The plant microbiome is a key determinant of health and productivity. However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p < 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. The dominant rhizosphere bacteria were Proteobacteria (29.70%), Acidobacteria (23.14%), Gemmatimonadetes (15.17%), Actinobacteria (8.31%), Chloroflexi (7.99%), and Bacteroidetes (5.15%). The dominant rhizosphere fungi were Ascomycota (83.52%), Mortierellomycota (7.67%), Basidiomycota (2.13%), Chytridiomycota (0.39%), and Olpidiomycota (0.08%). The distribution of dominant bacteria in different cotton rhizosphere soils and roots differed, with the dominant bacteria Pseudomonas (15.54%) and Pantoea (9.19%), and the dominant fungi Alternaria (16.15%) and Cephalotrichum (9.10%) being present in the greatest numbers. At sampling points in different ecological regions, the total numbers of cotton endophytic and rhizosphere microbiome OTUs from southern to northern Xinjiang showed an increasing trend. There were significant differences in the composition and diversity of rhizosphere microbes and endophytes during the entire cotton growth period and in representative ecological regions (p < 0.01), whereas rhizosphere microbes and endophytes showed no significant differences among the four growth periods and in representative ecological regions. RB41, H16, Nitrospira, and Sphingomonas play important roles in the microbial ecology of cotton rhizosphere soil. Pseudomonas accounted for a large proportion of the microbes in the cotton rhizosphere soil. This study provides an in-depth understanding of the complex microbial composition and diversity associated with cotton north and south of the Tianshan Mountains.

Drip irrigation under plastic mulch is widely used in Xinjiang, Northwest China. It can not only save water, but also reduce nutrient loss and improve fertilizer utilization. However, it is not clear whether the leaching occurs or not, what is the leaching amount? What is the relationship among fertilization, irrigation regimes, loss, cotton absorption, and cotton field under different fertilization and irrigation management under drip irrigation? Studying these issues not only provides reference for the formulation of fertilization and irrigation systems, but also is of great significance for reducing non-point source pollution. A long-term positioning experiment was conducted from 2009 to 2012 in Baotou Lake farm in Korla City, Xinjiang, with drip-irrigated cotton (Gossypium hirsutum L.) under different N fertilizer and irrigation amounts. The treatments were designed comprising Control (CK,0 N, 0 P, and 0 K with an irrigation of 480 mm) and the following three other treatments: (1) Conventional fertilize and irrigation (CON, 357 kg N hm–2, 90 kg P hm–2, 0 kg K hm–2, and irrigation of 480 mm); (2) Conventional fertilization and Optimizing irrigation (OPT, 357 kg N hm–2, 90 kg P hm–2, 62 kg K hm–2, and irrigation of 420 mm); and (3) Optimizing fertilization and irrigation (OPTN, 240 kg N hm–2, 65 kg P hm–2, 62 kg K hm–2, and irrigation of 420 mm). The results found that the leaching would occur in arid area under drip irrigation. The loss of total N, NH4+, P, N and P loss coefficient was higher under conventional fertilize and irrigation treatment while the loss of NO3- was higher under conventional fertilization and optimizing irrigation treatment. The correlations among N, P absorption by cotton, loss of NH4+ and total phosphorus were quadratic function. The total nitrogen loss and cumulative nitrogen application was lineally correlated. The loss of NO3- and cumulative nitrogen application was exponential. The nitrogen and phosphorus absorption by cotton under conventional fertilization and optimizing irrigation treatment was 24.53% and 35.86% higher than that in conventional fertilize and irrigation treatment, respectively. The cotton yield under conventional fertilization and optimizing irrigation treatment obtained higher than that in other three treatments. Therefore, the conventional fertilization and optimizing irrigation treatment was the optimal management of water and fertilizer in our study. These results demonstrate that reasonable water, nitrogen and phosphorus fertilize could not only effectively promote the absorption of nitrogen and phosphorus, but also reduce nitrogen and phosphorus losses under drip fertigation and plastic mulching.

Drip irrigation systems are becoming more and more mature and are now widely used to improve crop yield and nitrogen use efficiency in Xinjiang, NW China. However, it is not known if leaching is occurring or not and whether leaching will harm the water environment following N fertilization and drip irrigation. The purpose of our study was to estimate the leaching volumes, nitrogen losses, forms of nitrogen losses, and nitrogen loss coefficients under different N fertilization, P fertilization, K fertilization and irrigation regimes. A long-term field experiment was conducted from 2009 to 2015 in Baotou Lake farm in Korla City, Xinjiang, with drip-irrigated cotton (Gossypium hirsutum L.) being grown under different N fertilizer and irrigation regimes. The treatments were designed comprising 0 N, 0 P, and 0 K with an irrigation of 480 mm as the control(N0P0K0W480) and the following three other treatments: (1) 357 kg N·hm−2, 90 kg P·hm−2, 0 kg K2O hm−2, and irrigation of 480 mm (N357P90K0W480); (2) 357 kg N·hm−2, 90 kg P·hm−2, 62 kg K·hm−2, and irrigation of 420 mm (N357P90K62W420); and (3) 240 kg N·hm−2, 65 kg P·hm−2, 62 kg K·hm−2, and irrigation of 420 mm (N240P65K62W420). The results showed the following: (1) the leaching volume was determined by nitrogen fertilization, phosphorus fertilization, and the irrigation amount. In general, the leaching volume was highest under treatment N357P90K0W480. (2) The nitrogen loss was highest under treatment N357P90K0W480. (3) Nitrate nitrogen (NO3–) was the main form of nitrogen lost, followed by ammonium nitrogen (NH4+). (4) The annual nitrogen loss coefficients followed the order of: N357P90K0W480 > N357P90K62W420 > N240P65K62W420 > N0P0K0W480, with values of 0.85, 0.55, 0.30, and 0, respectively. The leaching volume, nitrogen loss, nitrate nitrogen, ammonium nitrogen, and annual nitrogen loss coefficient were lowest under the N240P65K62W420 treatment, except in the N0P0K0W480treatment. These results demonstrate that optimizing the management of water and nitrogen (N240P65K62W420 treatment) can effectively reduce nitrogen losses under drip fertigation and plastic mulching.