) where we used stable isotopes and pigment biom...

Cable bacteria are long, filamentous sulphur-oxidizing bacteria that induce long-distance electron transport in aquatic sediments. They turn the seafloor into an electro-active environment, characterized by currents and electrical fields, and when present, they exert a strong impact on the geochemical cycling in the seafloor. However, cable bacteri...

Nutrient (N and P) loading may affect functioning in aquatic ecosystems by restructuring producer assemblages with flow‐on effects to consumers. Trophic niche occupancy and trophic organization of consumers are key components of ecosystem function that have been increasingly investigated using quantitative isotopic niche indices. These indices are...

Estuarine sediments are critical for the remediation of large amounts of anthropogenic nitrogen (N) loading via production of N 2 from nitrate by denitrification. However, nitrate is also recycled within sediments by dissimilatory nitrate reduction to ammonium (DNRA). Understanding the factors that influence the balance between denitrification and...

Blooms of noxious N2 fixing cyanobacteria such as Nodularia spumigena are a recurring problem in some estuaries. Here we report the results of a palaeoecological study on a temperate Australian lagoon system (The Gippsland Lakes) where we used stable isotopes and pigment biomarkers in dated cores as proxies for eutrophication and blooms of cyanobac...

An external electron donor is usually included in wastewater and groundwater treatment systems to enhance nitrate removal through denitrification. The choice of electron donor is critical for both satisfactory denitrification rates and sustainable long-term performance. Electron donors that are waste products are preferred to pure organic chemicals...

The storage and release of phosphorus by sediments can act as an important control on the formation of noxious blooms of cyanobacteria in lakes and estuaries. Here we studied the uptake and release of phosphorus associated with iron oxides within sediments of a lagoon system affected by recurring summer blooms of the cyanobacterium Nodularia spumig...

Bedforms are a focal point of carbon and nitrogen cycling in streams and coastal marine ecosystems. In this paper we develop and test a mechanistic model-the "pumping and streamline segregation" or PASS model-for nitrate removal in bedforms. The PASS model dramatically reduces computational overhead associated with modeling nitrogen transformations...

Many consumers display flexible feeding strategies that vary among individuals or populations, through life-history, or spatiotemporally. Despite the recognized influence of flexible feeding on the structure and dynamics of food webs, the consequences of these feeding strategies on the actual shape and characteristics of trophic position distributi...

Increased nutrient loads stimulate estuary primary productivity and can alter the structure and function of biological communities within estuaries, particularly when producer groups respond differently to changes in nutrient availability. Here, the relative influence of riverine inputs of nitrogen and phosphorus were compared to determine their co...

Seagrass in Port Phillip Bay is dominated by the eelgrass, Zostera nigricaulis, which occurs around the margin of the bay from the shallow subtidal zone to depths of up to 8 metres. Zostera provides crucial ecosystem services such as stabilising sediments and improving water quality, reducing coastal erosion, and increasing biological productivity...

Nitrogen fixation is an ecologically significant process in marine systems because nitrogen is typically the key limiting nutrient controlling productivity. Seagrass beds are often hot spots for nitrogen fixation owing to the mutualistic relationship between seagrass and nitrogenfixing sulphate-reducing bacteria. The objectives of this study were t...

Bedform celerity, the migration rate of ripples along a sediment bed, has previously been shown to have dramatic effects on oxygen distribution and transport within the hyporheic zone of permeable sediments. This has the potential to influence denitrification rates – in particular by increasing the coupling of nitrification and denitrification. To...

Nitrate (NO3−) contamination in groundwater is a worldwide phenomenon and a pervasive environmental problem, particularly when NO3−-enriched groundwater discharges into a nitrogen-limited estuarine environment through submarine groundwater discharge (SGD). SGD is often associated with eutrophication which ultimately alters the coastal ecology of th...

Anthropogenic nitrogen inputs to aquatic ecosystems can detrimentally affect ecosystem function; therefore, we need methods that identify nitrogen sources consistently among catchments. Nitrogen sources may be distinguished with stable isotope values (δ15N). This study tested if the isotopic values of biota and inorganic oxides of nitrogen (NO3. +...

The Gippsland Lakes, listed under the Ramsar Convention in 1982, have undergone chronic salinisation since the cutting in 1889 of an artificial entrance to the ocean to improve navigational access, exacerbated in the mid–late 20th century by increasing regulation and extraction of water from inflowing rivers. Both developments have had substantial...