Introduction
Soils, plants and animals, as the primary objects of the grassland
study, have been investigated in the traditional researches separately.
Nevertheless, these issues are all the interconnected components in the
entirety of grassland ecosystem. Thus, new insight of internal
connections among biotopes of soil, phyllosphere and faeces in the
ecosystem are urgently needed to investigate the grassland. To evaluate
the components of the grassland ecosystem, the term “biotope” has been
applied for a long history. The concept of biotope has evolved with
quite different definitions along the development of ecology theory
(Dennis, Dapporto, & Dover, 2014; Olenin & Ducrotoy, 2006). With the
evolution of relative accompanying ideas, a new definition of the
concept biotope has been accepted extensively with the contemporary
meaning of the combination of substantial environment and assembled
organism species (Kobori, 2009; Rodiek & Thomas, 2007). Abiotic
components are attributed to the “habitat”, which means the physical
and chemical environment with the distinctive physiographic features and
geographical locations. The biotic components are attributed to the
“community”, which means groups of organism species in a particular
environment with the interaction of each other or the interconnection
between the organisms and environment (Dennis et al., 2014; Olenin &
Ducrotoy, 2006). Notably, compared to the entire ecosystem, Olenin and
Ducrotoy pointed out that the summation of all the biotopes does not
involve the energy and other linkages between the ecosystem components
(Olenin & Ducrotoy, 2006). In another words, apart from the biotopes,
the connections, especially the microbial linkages among the biotopes
also serve for the ecosystem running.
In a temperate grazed steppe, the ecosystem could be divided into three
biotopes of great importance: soil, phyllosphere and faeces. All of the
biotopes include the distinctive environmental features of abiotic
conditions. These abiotic conditions could also regulate and control the
distribution and migration of microbial community among the three
biotopes. Thus, every biotope with unique abiotic and biotic
characteristics is shaped into a sub-system of the pastureland
ecosystem. Concurrently, all these sub-systems interact with each other
by the web of food and predation. In such an environment, microbes play
a role of the vector and transporter for the energy flow (Andrés et al.,
2016; Bardgett & van der Putten, 2014; Wardle et al., 2004). This
function made microbiota as an important inhibitor for the environmental
disturbance to regulate and maintain the ecosystem (de Vries et al.,
2012).
As the main assembled organisms, soil, phyllosphere and fecal microbiota
play an essential role to regulate and control the ecosystem of the
grazed steppe. Initially, soil microbiota is deeply engaged participants
in the grassland ecosystem. Soil microbiota is the engine of the
biogenic elements in the soil-plant system to immobilize and regulate
the migration and transportation of nutrient elements owing to its role
of decomposer. Concurrently, soil microbiota plays a key role in the
soil assimilation process to the contaminant because the microbial
biotransformation is considerably correlated to the occurrence and fate
of the soil contaminants (Adrian, Szewzyk, Wecke, & Gorisch, 2000;
Bunge et al., 2003; Giller, Witter, & McGrath, 2009; Zhu, Yoshinaga,
Zhao, & Rosen, 2014). The last function of soil microbiota is
regulation of the greenhouse gas emission by affecting the
biogeochemical process of the elements (Brauer, Cadillo-Quiroz, Yashiro,
Yavitt, & Zinder, 2006; Erkel, Kube, Reinhardt, & Liesack, 2006; Lu &
Conrad, 2005; Mahecha et al., 2010; Yvon-Durocher et al., 2012). Another
critical microbial community controlling the grazed steppe ecosystem is
phyllosphere microbiota. Phyllosphere microbiota is termed as the
microbes who colonize in the aerial habitat on the surface of leaves
(Steven E. Lindow & Leveau, 2002; Vacher et al., 2016). The primary
phyllosphere microbial modification is the alteration to the properties
of plant surface (S. E. Lindow & Brandl, 2003). The substantial
heterogeneous aggregates of microbes also modify the traits of their
microhabitat to develop the nutrient availability expression of
phenotypes by the phylloplane (Horton et al., 2014; Monier & Lindow,
2003; Rastogi, Coaker, & Leveau, 2013; Whipps, Hand, Pink, & Bending,
2008). The phyllosphere epiphytic microbiota modify the plant by
controlling on plant disease and frost injury as well (Gourion,
Rossignol, & Vorholt, 2006; Knief, Ramette, Frances, Alonso-Blanco, &
Vorholt, 2010; Steven E. Lindow & Leveau, 2002; Melotto, Underwood,
Koczan, Nomura, & He, 2006). In addition, the microbial adaptation
regulates the resistance to the stress of the phyllosphere (Delmotte et
al., 2009; Vacher et al., 2016; Vorholt, 2012; Zimmerman & Vitousek,
2012). The last crucial compound to regulate the pasture is fecal
microbiota. The fresh fecal microbiota originates from the intestinal
tracts of large livestock. In a grazed grassland, 60-99% of the
nutrients ingested by the herbivorous livestock are returned into soil
as the excreta (Yanjiang Cai, Chang, & Cheng, 2017). After entering to
the soil through the faeces coverd patches, the fecal microbiota could
regulate the decomposition process of the faeces and control the release
of the nutrient element (Lin et al., 2009; Liu et al., 2018; Saggar,
Bolan, Bhandral, Hedley, & Luo, 2010). Furthermore, the physiochemical
properties, biological activities and plant growth are also influenced
by fecal microbiota (Y. Cai, Zheng, Bodelier, Conrad, & Jia, 2016;
Jost, Joergensen, & Sundrum, 2012). In the pasture, the fecal microbial
composition and the behavior of microbial community is a vital attribute
to impact the strategy and the method of livestock utilization and
management (Jost et al., 2012; Liu et al., 2018; Saggar et al., 2010).
Unfortunately, there is surprisingly little knowledge about the
migration and cycle of the microbial community among three substantial
biotopes: soil, phyllosphere and faeces in a grazed grassland. Although
the studies on soil, phyllosphere and fecal microbiota have been carried
out separately, the lack of the demonstration for microbial
transportation among these three biotopes limits the insight to the link
among components and energy flow path in the ecosystem. Neither any
study for how these microbial linkages served for the stability of the
ecosystem has been made.
In this study, we investigated the distribution of soil, phyllosphere
and fecal microbiota to figure out the microbial migration and cycle
among these biotopes using molecular method such as high-throughput
sequencing and real-time Polymerase Chain Reaction (qPCR) combining with
genomic analysis and machine learning classification. The hypotheses are
advanced as following: (1) Are there significant different distributions
among soil, phyllosphere and fecal microbiota? (2) What are the
interactions of the microbiota among three biotopes? and (3) What are
the dominant microorganisms playing key role in this migration and
cycle?