Marine Bacteria and Archaea

1. Marine Bacteria and Archaea:
Diversity,
Adaptations, and Culturability
Prepared by: Emelyn C. Azucenas
Insructor I
Subject: MB 9 Microorganisms

2. Bacteria and Archaea represent major drivers
of the biogeochemical
large abundance,
high cell-specific activity, and
unique metabolic capabilities that include,
among others,
nitrogen fixation, (anaerobic) ammonia
oxidation, and
methane oxidation
Introduction
Gammaproteobacteria

3. • Total numbers of bacterial cells (Whitman et al. 1998):
• marine pelagic :
• surface sediments:
• and coastal waters:
Biomass, Diversity and Phylogenetic Composition
of Marine Bacterial Communities

4. Global bacterial biomass in the sub-seafloor biosphere:
5.4 x 1029 cells (Parkes et al. 2014)
 ~ 24% of global number and biomass of bacteria and archaea
 numbers demonstrate that the global
bacterial biomass of the open ocean and the marine subsurface is
similar to that of what is present in soils (2.6 10 29 cells) and that
marine Bacteria and Archaea
constitute a considerable part of the microbial biomass on Earth.

5. • Open ocean surface marine bacterioplankton typically consists of a few
dominant (sub)-phyla that decrease in abundance in the order
Alphaproteobacteria > Gammaproteobacteria > Flavobacteria and
Cyanobacteria.
• . Additional groups that are usually detected at low abundances are
the Betaproteobacteria, Firmicutes and Actinobacteria

6. • In oceanic deep waters,
• Gammaproteobacteria, Deltaproteobacteria and Actinobacteria
occur in higher relative abundances than at the surface. In coastal
waters, however, the relative proportion of Flavobacteria is
significantly higher (17 %) than in all other marine pelagic habitats
(Zinger et al. 2011).

7. In oxic surface sediments,
• Gammaproteobacteria and Deltaproteobacteria are dominant groups;
in addition Alphaproteobacteria, Acidobacteria, Actinobacteria and
Planctomycetes are abundant.
 The diversity of Archaea at the sediment surface
• is low where marine group I Thaumarchaeota dominate (Orcutt et al.
2011). In the first meters below the sediment surface,
• the high phylum level diversity of bacterial communities persists, and
also comprises Epsilonproteobacteria, Chloroflexi and
Thaumarchaeota (Parkes et al. 2014).

8. • In contrast, bacterial communities in the deep marine biosphere are
dominated by Gammaproteobacteria, Chloroflexi, and members of
the candidate phylum JS1, which together contribute an average of
>50 % of all 16S rRNA gene sequences.

9. • The estimates of the bacterial species richness even of individual
marine samples are twice as high as the total number of species that
has so far been validly described (

10. • Correlating phylogenetic similarity of marine bacterial communities or
the relative abundance of particular target phylotypes of Bacteria and
Archaea with the physicochemical characteristics of their respective
environment can yield initial information about potential drivers of
bacterial diversity and the niches of individual phylotypes.
Patterns and Potential Drivers of Marine Bacterial Diversity

11. • In taxonomy,
• Phylotype refers to an observed similarity used to classify a group of organisms based on their phenetic
relationship.
• This similarity, especially in the case of asexual organisms, may reflect their evolutionary relationships. The
term “phylotype” is rank-neutral, meaning it can describe groups at different levels, such as species, class, or
based on 97% genetic similarity or homology1.
•
• In the realm of microbiology, where the genomes of prokaryotes freely exchange genetic material,
phylotypes are particularly relevant. Unlike many eukaryotes (such as plants and animals), prokaryotes do
not fit neatly into Linnean taxonomy due to their unique genetic characteristics1.
• In summary, a phylotype helps us understand the relatedness of organisms based on observed similarities,
even when traditional taxonomic categories might not apply easily. 🌱
•

12. • Based on analyses of similarities between metagenomic sequences of
marine bacterioplankton communities, water temperature and
salinity were identified as the major environmental factors that
correlated with community composition. Water depth, primary
productivity and proximity to land constituted additional relevant
factors (Rusch et al. 2007)

13. Salinity was identified as the major environmental determinant of community
• composition on a global scale (Lozupone and Knight 2007).
• also the major environmental variable that is associated with the phylogenetic
differences of bacterial communities in freshwater, brackish and marine
sediments (Wang et al. 2012) and
• constitutes an important driver of the composition of bacterioplankton in
• inland waters (Wu et al. 2006).

14. • with increasing salinity, the abundance of Alphaproteobacteria
• and Gammaproteobacteria increases whereas that of
Betaproteobacteria, Actinobacteria and Verrucomicrobia decreases
(Cottrell and Kirchman 2003; Herlemann et al. 2011; Zhang et al.
2006).
• The bacterioplankton in brackish waters of the Baltic Sea appears to
be autochthonous and also harbors sequence types unique to this
environment, e.g., an uncharacterized member of the
Spartobacteriaceae (Verrucomicrobia).
• Unlike multicellular organisms, however, bacterial diversity in brackish
waters is not decreased compared to marine or freshwater
communities (Herlemann et al. 2011).

15. Life Strategies and Adaptation Mechanisms of Marine Bacteria and Archaea
Fig. 2.1 Conceptual representation of
the canonical adaptations of marine
Bacteria and Archaea, including the
copiotrophic lifestyle on marine
aggregates (A), chemotaxis towards
higher nutrient
concentrations liberated from marine
aggregates (B), and the adaptation to
oligotrophic conditions
in the free water (C

16. • The dominant primary producers in the nutrient limited euphotic
zone of the open oceans are cyanobacteria of the genera
Synechococcus and Prochlorococcus (see Chap. 3).

17. • Primary production by microalgae and cyanobacteria constitutes the
main source of organic carbon substrates of bacteria in the open ocean.
However, concentrations of carbohydrate monomers and amino acids
that can be taken up directly are only in the nanomolar range (Kirchman
et al. 2001; McCarthy et al. 1996).

18. • In the ocean,
higher substrate and nutrient concentrations are found on the
continental shelves (<150 m water depth) that cover 7 % of the surface
area of the world ocean but due to their often higher productivity
harbor a much larger proportion of the global number of bacterial cells
(Kallmeyer et al. 2012).
Adaptations to Temporal and Spatial Heterogeneity

19. • Diversity: Most marine bacterial communities are highly
diverse, and individual samples can comprise over 20,000
species. Different marine habitats, such as coastal surface
waters, subsurface open ocean waters, and sediments, are
colonized by distinct bacterial communities. Consequently,
global marine bacterial diversity must be very high but has
remained largely uncharted to date.

20. • Culturability Challenge: Despite their abundance, one major
obstacle is the difficulty in culturing most of the dominant
marine bacterial and archaeal phylotypes. These challenges
arise from an insufficient appreciation of their specific
physiological requirements and adaptations.

21. • Adaptations to Oligotrophic Conditions: Marine
environments often have low nutrient availability. Known
bacterial adaptations to oligotrophic (nutrient-poor) growth
conditions include:

22. • High affinity uptake systems: Efficient nutrient uptake.
• Low growth rates and cell sizes: Adaptations to conserve
resources.
• Streamlined genomes: Minimalistic genetic makeup.
• Little regulatory flexibility: Rigidity in gene expression.
• Physiological specialization: Tailored functions.
• Low loss rates due to grazing and viral lysis: Strategies to
survive in nutrient-scarce environments.

23. • Motility and chemotaxis: They actively move toward nutrients.
• Large cell sizes: Adaptations for efficient resource utilization.
• Adherence to particles: Staying close to nutrient sources.
• Specialized uptake systems for high molecular weight
substrates: Efficient nutrient acquisition.
• Excretion of exoenzymes: Breaking down complex
compounds.
• Broad substrate spectrum: Versatility in utilizing different
nutrients.

25. • Exploitation of Nutrient Hot Spots: Some lineages thrive in
nutrient-rich hot spots. These bacteria and archaea exhibit
contrasting features:

26. • Across their different habitats, marine bacteria are distributed rather
unequally.
• Surface seawater harbors between 10 4 and 10 7 cells ml−1 with an
average of 5 10 5
• cells ml−1 for epipelagic and coastal shelf waters. Deeper water layers
on average are
• colonized by 5 10 4 cells ml−1 (Whitman et al. 1998).

27. • Accordingly, the species richness of marine environments is similar to those
esti-
• mated for soils using comparable experimental approaches (Roesch et al.
2007).
• The total species diversity of marine Bacteria and Archaea most likely is
under-
• estimated by the above. This is suggested by the fact that a significantly
higher
• number of 799,581 of 16S rRNA gene sequences in GenBank is of marine
origin
• (Benson et al. 2013).
Biomass, Diversity and Phylogenetic Composition
of Marine Bacterial Communities