Partial replacement of fertiliser nitrogen with organic material derived from animal and human waste in a two year field experiment in China: bacterial community results

Ensuring global food security by increasing yields while reducing environmental impacts is currently a major agricultural challenge. This will require transition towards more sustainable practices such as reduction in chemical fertilisation. We conducted a field experiment with vegetable production in China examining partial substitution of chemical fertiliser with organic forms considering key sustainability metrics: productivity, soil health, environmental impacts and microbial communities. A 2-year vegetable growth field experiment in China was used to assess impacts of partial replacement of fertiliser N with organic material derived from animal and human over eight rotations. The experiment began in July 2017 with the application of six di?erent fertilisation treatments. With the exception of a zero N fertiliser addition control the treatments aimed to balance fertilisation on the basis of total N added as follows: 1) ZeroN (non-N fertilisation control); 2) ConN (conventional chemical fertiliser as urea 3) M25 (25% substitution of chemical fertiliser N with composted pig manure); 4) M50 (50% substitution with composted pig manure); 5) S25 (25% substitution with composted municipal sludge); and 6) S50 (50% substitution of chemical fertiliser with composted municipal sludge). Four vegetable crops were cultivated in each year: water spinach (Ipomoea aquatica), spinach (Spinacia oleracea L.), pak choi (Brassica chinensis L.), and amaranth (Amaranthus tricolor L.). Composite soil samples were collected from the 24 plots (4 reps × 6 treatments) at four time points (96 samples in total) at harvest of spinach in December 2017 and 2018 (second and sixth crop cycle, 6 months and 18 after treatment inception); and 2 times on amaranth harvest in June 2018 and 2019 (fourth and eighth crop cycle, after 12 and 24 months). Six independent soil cores (5 cm diameter covering 0–20 cm depth) were taken per plot and mixed. DNA was extracted from soil using the Fast DNA SPIN Kit (MP Biomedicals, Santa Ana, CA, USA) according to the manufacturer's instructions. Bacterial 16S rRNA gene fragments (V4-V5) were sequenced following PCR amplification with primers 515F (5'-GTGCCAGCMGCCGCGGTAA-3'; Turner et al. 1999) and 907R (5'-CCGTCAATTCMTTTRAGTTT-3'; Lane et al. 1985). Products were purified, pooled in equimolar concentrations and paired-end sequenced (2?×?300bp) on an Illumina MiSeq platform (Illumina, San Diego, USA) by Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China) using standard protocols. We observed a significant, but small effect of fertiliser treatment on alpha bacterial diversity. This contrasted with assessments of community structure where there was a strong, significant effect of fertiliser with the no fertiliser and organically amended samples being quite similar, but the conventional fertiliser samples being distinct from all other treatments. Moreover, differences in bacterial communities between fertiliser treatments appeared to increase through time. Analysis of bacterial communities using the 16S rRNA gene amplicons in addition to other measures including the abundance of key genes involved in the nitrogen cycle and soil chemical parameters, suggests a mechanistic link to the observed differences in agroecosystem functioning in this experiment. The study provides key insights and novel ideas on how different fertilisers may impact microbial communities and the potential consequences of those changes.