Global Bunker Prices
Last update --:-- UTC
Home › Engine Room › Engine Room, Engine Room Operations, Fuel Systems, maintenance, marine engineering, Safety

17 February 2026 17 min read Engine Room, Engine Room Operations, Fuel Systems, maintenance, marine engineering, Safety
Share: X LinkedIn Email

Microbial Growth: Risks to Marine Fuel Tanks – Practical Management and Safe Operation

Microbial contamination in marine fuel tanks is an increasing concern as vessels contend with changing fuel blends, stricter regulations, and unpredictable voyages. Left unchecked, microbial growth can undermine propulsion, damage components, and threaten safety. This article delivers a comprehensive, chief engineer-level insight for managing micro-organisms in marine fuel tanks, based on real-world operational experience.

Contents

Introduction

Microbial growth, often called ‘diesel bug’, is an established threat to marine fuel systems, especially with the uptake of low-sulphur fuels and increased exposure to water ingress. Bacteria, yeasts and fungi thrive in the fuel–water interface or aqueous phase at the tank bottom, unseen during routine operation, but progressively compromising fuel quality, blocking filters, and damaging engines when conditions are right.

Historically, microbial contamination was sporadic, largely due to water ingress in poorly maintained tanks. Modern marine operations, regulatory-driven fuel changes, and less frequent tank cleaning have all contributed to a sharper risk profile. Understanding the precise mechanisms of contamination, detection, and remedy is now essential for every engineer at sea.

This article will describe operational risks, symptoms, and effective countermeasures, providing concrete procedures and lessons learned from actual shipboard incidents. The chief engineer must foster a culture of vigilance, regular maintenance, and knowledge sharing for microbial control.

The consequences of mismanaging microbial growth range from loss of propulsion to catastrophic engine damage, with compounding effects on safety, compliance, and cost. This guide aims to close practical knowledge gaps and foster robust, repeatable fuel system management.

Mechanisms of Microbial Contamination

Microbial contamination in marine fuel tanks is primarily driven by two factors: the ingress of water and the introduction of micro-organisms. Water may enter the tank via condensation, tank venting, contaminated bunkers, or leaks in tank structures. Wherever water and fuel meet, a niche exists for microbial activity.

The fuel itself, under modern refinery processes, frequently supports microbial growth as additives and reduced sulphur remove many natural inhibitors. Microbes hitchhike into the tank from bunkered fuel, dirty hoses, tank residues, or atmospheric exposure. Once introduced, their survival depends on nutrients (carbon sources in fuel), water, warmth, and oxygen content at the interphase.

Within the tank, micro-organisms congregate at the boundary layer. Anaerobic bacteria thrive in anoxic sludge; aerobic species colonise surfaces and the tank bottom, aided by tank construction features (strakes, dead zones, and poorly sloped floors). Biofilms quickly form, allowing resistance to biocides and cleaning, and supporting diverse microbial communities.

Microbial communities accelerate corrosion by secreting acids and byproducts as they digest fuel, producing hydrogen sulphide, organic acids, and gas. Once established, these populations become self-perpetuating unless aggressively removed.

Risk Factors and Fuel Types

Marine fuel risk profiles depend heavily on fuel type, bunkering habits, geographic location, and ship operational profile. Ultra low sulphur fuels (ULSF), VLSFO, and MGO/MDO fuels all tend to have higher risk due to decreased biocidal properties. Blended fuels tend to have increased phase separation and sludge formation, amplifying water retention at tank bottoms.

High humidity and temperature, characteristic of tropical trades, induce greater condensation in uncoated steel tanks. Ships which run mostly on one specific tank (leaving others cold and uncirculated) increase stagnation risk and allow stratification, perfect for microbe colonisation. Irregular tank cleaning, poor scupper and tank vent drainage, or defective tank coatings can all be factors for increased contamination.

Operational scenarios showing increased risk typically include: frequent short sea voyages, mixed fuel streams, erratic bunkering sources, or extended layup. Older vessels, where access to tank internals is limited, also run higher operational risk as residues are not thoroughly removed.

Even newly delivered ships are not immune, as contamination can arise rapidly in the presence of construction residues if commissioning flushing and drying are not performed with diligence. Premature filter clogging, even on new fuel systems, is often an early signal of this root cause.

Microbial Growth Life Cycle in Fuel Tanks

Once introduced, micro-organisms undergo a rapid multiphase growth cycle. Initially, they ‘lag’ as they adapt to tank fuel composition, temperature, and available water. Given suitable conditions, an exponential growth phase follows, quickly accelerating biofilm and sludge formation.

The fuel–water interface becomes colonised by bacteria and fungi, which develop sticky biofilms over the tank surfaces and in low-velocity zones. These films are notoriously resistant to basic cleaning and may shelter other microbial species, forming complex, resilient communities.

Over time, active communities metabolise hydrocarbons, generating dense biomass (sludge) which accumulates on tank walls, floors, and sumps. The sludges and biofilms impede drainage systems, block strainers, feed pumps, and clog filters repeatedly. By-products of metabolism, such as organic acids, promote corrosion (pitting and MIC – microbially influenced corrosion), frequently observable in tank bottom plate inspections.

Eventually, nutrient depletion or disruptive interventions (biocide treatment, cleaning) may lead to a temporary population crash. However, unless all residues are effectively removed, small surviving populations rapidly rebound, highlighting the need for persistent monitoring and cyclic maintenance intervention.

Failure Modes and Symptoms Onboard

Failure due to microbial growth manifests in several stages, often first detected by subtle symptoms before an outright system breakdown. The most frequent symptom is premature filter obstruction; what appears to be a fuel quality issue or filter installation defect may in fact have a biological root cause.

Other tell-tale failures include loss of fuel injector pressure, erratic engine performance due to fuel starvation, or difficulty maintaining fuel transfer pump suction. Shutdown of main engines or generators, in severe cases, can be traced to microbe-induced sludging of supply lines or persistent pre-filter clogging, with soft black or slimy contaminant visible on filter elements.

Persistent water separation in settling tanks, an increase in fuel-water interface volumes, and tank bottom sampling yielding hazy, black or viscous residues (distinct odours of rot or sour organic matter) are significant warning signs. Corroded uptake pipework and unexplained pitting within the tank structure are further diagnostic clues.

In extreme cases, contaminated fuel can deliver damaging acids and particulates to high pressure injection systems and pumps, leading to wear, galling, and complete mechanical failure. Prolonged cases effect regulatory compliance, as exhaust emissions or overboard discharges exceed required standards. Recognising progression of failure, through systematic symptom gathering, is essential to timely intervention and escalation.

Case Study: Operational Failure Due to Microbial Growth

Consider an 8,000 TEU container vessel operating on VLSFO, trading in the tropics. After a routine bunker, the engineering team observed that service filter DP (differential pressure) alarms tripped every 8–12 hours, despite filter cartridge renewals. Black, jelly-like mass adhered to filter surfaces, but fuel appearance in sight glasses remained normal. Initially, engineers attributed this to bad bunkers.

As the voyage continued, transfer pump suction pressure dropped sporadically (cavitation noise at pump), and standby generator began to trip on low fuel header pressure. A tank bottom sample was drawn, yielding a pungent smell and viscous emulsion at the water–fuel interface, confirming advanced microbial growth. Engine performance deteriorated further despite multiple filter changes and transfer line purges.

Interim actions involved switching tanks and dosing biocide via the settling tank in consultation with technical management. Within 24 hours, filter clog frequency dropped and header pressure stabilised, allowing safe arrival at port.

During layover, both fuel tanks were opened, revealing extensive pitting, black sludge, and persistent biofilms on surfaces and structural members. A full chemical clean was executed, and tank bottom plating was scheduled for recoating at the next drydock. This case underscores failure progression, the importance of integrating warning symptoms, and decisive, systematic response to avoid catastrophic engine failure.

Detection and Measurement Methods

Proactive detection is essential for shipboard microbial management. The routine practice involves drawing representative tank bottom samples and visually inspecting for phase separation, cloudiness, or sludge. However, visual checks alone are unreliable; modern kits provide more accurate on-site detection.

ATP bioluminescence tests and dip-slide test kits offer semi-quantitative readings for bacterial, yeast, and mould count. ATP-based meters identify all living microbial mass, while dip-slide tests, cultured at set temperatures, show specific colony growth after 24–72 hours. Both can identify the presence before major engine symptoms arise.

In advanced cases, specially commissioned laboratory analyses (fuel, sludge, and swab samples) will provide species-level identification and population density, informing management of persistent or resistant infestations. The standard for tank water content (Karl Fischer test) is also a crucial proxy, as high water correlates with elevated risk.

Onboard, measuring fuel filter DP, and noting changes in scheduled filter use rate, is an indirect method to spot building contamination, particularly where strainers or coalescers are prone to repeated, rapid clogging. Record filter change intervals systematically for trending.

Common Tools and Test Kits

For the practical shipboard engineer, several test kits are recommended. ATP swab or meter kits, such as those by 3M or Aquasnap, permit rapid detection of living biomass with immediate results, aiding in decision making before significant engine risk accumulates. Their use requires accurate sampling technique and prompt processing for reliability.

Dip-slide or paddle tests are cost-effective, requiring simple incubation (often in the ECR or galley oven at the recommended 28–30°C), for early warning. These tests yield visible colony growth, offering both qualitative and semi-quantitative results. While slower than ATP meters, they cost less and don’t require specialist handling.

Water detection pastes (Kolor Kut, etc.) are used in sampling rods, identifying water phase within sounding pipes. Karl Fischer titration on board (rarely, but more common on larger vessels) gives direct ppm moisture data, correlating closely with risk. Bacterial biocide dosers or injection pumps may also form part of the engineer’s toolkit during treatment cycles.

Ensure that all testing equipment is stored dry, away from fuel vapours and extreme heat, and is serviced/calibrated per manufacturer instructions. Train all junior engineers in both sampling and safe interpretation of microbial test kit results.

Containment and Remediation Options

On detecting microbial activity, immediate containment is crucial. Isolate affected tanks where possible and prioritise clean fuel use for propulsion. Water removal, by regular stripping and draining of all sumps and settling tank bottoms, is a top priority.

Dosage of suitable biocides (see dedicated section) is the industry standard for initial remediation, targeting live colonies before further biofilm formation or filter blockade. Biocide selection must be compatible with both fuel type and engine systems; refer to manufacturer recommendations and consult with fuel suppliers before application.

Should contamination become severe, tank-by-tank disinfection may be necessary. This involves emptying tanks (return all on-spec fuel through purifiers if possible), entering under permit with breathing apparatus and chemical PPE, and cleaning all surfaces of residue and biofilm. Manual removal of sludge is critical, supported by chemical washes and high pressure washing equipment designed for marine use.

For minor incidents, chemical fuel additives alone may suffice if mould blockage is not severe. But where filters are persistently blocking or engine reliability is threatened, only thorough tank cleaning and complete residue removal are effective in the medium-term.

Tank Cleaning Protocols

Safe, effective tank cleaning post-microbial contamination is a staged and controlled process. Plan tank entry via company isolation and confined space entry procedures. All personnel must be briefed on safety, including LEL (lower explosive limit) monitoring, continuous atmospheric testing, and rescue procedures.

The tank must be fully emptied, and remaining sludge manually stripped using scoops, squeegees, and suction hoses. Mechanical scrubbing tools, followed by application of manufacturer-approved chemical detergents, are applied to surfaces with visible biofilm. Allow dwell time per chemical instructions to ensure complete breakdown.

Rinse tanks thoroughly using fresh water at high pressure, removing all residues into approved sludge tanks or containers. Inspect tanks visually for remaining residues; manual spot scrubbing may be needed for persistent deposits. Multiple cycles of wash/rinse/dry are standard before tanks can be declared clean and put back into service.

After tank cleaning, all manhole gaskets must be checked/replaced, and further microbiological test samples should be recorded to certify cleanliness. Only then can tanks be considered fit for new fuel loadings. Record all cleaning cycles in the engine logbook and report to the management company for future audit and compliance.

Biocide Use and Dosing

Biocides remain the cornerstone of non-invasive microbial risk management. Use only approved, marine-grade fuel biocides compatible with your tank materials and engine/fuel system. Selection should be based on supplier fuel sample lab reports, with dosing calculated to achieve the recommended ppm levels for eradication or prevention.

Administer biocide as early in the fuel transfer process as practical, ideally directly to settling tanks during stripping/bunkering. Agitation ensures mixing throughout the fuel mass; recirculate for several hours if possible to ensure thorough contact. Dosing rates are critical: insufficient dose may select for resistant microbes; excess can cause problems with fuel combustion and system material compatibility.

Monitor the treated fuel system for filter blockages and dead biomass post-treatment. Biocides inactivate but do not remove dead organic matter; filter change frequency may rise initially as organisms die and slough off tank and pipe surfaces. This is normal but requires vigilance to avoid fuel starvation of vital systems.

Avoid over-reliance on chemicals alone. Biocide use is an interim and sometimes repeat measure pending thorough manual cleaning. Document all dosing, including rate, fuel volume, and time, in engine records for later review and trending.

Ongoing Preventative Practices

Routine prevention measures are the engineer’s best weapon against microbial recurrence. Schedule weekly stripping of all tank bottoms to remove free water and monitor soundings for unusual increases after heavy weather, major bunkers, or temperature swings.

Keep tank vent closures and overflows in top mechanical condition, checking for rust, open breaches, or blockages that enable water ingress. Monitor all deck access points, scuppers, and air pipes for signs of leakage or poor drainage after rain. Regular visual examination of sampling points for emulsion or foul odour is essential.

Add biocidal or stabilising additives into the settling tank after major bunkering, particularly if unfamiliar fuel sources or extended storage are anticipated. Routinely review bunkering reports for delivered water and microbiological contaminant readings, feeding into the ship’s risk matrix.

Implement a filter monitoring regime, logging all pressure differentials, changeout intervals, and associating events with fuel/oil transfers. Trend this data to identify evolving problems before they threaten safety. Engage junior officers and cadets in regular sampling, ensuring ship-wide expertise in detection and interpretation of early warning signs.

Troubleshooting Process Onboard

A structured troubleshooting approach is essential for effective response. Upon detection of filter blockages or odd odours/sludge from samples:

1. Confirm filter type and installation, check if blockages are not due to operational error or filter manufacturing defect.
2. Draw systematic samples from all tanks – top, mid, and bottom – visually inspect and test for water and biological contamination.
3. Assess recent fuel consumption, bunkering, and humidity data for abnormal exposures.
4. Use ATP/dip-slide kits, if available, to quantify the problem.
5. Strip and drain all affected tanks, routing contaminated fuel for shore disposal/purification where possible.
6. Dose with biocide as per dosage chart(s).
7. Increase filter monitoring/replacement frequency, and purge supply pipes if evidence suggests line blockage.
8. If blockages persist after biocide and water removal, plan for complete tank cleaning at the next available opportunity.

Escalate systematically: Only seek management company advice or technical support when the problem exceeds onboard resources or where system redundancy and safety are threatened. Record all troubleshooting steps in logbooks, including sample photos where possible.

Escalation and When to Seek External Support

Judicious escalation is key. Engage external support in cases of repeatable equipment failure post-intervention (after two or more cycles of biocide and stripping), evidence of advanced tank corrosion, or lack of effective access to internal tank components. Seek classification society advice if tank integrity (pitting, structural steel loss) threatens regulatory compliance or class rules.

Specialist laboratory analysis is warranted when in-house tests are inconclusive or where atypical symptoms (e.g., high acid gas emissions, unusual sludges) are encountered. Arrange shore-based cleaning when tank entry is hazardous, limited by working hours, or where large volumes of sludge exceed onboard disposal capacity.

Report all major contamination events to the management company, providing sample data, test results, and photos. Early notification enables procurement of specialist services, spares, and tailored shore support ahead of scheduled arrivals.

Failure to escalate at the right time can leave the vessel immobilised or non-compliant, with consequential cost and reputational risk. Encourage transparent reporting up the command chain, with documented approval for all extraordinary actions.

Summary and Key Takeaways

Microbial growth in marine fuel tanks is a routine but serious operational risk, accelerated by modern fuel trends and maintenance practices. The chief engineer must champion robust, routine water removal, tank cleaning, filter monitoring, and prompt biocide treatment at first sign of contamination.

Systematic sampling and trending of both biological and operational metrics are essential for developing a shipboard risk register. Early recognition, decisive containment, and full cleaning cycles ensure safe, reliable engine performance and regulatory compliance.

Train engine teams, maintain routine checks, and upgrade tools/test kits to support early intervention. Always escalate when operational or regulatory risk exceeds onboard control. Detailed logs, records, and visual evidence are critical for both internal review and external support.

A culture of vigilance and continuous improvement sets the standard for microbial growth management, preserving fuel quality, engine reliability, and ultimately, vessel safety at sea.

Review Questions

  1. What are the primary factors leading to microbial contamination in marine fuel tanks?
  2. Why are low sulphur fuels more susceptible to microbial growth?
  3. How does water promote microbial colonisation in fuel tanks?
  4. Describe the typical failure modes associated with microbial contamination.
  5. What are common operational symptoms of advanced microbial presence?
  6. How does biofilm formation complicate remediation efforts?
  7. What sampling strategy gives the most accurate indication of contamination?
  8. What precautions must be taken when entering a contaminated fuel tank?
  9. How should biocides be selected and dosed?
  10. What effect does biocide use have on subsequent filter maintenance?
  11. Which test kits provide rapid vs. longer-term detection of tank microbes?
  12. Describe the relationship between condensation and microbial proliferation.
  13. Why is filter DP trending an effective monitoring tool?
  14. When should external support or management advice be sought?
  15. What are the risks of incomplete remediation cycles?
  16. Explain the troubleshooting steps after rapid filter blockage events.
  17. What are the signs of microbially influenced corrosion (MIC)?
  18. Why is it important to log all maintenance and dosing details?
  19. Which shipboard practices reduce the recurrence of microbial contamination?
  20. What limitations exist for on-board detection kits?

Glossary

  • ATP Bioluminescence: A testing method that detects living cells by measuring the light released by ATP presence.
  • Biofilm: A sticky, resistant layer of microbial cells and their excretions attached to tank surfaces.
  • Biocide: Chemical agent used to kill living micro-organisms contaminating fuel.
  • Dip-slide: A laboratory tool/card used to culture and assess microbial activity in fluid samples.
  • Filter DP: Differential pressure monitoring across a filter, indicates blockage/clogging frequency.
  • MIC (Microbially Influenced Corrosion): Corrosion caused or accelerated by microbial action, often resulting in pitting.
  • Settling Tank: Tank allowing gravitational separation of water and contaminants from fuel before purification or use.
  • Sump: A low point in a tank designed for collecting water and sludge for later removal.
  • VLSFO: Very Low Sulphur Fuel Oil, a common marine fuel under IMO 2020 sulphur regulations.
  • Water Paste: A reagent used to detect the presence of water in fuel tanks via colour change.

ASCII Diagrams

Diagram 1: Typical Fuel Tank Cross-section with Microbial Risk Zones

+----------------------+
|                      | <-- Fuel
|      (Biofilm)       |
|----------------------|
|   (Water/Sludge)     |
+----------------------+
 ^                    ^
 |                    |
Tank Wall          Sump/Bilge
(Colonised)         (Drain)


Diagram 2: Filter and Supply System Failure Points

[Fuel Tank]--->[Strainer]--->[Pump]--->[Service Filter]--->[Engine]
                  |             |           |
                (Sludge)   (Blockage)  (DP increase)