SOILS, SEC 5 • SOIL AND LANDSCAPE ECOLOGY • RESEARCH ARTICLE
Do genetic diversity patterns of soil ammonia-oxidizing microorganisms
(AOM) match the habitat types of the NATURA2000 scheme?
Received: 27 February 2018 /Accepted: 21 May 2018
Springer-Verlag GmbH Germany, part of Springer Nature 2018
Purpose Despite the important role of soil ammonia-oxidizing microorganisms (AOM) in the biogeochemical cycle of nitrogen,
a unified view of the factors driving their spatial pattern of abundance and genetic diversity in terrestrial ecosystems is still
lacking. The objective of this study was to explore whether abundance and genetic diversity of AOM follow the existing diversity
of habitat types of the NATURA2000.
Materials and methods We evaluated the relative abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well
as their genetic diversity in pastoral landscapes of an eastern Mediterranean island. Focusing on six different NATURA2000
habitat types of Crete, the study of AOM was based on culture-independent techniques, while vegetation and soil data of each
habitat type were also collected and incorporated in the analysis.
Results and discussion Our results suggest that the relative abundances of soil AOB and AOA in the pastoral landscapes of Crete
are related to a limited number of soil factors, while their genetic diversity patterns are mainly explained by the dominant woody
plant families, and partially by the soil parameters, but do not match the habitat types of the NATURA2000 scheme.
Conclusions The variation of genetic diversity of soil AOM is not predicted from the habitat types of the NATURA2000 scheme.
Thus, NATURA2000 habitat types cannot serve as a management scheme of soil AOM.
Keywords Ammonia-oxidizing microorganisms
Aerobic ammonia oxidation to nitrite ions (ΝΟ
) is the first
and often rate-limiting step in nitrification and is driven by
ammonia-oxidizing microorganisms (AOM). For more than
a century, the role of ammonia-oxidizing bacteria (AOB)
was considered to be predominant in this process. However,
relatively recently, the discovery of archaea domain members
(ammonia-oxidizing archaea, AOA) capable of oxidation of
ammonia (Venter et al. 2004; Könneke et al. 2005; Treusch et
al. 2005) promoted the joint examination of both groups of
microorganisms (Leininger et al. 2006;Heetal.2007; Zhang
et al. 2012; Prosser and Nicol 2012;Huetal.2014), while
very recently, the exciting discovery of comammox (complete
ammonia oxidizers) within the Nitrospira genus that are ca-
pable of converting ammonia to nitrate in a single organism
and their broad environmental distribution added a new di-
mension to our knowledge of the biochemistry and physiolo-
gy of nitrification (Hu and He 2017).
Several studies have been conducted on the structure,
abundance, and diversity of AOA and AOB in a range of
terrestrial habitat types including forests (Stempfhuber et al.
2015), drylands (Sher et al. 2012, 2013;Huetal.2013),
grasslands (Yao et al. 2013), agriculture lands (He et al.
2007; Jia and Conrad 2009;Shenetal.2008; Gubry-Rangin
Responsible editor: Jizheng He
Electronic supplementary material The online version of this article
(https://doi.org/10.1007/s11368-018-2039-7) contains supplementary
material, which is available to authorized users.
* Stergios Pirintsos
Department of Biology, University of Crete, 714
09 Heraklion, Greece
Botanical Garden, University of Crete, Gallos Campus, 741
00 Rethymno, Greece
Journal of Soils and Sediments