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Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Sustainable management practices, such as tillage and residue management, can influence structure and function of the soil microbiota, with direct consequences for the associated ecosystem services. Although there is increasing evidence that different tillage regimes alter the soil biological indices, we only have a limited understanding of their temporal changes in a rice (Oryza sativa L.)–wheat (Triticum aestivum L.) cropping system. We evaluated the effects of combinations of tillage, crop residue management and green manuring on soil biological indicators after 5 years of the practising rice–wheat system (RWS). Four main plot treatments in rice included the following: (a) PTRW0, puddled transplanted rice with no wheat straw retained; (b) PTRW25, puddled transplanted rice with 25% anchored wheat stubbles retained; (c) PTRW0 + Sesbania aculeate L. green manure (GM); and (d) PTRW25+GM, puddled transplanted rice with 25% anchored wheat stubbles retained+ GM. There were three subplot treatments in the subsequent wheat crop: (a) CTWR0, conventional tillage wheat with rice residue removed; (b) ZTWR0, zero tillage wheat with rice residue removed; and (c) ZTWR100, ZTW with 100% rice residue retained as mulch. The PTRW25+GM treatment, followed by ZTWR100, significantly increased soil microbial biomass carbon, basal soil respiration, microbial quotient and mineralization quotient measured during wheat‐growing season. These biological indicators were higher at vigorous vegetative wheat growth stage than at flowering stage and decreased at maturity. The principal component analysis of the assayed variables showed that all the variables significantly contributed to the variability in parameters examined and were more related to maximum tillering stage of wheat growth than to maturity or at sowing of wheat. Three highly effective biological indicators were microbial biomass carbon, microbial quotient and mineralization quotient, which responded significantly to changes in tillage and residue management practices in the RWS. We conclude that crop residues and green manure have significant to improve soil biochemical processes by improving soil organic carbon and soil biological indicators in rice–wheat cropping system. [ABSTRACT FROM AUTHOR]

• β-Glucosidase, cellulose and phenol oxidase identified as key soil quality indicators. • Maximum tillering is an optimum growth stage of wheat for soil sampling. • Wheat yield increased significantly in puddled transplanted rice plus green manure and zero tillage with residue retention compared to residue removal. Soil quality degradation in the last four decades is threatening the sustainability of puddled transplanted rice (Oryza sativa L.) – wheat (Triticum aestivum L.) (RW) system in north-western region of India. Hence comprehensive information on the influence of soil and crop management practices in intensive and nutrient exhausting RW system on soil quality is urgently needed. The present study evaluated the effects of crop residues, green manure and tillage on the changes in soil biochemical properties at different growth stages of wheat after five cycles of RW system. Four main plot treatments in rice included combinations of wheat straw and Sesbania green manure management: (1) PTR WS0, puddled transplanted rice (PTR) with no wheat straw (2) PTR WS25 , puddled transplanted rice with 25% anchored wheat stubbles retained (3) PTR WS0 plus green manure (GM), and (4) PTR WS25 plus GM. Three sub-plots treatments in subsequent wheat included (1) CTW RS0 , conventional tillage wheat without rice straw (2) ZTW RS0 , zero tillage wheat without rice straw and (3) ZTW RS100 , ZTW with 100% rice straw retained as surface mulch. The results showed that PTR WS25 plus GM and ZTW RS100 increased significantly all the soil biochemical properties (enzyme activities and glomalin related soil protein concentration) except phenol oxidase and peroxidase activities. The activities of dehydrogenase, β-glucosidase and concentration of easily extractable glomalin and total carbohydrate carbon under ZTW RS100 were 36.8, 24.6, 25.9 and 23.3% higher than CTW RS0. Application of GM and wheat straw retention in previous rice significantly increased grain yield of subsequent wheat crop by 26.5%. The majority of the increases in biochemical properties were higher at vegetative growth (at 40–45 days after sowing) and flowering (at 80–85 days after sowing) stages compared to the initial and at maturity. Principal component analysis identified β-glucosidase, cellulase and phenol oxidase activities as the most sensitive and reliable indicators for assessing soil quality for conservation agriculture based RW system. [ABSTRACT FROM AUTHOR]