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.