Introduction:
Shifting agriculture is practiced in 57 countries and contributes
significantly to the livelihood of approx. 250 million rural and
indigenous people worldwide (1). Based on combined data of existing
global Landsat-based deforestation data (2000-2014) and a very
high-resolution satellite image on the spatio-temporal pattern of
shifting cultivation, a recent study (1) puts 280 million hectares of
land under shifting cultivation worldwide inclusive of both cultivated
fields and fallows of the system. The majority of this is in the humid
and sub-humid tro{Heinimann, 2017 #1}pics, with 22 % of this in
Asia. Although many consider that this traditional practice is
environmentally sustainable and is successful for in-situ conservation
of agricultural/horticultural crop diversity, shifting agriculture has
also been reported as one of the causes of degradation of the forest
ecosystem (2). Thus, shifting agriculture is linked with the issues of
livelihood security and resilience among economically poor indigenous
people in the tropics and sub-tropics, and there is an urgent need to
understand the system empirically and to explore means to enhance its
productivity sustainably.
Shifting agriculture is known as ‘jhumming ’ in North-east India
(NEI), the Indian region of the Indo-Burma biodiversity hotspot, where
this practice is widespread. Sixty-five percent of the geographical area
of NEI is mountainous, where nearly about 1.73 million ha land is underjhum agriculture as a means of livelihood for 6,23,000 families
(3). Available research data on this indigenous system of agriculture is
limited and mostly confined to the description of cultivated crops, weed
problems during the cropping phase (4), the intensity of soil erosion
(5,6), although physiochemical properties of soil of shifting
agriculture fields and fallows have been better studied (7-10).
Although studies on the soil microbial community and its dynamics in
permanent agriculture (11-13) have established their role in maintaining
soil ecosystem health and crop productivity, biological properties and
below-ground microbial diversity in crop fields and fallows under
shifting agriculture have been very poorly studied. Whilst enumerations
of the bacterial and fungal populations in jhum fields during the
cropping phase have been made (5), there is no report on comparing
microbial diversity in the soil of adjacent fields of varying fallow
periods or associated with different crops. The composition of the soil
bacterial community is influenced by factors such as a) soil
disturbance, b) organic matter removal (16, 17) as well as c) dominant
tree species (18) in the region. Bacterial community
composition in soils also varies depending upon the root activity and
the type of crop/tree species that are unique in their rhizosphere
activity. A recent study showed that initial soil microbiome diversity,
explained the most similar in plant and herbivore associated microbial
communities (19). Accordingly, bacterial functioning in rhizosphere
niches and bulk soil can influence the overall health of crops, soil
fertility (20), and nutrient cycling (21).
A shifting agriculture system area represents fields of varying fallow
periods located close to each other with different plant species
composition and accumulation of plant biomass. This system provides an
opportunity for determining bacterial community changes in rhizosphere
and bulk soils of crops grown in fields established by burning
vegetation of different fallow periods of jhum cycles. A site in
the Mizoram state of NEI with 5, 8, and 20 years old fallow fields, each
of which was cultivated with rice (Oryza sativa ), maize
(Zea mays ), and arahar/pigeon pea (Cajanus cajan ) and
bacterial community dynamics in rhizosphere niches and bulk soil were
studied. We used both a conventional culture-based approach which is
limited to getting information of only 1% of total bacterial diversity
(21, 22), and NGS technologies which allowed high throughput screening
to study complex microbial communities and better insight into the
interaction between their plant host and abiotic environment (23). The
present study is based on our hypothesis that the bacterial community
present in the non-rhizosphere, rhizosphere, and root endophyte niches
determines the community structure in long and short fallow periods of
shifting cultivation. Accordingly, to test the hypothesis, we determined
the bacterial community composition by using (a) culture-independent
methods and (b) NGS sequencing in non-rhizosphere, rhizosphere, and root
interior endophyte niches of three different crops grown in three
different fallow period fields of shifting agriculture in the state of
Mizoram, North-east India.