48
1998b)) nifH sequences suggested that they were unicellular even though they could
not be visualized or confirmed by microscopy (Zehr et al. 2016). Subsequent application of flow cytometry, probing by nifH PCR and single cell analysis showed that
UCYN-A was an unusual cyanobacterial symbiont with a greatly reduced genome
that had lost photosystem II, Rubisco, the entire TCA cycle and many other metabolic pathways (Thompson et al. 2012; Tripp et al. 2010; Zehr et al. 2008, 2016). It
also lacked pigment genes, which explained why it was not detected by conventional or fluorescence microscopy. UCYN-A has been reported from cooler waters,
including the Arctic, which has extended the range of habitats where N 2 fixation is
known to occur (Harding et al. 2018).
Heterotrophic N 2 Fixers
In addition to cyanobacteria, other noncyanobacterial Bacteria and Archaea may be
involved in N 2 fixation in the surface ocean (Figs. 4.2 and 4.4). Bacteria and Archaea
are diverse and abundant in the surface ocean, although dominated by species that
do not have nitrogenase genes. PCR (Farnelid et al. 2011) and metagenomic
(Delmont et al. 2018; Gradoville et al. 2017) studies have uncovered diverse nitrogenase genes (Fig. 4.4), but their significance, even now, is not yet known. In more
eutrophic regions, and in low O 2 waters, heterotrophic N 2 -fixing bacteria have been
detected and characterized by nifH sequencing (Farnelid et al. 2014; Löscher et al.
2014; Turk-Kubo et al. 2013). Heterotrophic genes have also been found associated
with detrital aggregates and algal cells (Farnelid et al. 2018), and in invertebrate
plankton (copepod) guts (Conroy et al. 2017), some of which are native to the copepod microbiome (Scavotto et al. 2015).
A few reports have attributed N 2 fixation to marine heterotrophs (Halm et al.
2012), but the evidence is indirect and heterotrophs have not been directly shown to
fix N 2 in low nutrient surface waters (Turk-Kubo et al. 2013). While they can have
gene abundances similar to that of the cyanobacterium UCYN-A (Moisander et al.
2014, 2017), only a small fraction of the heterotrophic nifH gene sequences present
have also been detected in mRNA (e.g. (Farnelid et al. 2011)) indicating that at
times not all are active (Langlois et al. 2015; Moisander et al. 2014) (see also Chaps.
7 and 8). A relatively large fraction of heterotrophic nifH genes were expressed and
coincident with high N 2 fixation rates in relatively eutrophic Danish estuarine waters
(Bentzon-Tilia et al. 2015). However, it is unclear given the energy requirements for
N 2 fixation and the sensitivity to O 2 inactivation how bacteria in oligotrophic environments can obtain sufficient organic matter and have high enough respiration
rates to protect nitrogenase from O 2 for nitrogenase activity (Riemann et al. 2010;
Turk-Kubo et al. 2013). A plausible explanation is that heterotrophic N 2 -fixing bacteria are largely associated with particles (Farnelid et al. 2018; Pedersen et al. 2018)
where there is a richer supply of organic matter for energy and where the physical
structure of the particle can restrict diffusion, allowing O 2 concentrations to be
reduced and N 2 fixation to occur.
4 Microorganisms and Habitats
1998b)) nifH sequences suggested that they were unicellular even though they could
not be visualized or confirmed by microscopy (Zehr et al. 2016). Subsequent application of flow cytometry, probing by nifH PCR and single cell analysis showed that
UCYN-A was an unusual cyanobacterial symbiont with a greatly reduced genome
that had lost photosystem II, Rubisco, the entire TCA cycle and many other metabolic pathways (Thompson et al. 2012; Tripp et al. 2010; Zehr et al. 2008, 2016). It
also lacked pigment genes, which explained why it was not detected by conventional or fluorescence microscopy. UCYN-A has been reported from cooler waters,
including the Arctic, which has extended the range of habitats where N 2 fixation is
known to occur (Harding et al. 2018).
Heterotrophic N 2 Fixers
In addition to cyanobacteria, other noncyanobacterial Bacteria and Archaea may be
involved in N 2 fixation in the surface ocean (Figs. 4.2 and 4.4). Bacteria and Archaea
are diverse and abundant in the surface ocean, although dominated by species that
do not have nitrogenase genes. PCR (Farnelid et al. 2011) and metagenomic
(Delmont et al. 2018; Gradoville et al. 2017) studies have uncovered diverse nitrogenase genes (Fig. 4.4), but their significance, even now, is not yet known. In more
eutrophic regions, and in low O 2 waters, heterotrophic N 2 -fixing bacteria have been
detected and characterized by nifH sequencing (Farnelid et al. 2014; Löscher et al.
2014; Turk-Kubo et al. 2013). Heterotrophic genes have also been found associated
with detrital aggregates and algal cells (Farnelid et al. 2018), and in invertebrate
plankton (copepod) guts (Conroy et al. 2017), some of which are native to the copepod microbiome (Scavotto et al. 2015).
A few reports have attributed N 2 fixation to marine heterotrophs (Halm et al.
2012), but the evidence is indirect and heterotrophs have not been directly shown to
fix N 2 in low nutrient surface waters (Turk-Kubo et al. 2013). While they can have
gene abundances similar to that of the cyanobacterium UCYN-A (Moisander et al.
2014, 2017), only a small fraction of the heterotrophic nifH gene sequences present
have also been detected in mRNA (e.g. (Farnelid et al. 2011)) indicating that at
times not all are active (Langlois et al. 2015; Moisander et al. 2014) (see also Chaps.
7 and 8). A relatively large fraction of heterotrophic nifH genes were expressed and
coincident with high N 2 fixation rates in relatively eutrophic Danish estuarine waters
(Bentzon-Tilia et al. 2015). However, it is unclear given the energy requirements for
N 2 fixation and the sensitivity to O 2 inactivation how bacteria in oligotrophic environments can obtain sufficient organic matter and have high enough respiration
rates to protect nitrogenase from O 2 for nitrogenase activity (Riemann et al. 2010;
Turk-Kubo et al. 2013). A plausible explanation is that heterotrophic N 2 -fixing bacteria are largely associated with particles (Farnelid et al. 2018; Pedersen et al. 2018)
where there is a richer supply of organic matter for energy and where the physical
structure of the particle can restrict diffusion, allowing O 2 concentrations to be
reduced and N 2 fixation to occur.
4 Microorganisms and Habitats