The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from
streams of marine data. This metadata record describes the Expert Assessment "The state and trends of marine microbial community
composition". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where
available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section
of this record.
DESCRIPTION OF ECOLOGICAL PROCESS FOR EXPERT ASSESSMENT
The microbial community composition is a sensitive indicator of ecosystem status and health.
Marine waters typically contain 104-106 microbial (bacteria, archaea and unicellular algae) cells per milliliter, belonging
to hundreds to thousands of different species. This highly diverse and abundant community has an intimate connection with
its environment, the marine water. Marine microbial assemblages are the first responders to changes in the chemistry and
physical properties of the surrounding water. At the same time, microbes also shape the marine environment by driving most
of the biogeochemical cycles, supporting phytoplankton and primary productivity, contributing to the ocean carbon pump and
the sequestration of carbon in recalcitrant forms, and removing a wide range of organics and pollutants. Photoautrophic
microorganisms both form the base of the marine food-web and are responsible for ocean CO2 draw-down, while nitrogen fixing
bacteria are often essential for fueling the food-web with bioavailable nitrogen.
To this end, marine microbial assemblages display systematic and predictable change over seasons, across temperature climates,
with distance to shore, with depth in association with different water masses and in response to nutrient enrichment, eutrophication
and pollution, and the traits of marine microorganisms accurately reflect their niche adaptation.
Many of the most abundant clades of marine bacteria, including the Prochlorococcus, Synechococcus, Pelagibacter, Roseobacter
and the SAR86 cluster of the gammaproteobacteria have a very broad, if not a cosmopolitan distribution. However this is
not reflected in an underlying genetic identity. Rather, widespread distribution in these organisms is achieved by the existence
of closely related but discrete ecotypes that display niche adaptations. Closely related ecotypes display specific nutritional
or energy generating mechanisms and are adapted to different physical parameters including temperature, salinity, and hydrostatic
There is a global trend for rising incidence of disease in marine habitats. Within Australia there have recently been a number
of significant disease outbreaks in organisms including corals, starfish, oysters and fin-fish. While pathogenic microbes
constitute a very small minority of the marine microbial communities, their presence is of particular importance and interest.
DATA STREAM(S) USED IN EXPERT ASSESSMENT
This assessment is based on peer-review papers and reports. Data on state and trends and associated spatial and temporal
coverage are detailed in the publications provided in the reference list.
2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details]
• 2016 •
Assessment grade: Unclear
Assessment trend: Unclear
Confidence grade: Evidence and consensus too low to make an assessment
Confidence trend: Evidence and consensus too low to make an assessment
Comparability: Grade and trend are not comparable to the 2011 assessment
• 2011 •
Assessment grade: Very good
Assessment trend: Stable
Confidence grade: Limited evidence or limited consensus
Confidence trend: Limited evidence or limited consensus
CHANGES SINCE 2011 SOE ASSESSMENT
The 2016 assessment is similar to the 2011 assessment. With very little information on marine microbial communities with
which clear trends could be determined it was considered appropriate to alter the state assignment to ‘unclear’ rather than
‘very good’ and trend assignment to ‘unclear’ rather than ‘stable’ to avoid assumptions on the current state and recent trends.
Beman JM and Carolan MT (2013) Deoxygenation alters bacterial diversity and community composition in the ocean’s largest
oxygen minimum zone. Nature Communications 4, 2705
Brown et al (2009) Microbial community structure in the North Pacific Ocean. ISMEJ 3, 1374–1386
Brown et al (2012) Global Biogeography of SAR11 marine bacteria. Mol Syst Biol 8, 595
Brown et al (2014) A trait based perspective on the biogeography of common and abundant marine bacterioplankton clades.
Mar Genomics 15, 17-28
Canfield DE, et al. (2010) A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast. Science 330:1375–1378.
Carlson et al (2009) Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso
Sea. ISMEJ 3, 283-295
D’Souza et al 2016 Elevated surface chlorophyll associated with natural oil seeps in the Gulf of Mexico. Nature Geosciences
Fuhrman et al (2006) Annually reoccurring bacterial communities are predictable from ocean conditions. PNAS 103, 13104-13109
Giovanonni et al (2006) Genome streamlining in a cosmopolitan marine bacterium. Science 309, 1242-1245
Johnson et al (2006) Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science
Kalvelage et al 2015Aerobic Microbial Respiration In Oceanic Oxygen Minimum Zones. PLoSONE doi.org/10.1371/journal.pone.0133526
Kostka et al (2011) Hydrocarbon-Degrading bacteria and the bacterial community response in the Gulf of Mexico beach sands
impacted by the Deepwater Horizon oil spill. Applied and Environmental Microbiology 77, 7962-7974
Mazard et al (2012) Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus. Environmental
Microbiology 14, 372-386
Seymour et al (2012) Contrasting microbial assemblages in adjacent water masses associated with the East Australian Current.
Environ Microbiol Rep 4, 548-555
Ulloa O, Canfield DE, DeLong EF, Letelier RM, Stewart FJ (2012) Microbial oceanography of anoxic oxygen minimum zones. Proceedings
of the National Academy of Sciences, USA 109, 15996-16003
Wright JJ, Konwar KM, Hallam SJ (2012) Microbial ecology of expanding oxygen minimum zones. Nature Reviews Microbiology
QUALITY OF DATA USED IN THE ASSESSMENT
Data used to determine state and trend are based on systematic surveys and genomic studies describing microbial communities.
Methods and associated quality of data produced by those surveys are detailed in the publications provided in the reference
CUSTODIAN AND LOCATION OF DATA
Data in individual peer-review papers and reports are the IP of the relevant authors and institutions (details of specific
data sets used to generate the assessment have not been provided).
METHOD USED TO DETERMINE STATE OR RECENT TREND
An assessment of the current information available.
When citing this Expert Assessment in a list of references use the following format:
citation author name/s (year metadata published), metadata title. Citation author organisation/s. File identifier and Data
accessed at (add http link).