MCB 411: PETROLEUM MICROBIOLOGY: 4 UNITS

MICROBIOLOGICALLY INFLUENCED CORROSION

Corrosion is the destructive attack of a metal by its reaction with the environment. It is a

major key problem in oil and gas industries. It occurs in all areas of this industry from

exploration and production to transportation through pipeline systems. It resulted as a

result of production of High impurity products in crude oil and natural gas such as H 2S, CO2

Despite corrosion being of many mechanisms, the most important in this course is derived

from microorganisms and microbiological activities within a system, the form thus named

as microbiologically influenced/induced corrosion (MIC).

MIC is of significant interest and importance in oil and gas industry. It is defined as “An

electrochemical process in which micro-organisms can initiate, facilitate and accelerate

the corrosion reaction by the interaction of three components that make up this system:

metal, solution, and micro-organisms”. It accounts for more than 75% of corrosion in

productive oil wells and more than 50% of the failures in the pipeline system.

Microorganisms Associated with MIC

i. Fungi: These include filamentous fungi which enhance the corrosion by releasing organic
acids as well as yeasts. Fungi increase the acidity by producing acetic, formic, oxalic and

citric acid which results in accelerated corrosion.

ii. Bacteria

a) Sulphate Reducing Bacteria

They are anaerobic and reduced oxidized Sulphur compounds such as sulphate, sulphite

and thiosulphate, as well as sulphur to H2S.

b) Sulphite/Sulphide Oxidizing Bacteria

These are aerobic and produce sulphuric acid from Sulphur or sulphide.

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 c) Metal Reducing Bacteria

These could be aerobic or anaerobic or facultative aerobic in nature. They reduce

insoluble ferric compounds to ferrous ions.

d) Metal Oxidizing Bacteria

They are commonly referred to as iron oxidizing bacteria. They oxidize manganous ions

with manganic ions with associated deposition of manganese dioxide.

e) Acid Producing Bacteria

Many bacteria produce good amounts of organic and inorganic acids such as nitric acid

(HNO3), sulphorous acid (H2SO3), sulphuric acid (H2SO4), nitrous acid (HNO2) and carbonic

acid (HCO3).

Mechanisms of MIC

i. Cathodic Depolarization Theory

Cathodic depolarization theory demonstrates the corrosion derived by SRB through the

oxidation of cathodic hydrogen by an enzyme called hydrogenase.

ii. Iron Sulphide Mechanisms

This results because of the formation of sufficient amount of FeS is formed into the

system. The area covered with FeS starts to act like cathode whereas the biofilm area

starts to act like anode. The higher concentration of Fe 2+ ions in the system causes a

crack in the protective film, and results in an accelerated corrosion.

iii. Volatile Phosphorous Compounds

In this phenomenon, it was assumed that SRB accelerates the corrosion reaction through

the formation of corrosion products such as phosphine (H 3P), followed by the formation

of iron phosphide (FE2P)

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 iv. Anodic Depolarization

This forms the corrosion of forms the corrosion product FE(OH) 2. SRB reduces SO42- to

H2S followed by which further dissolution of H 2S directly influences the H + concentration

in the system. With the increased concentration of H + ions, the corrosion rate is

expected to be increased.

v. Metal Binding Exopolymers

Biofilms consists of microorganisms and extracellular polymeric substances (EPS). EPS

produces by sulphate reducing bacteria are capable of binding with metal ions to

expedite corrosion. The four steps of biofilm formation on the metal surface are as

follow:

 Transportation of organic material to metal surface

 Transportation of microbial cells from bulk to surface
 Attachment of microbial cells
 Growth within the biofilm.

Prevention and Control of MIC

MIC can be prevented and controlled in a number of ways such as use of cleaning methods

which could be mechanical or chemical. However, the most important and common method

is through the use of biocides.

Properties of a Biocide

 Selectivity against target microorganisms

 Capability to maintain its inhibitory effect in the presence of other compounds and
under operating conditions of the system
 Lack of corrosivity
 Biodegradability
 Low cost

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BIOFOULING

The attachment and growth of microorganisms on surfaces (the buildup of a slimy biofilm

layer generally termed biofouling) are well established phenomena in many environments

and industries. Despite the early recognition of the importance of biofilms and biofouling,

serious study only really began in the early 1940s with the pioneering work of ZoBell (1943),

who developed the early concepts for the different stages in biofilm development, which

lasted for 20 years or more.

In the simplest descriptive terms, a biofilm is a microbial accretion, adherent to a biological

or nonbiological surface, and enclosed in an extracellular polymeric matrix of its own

production. Biofilms (especially industrial biofilms) may also contain a significant amount

of inorganic substances (silt, scale, sand, and corrosion products), entrapped within the

extracellular polymeric matrix. Since planktonic marine bacteria were first observed to

preferentially attach to available surfaces (ZoBell, 1943), bacterial biofilms have been

implicated as the causative agent in a wide range of petroleum production and refining

problems. Their ability to thrive over a remarkable range of growth niches, from organic-

rich oil-water emulsions to the relatively oligotrophic seawater injection well environment,

suggests that bacterial communities can survive in virtually all fluid streams associated with

petroleum extraction and processing. An active microbial consortium has, indeed, been

confirmed throughout virtually all oil field process systems. Over the past 2 decades, it has

become increasingly apparent that biofilms are the preferred mode of growth for most

bacteria (Costerton et al., 1978), including those microorganisms of greatest interest to

hydrocarbon extraction and petroleum-refining industries.

Biofilms develop in response to both system conditions (external stimuli) and cell produced

chemical signals (internal stimuli). Both these stimuli have significant effects on the

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structure and activity of biofilms. Biofilms grown under high-shear conditions typically

develop a tenacious extracellular matrix and have a relatively thin cross-sectional

thickness, whereas those grown in quiescent, nutrientrich environs are typically thicker

(>lo0 pm in many cases) (Stoodley et al., 1997)

STEP 1: INITIAL ATTACHMENT

Biofilm formation on surfaces occurs rapidly following contact of a surface with nonsterile

fluids. Typically, within minutes, a conditioning film of organic molecules develops,

facilitating initial cell attachment to solid phases such as pipe walls, process plant vessel

interiors, or porous media.

STEP 2: BIOFILM INITIATION AND EPS PRODUCTION

Following initial surface attachment, many species of bacteria undergo a shift in protein

synthesis, which results in the production of extracellular polymers that serve to irreversibly

anchor the cell to the surface. Physiologic and metabolic changes resulting from transition

of the cell from a planktonic to a sessile state have led to the identification of a biofilm

phenotype. This phenotypic change may be accompanied by a lag phase of several hours as

the cell up-regulates biofilm-specific protein synthesis. Major observable changes in cell

phenotype as a result of cell attachment include the production of extracellular polymer

and the loss of flagella, and comparison of proteomic analysis of Pseudomonas putida under

sessile and planktonic condtions showed that attachment resulted in 15 up-regulated

proteins and 30 down-regulated proteins, confirming major changes in bacterial metabolic

pathways upon attachment to a surface (Sauer and Camper, EPS production serves to build

a threedimensional matrix in which cells may occupy <15% of the total biofilm volume

(Costerton and Stoodley, 2003). This three-dimensional structure influences the movement

of dissolved chemical species into and out of the biofilm, entraps particulate material and

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cell clusters from the bulk fluid, and creates diffusion gradients that lead to localized water

chemistry conditions, which may vary significantly from the bulk fluid interface to the

substratum.

STEP 3: BIOFILM STRUCTURAL DEVELOPMENT

The early simplistic model of a multilayered structure of biofilms developed in the 1980s

has been replaced by a more complex model for mature biofilms. Recent advances in

techniques such as microscopy, microelectrodes, biochemical markers, and

immunofluorescent staining have shown that as biofilm matures, bacterial growth tends to

concentrate in cell clusters, a condition which leads to the development of a complex

biofilm architecture.

STEPS 4 AND 5: BIOFILM MATURATION AND DETACHMENT

Biofilms are ever-changing entities, but biomass concentration typically reaches stasis after

a period of days or weeks, if left untreated. Depending on the species composition and

structure of the biofilm, bacteria located deep within a cell cluster may enter a stationary

phase. This condition of reduced activity has been shown to make cells less susceptible to

antimicrobial treatments that depend on active cell growth, such as antibiotics and more

likely to detach from the substratum. Biofilm maturity is characterized by periodic

detachment events, which include the release into the bulk fluid of either individual cells

or multicell clusters. As a result of these detachment events, overall biofilm thickness may

remain in a quasi-static state in the mature biofilm. Recent biofilm studies have shown that

cell detachment can occur as what has been termed swarming dispersal, where an inner

region of a cell cluster liquefies, with the interior biofilm cells reverting to the planktonic

state, complete with flagella. These cells then “swim” from the biofilm into the bulk fluid,

completing the biofilm life cycle

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ENVIRONMENTAL POLLUTION BY PETROLEUM HYDROCARBON

Pollution has been defined as an undesirable change in physical, chemical and biological

characteristics of air, water and land. The sudden input of large amount of hydrocarbon

(HCO(s) associated with spillages stresses the environment in a way not imposed by natural

hydrocarbons. Oil spillage as it is referred to have deleterious impact on flora, fauna and

microbiota of the ecosystem.

The economic life of the populace in the affected area is disrupted and the fragile

ecobalance is usually disturbed. Farm lands, navigational activities, availability of clean

potable water and fishing resorts are badly affected. Spill incidence remains amongst the

various mean by which petroleum HCO pollute the environment. Crude oil spillage can occur

at different stages of production and transportation either for export or refining processes.

The spillages can be categorized depending on the barrels of oil spilled into three (3):

Minor Impact: < 25 bbl in inland water or 250 bbl on land that does not pose a threat to

public health.

Medium Impact: Discharge of oil 25 – 250 bbl on inland water or 250 – 2,500 bbl on land

offshore and coastal waters.

Major Impact: Any discharge over > 250 bbl in inland water or > 2,500 on land offshore and

coastal water. Any uncontrolled well blow out, pipe rupture or storage tank failure.

Tanker Wreckages

It results from the wreck of oil tankers whose sizes and capacity have increased

tremendously in recent times with advance in technology. In 1957, a tanker wrecked off

Baja, California spilling about 9,000 tonnes of diesel fuel containing a high proportion of

Aromatics. Argea Prima in July, 1962 spilled about 5,000 tonnes of oil in the port of

Guatemalla, Puerto Rico.

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Well blow out

Well blow out does not occur frequently, however it results in the largest volume loss per

time if not brought under control on time. The Ixtoc oil well blow out in 1979 remain a case

study in history with about 500,000 tonnes of oil loss. Ekofisk, in the North Sea recorded

200,000 tonnes of oil losses. In Nigeria, 400,000 tonnes of oil was spilled in the ‘Funiwa 5’

oil well blow out of 1980. Also, Shell 2, Sefrap (Elf), and Obagi 21 blow out of 1972

respectively.

Causes of Oil Pollution incidence in Nigeria

Causes of oil pollution incidences in Nigeria can be attributed to:
i. Burst/Rupture/Corrosion of flow-line/Pipelines
ii. Over pressure failure/Overflow of process equipment components.
iii. Sabotage of well heads and flowlines.
iv. Hose failure during tanker loading.
v. Failure along pump discharge manifolds.
vi. Blow outs.
vii. Sabotage
viii. Illegal bunkering

Oil spills incidences in Nigeria (1976 – 1986)

YEAR NET VOL. SPILLED (BBLS)

1976 26,157
1977 32,879
1978 489,294
1979 694,117
1980 600,511
1981 42,723
1982 42,841
1983 48,351
1984 40,209
1985 11,876
1986 2,038,710

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Selected oil spill incidences around the world

VESSEL DATE QUANTITY SPILLED LOCATION

Arrow 1970 12,000 Canada
Bohlen 1976 10,000 Brittany
Chryss 1970 31,000 N. E. Bermuda
Ennerdole 1971 42,000 Seychelles Island
Gino 1979 40,000 Brittany
Poly Commander 1970 13,000 Spain
Urqiola 1976 107,000 Spain
Amoco Cadiz 1978 230,000 Brittany

Effect of Oil pollution

Marine ecosystem Is the ultimate recipient of surface run-off from soil and rivers which

finally go into lagoons. Devastating oil spills occur more often in the oceans. e.g Gulf of

Mexico. The response of microbes to spillages in various ecosystems varies but usually there

is increase in number of hydrocarbon degraders. Algal diversity and consumption will shift

as a result of pollution. The species diversity in the coral reefs is badly affected.

Invertebrates such as zooplanktons, crustaceans as well as vertebrates are adversely

affected. The larval stages of shrimps are very susceptible to oil spill. Studies on the toxicity

of oil to mangroves reveals that Avicenia sp will die within a week while it is mild on

Rhizophora sp.

Freshwater ecosystem

It has been reported that there are drastic changes in the levels of microbial populations

and the ability of indigenous microorganisms to degrade the hydrocarbon spilled/polluting

the environment. Nitrogen fixation is reduced to about 8% after exposure to HCO. It has

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been reported, that some hydrocarbons not originally present in the crude were found

present, after exposure to the estuarine community in the water body.

Soil ecosystem

Contamination of the terrestrial ecosystem affects not only the microbiota of the soil but

also the resident microcommunity. It has negative effects on the pH community both by

contact toxicity and indirect deleterious effects. Among the various effects are oxygen

deprivation of roots and generation of phytotoxic compounds such as hydrogen sulphides.

Herbaceous vegetation is quickly killed.

MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

Susceptibility to degradation varies with the type and size of the hydrocarbon molecule.

N-alkane of intermediate chain length (C10 – C24) is degraded most rapidly. Short chains are

toxic to many microorganisms, but generally evaporate from oil slick, rapidly. Very long

chain alkanes become increasingly resistant to biodegradation. As the chain length

increases and the alkanes exceed a molecular weight of 500, the alkanes do not serve as

carbon sources.

Branching, in general reduces the rate of biodegradation. Aromatic compounds, especially

of the condensed polynuclear type are degraded more slowly then Alkanes. Alicyclic

compounds are frequently unable to serve as the sole carbon source for microbial growth

unless they have a sufficiently long aliphatic side chain, but they can

be degraded via cometabolism by two or more co-operating microbial strains with

complementary metabolic capabilities.

Alkanes

The preliminary attack on alkanes occurs by enzymes that have a strict requirement for

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molecular oxygen, that is monooxygenases or dioxygenases. One atom of 02 is incorporated

into the alkane, yielding a primary alcohol.

Pathway of degradation of Aliphatic hydrocarbons by Microorganisms

Though not in all cases, the initial attack is targeted at the terminal – CH3 (Methyl group)

thereby forming a primary alcohol. This is in turn oxidized to an aldehyde and fatty acid.

Occasionally both terminal-CH3 are oxidized in this manner, resulting in the formation of a

dicarboxylic acid. This variation is referred to as diterminal or ω-oxidation. This is one of

the several ways to bypass a block to β-oxidation due to branding of the carbon chain. Once

a fatty acid is formed, further catabolism occurs by the β-oxidation sequence. The long-

chain fatty acid is converted to its acyl coenzyme-A form and is acted upon by a series of

enzymes with result that an acetyl CoA group is cleared off and the fatty acid is shortened

by a two-carbon unit. This sequence is then repeated. The acetyl CoA units are converted

to CO2 through the TCA cycle. Thus the end products of hydrocarbon mineralization are CO 2

and H2O.

FUTURE PROSPECTS: THE ROLE OF MICROBIOLOGY IN THE ENERGY TRANSITION AGENDA

OF THE PRESENT ADMINISTRATION

From petroleum to renewables, microorganisms plan an integral role in our society. The

degree of their impact is evaluated based on several factors, including the environment,

geological conditions, temperature, nutrient availability, and microbial community

structure. Microorganisms can radically influence the energy sector, both positively and

negatively. On the one hand, microbes are potential energy “powerhouses” through their

abilities to capture and convert CO2 into other energy carriers, such as sugars and hydrogen.

For example, the photosynthetic cyanobacterium Synechococcus elongatus utilizes solar

energy to directly convert CO2 into chemicals such as omega-3 fatty acids and alcohols.

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Scaling-up microbial-based solar capture into a form of energy “refinery” has been under

development across several nations with the hope of one day providing fuel on a commercial

level. Similar technological advances have also been made on microbial fuel cell and biofuel

production, to further increase the fraction of bio-generated fuels in our current economy.

For example, microbial fuel cells are seen as a highly promising alternative technology for

self-sustaining wastewater treatment, that theoretically ends with a net energy positive

reaction while recovering heavy metals such as cobalt, cadmium, and chromium.

However, constructing a large-scale microbial fuel cell is challenged with operation-related

energy losses, as well as the high costs associated with the infrastructure, that is, electrode

materials and platinum-based catalysts. In addition, the shifts in the microbial community

due to changes in the environment, that is, electron acceptor and donor availability, pH,

and temperature will nonetheless impact the performance of the microbial fuel cell. This

is further complicated by the production of negative metabolic products such as hydrogen

sulfide due to the activities of sulfate-reducing prokaryotes (SRPs). In fact, production of

hydrogen sulfide by the SRPs is a universal issue that is observed across several energy

sectors, ranging from petroleum to renewables. The earliest recorded observation on

microorganisms-induced oilfield reservoir souring was in 1926, and since then several groups

of SRPs have been isolated and studied with the ultimate goal to find an effective mitigation

strategy. In addition to the SRPs, characterization of microorganisms from other metabolic

groups has expanded our knowledge on MIC, microbial-induced carbonate precipitation,

microbially enhanced oil recovery, etc., and since then several groups of SRPs have been

isolated and studied with the ultimate goal of finding an effective mitigation strategy. In

addition to the SRPs, characterization of microorganisms from other metabolic groups has

expanded our knowledge on MIC, microbial-induced carbonate precipitation, microbially

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enhanced oil recovery, etc. Interestingly, the same concerns studied within the petroleum

sector is being raised again within the renewable storage systems, particularly for hydrogen

storage, CO2 storage, and geothermal energy system. As our energy system undergoes rapid

transitions with an increased number of pilot studies conducted on new underground energy

technologies, new possibilities were opened to expand the current understanding of

microbial activity and impact. For example, the impact of high hydrogen partial pressure

within underground hydrogen storage on microbial growth is currently unclear. Whether

such high partial pressure will decrease microbial activity by inhibiting hydrogen-oxidizing

enzymes, such as hydrogenases, is largely unknown. In addition, many of these underground

storage systems are considered hostile to microorganisms due to high salinity and low

nutrient availability, yet microorganisms specifically adapted to such environments have

been isolated, with many of them capable of producing sulfide, methane, acids, and other

undesirable metabolic products.

These clearly put forward the importance of knowledge transfer from petroleum

microbiology to renewables. Many of the microbial techniques developed within the oil and

gas sector, such as functional gene detection to target MIC microorganisms, can be applied

to other energy systems, including hydrogen storage. Furthermore, the use of depleted oil

reservoirs for hydrogen storage offers new potential for microbially triggered effects and

risks due to the supply of oil organics for microbial growth. As learned previously from

petroleum microbiology, this is a field that requires multidisciplinary research between

microbiologists, geochemists, physicists, reservoir engineers, and operators. Such

collaboration will need to continue with the addition of modeling research to make accurate

predictions on microbial risks and ensure a smooth and safe energy transition for our

society.

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