We simultaneously incubated soils from long-term manure and fertilizer application, for a paddy field and a dry-land cropland.

I'm sure you've thought of it, but i would suggest it must because of different soil micro-organisms. Looking at the composition of broad groups of soil organisms might reveal key differences between dry-land and paddy fields that might expalin this difference. Certainly intriguing results!

Thanks, Philip. It is a pity that I did not anything about the composition of soil organisms. If you suggest that what possible difference in microbes between the dry-land and paddy fields, or recommend some related papers? I will be deeply grateful.

I can't help with the paddy fields - no expertise in that area, however you might want to check a couple of my papers on micro-organism diversity and ecosystem functioning available through my RG account: 

Staddon P, Lindo Z, Crittenden PD, Gilbert FS, Gonzalez A (2010) Connectivity, non-random extinction and ecosystem function in experimental metacommunities. Ecology Letters 13: 543-552.

Bradford MA, Jones TH, Bardgett RD, Black HIJ, Boag B, Bonkowski M, Cook R, Eggers T, Gange AC, Grayston SJ, Kandeler E, McCaig AE, Newington JE, Prosser JI, Setälä H, Staddon PL, Tordoff GM, Tscherko D, Lawton JH (2002) Impacts of soil faunal community composition on model grassland ecosystems. Science 298: 615-618.

OK， thank you very much!

I don't know when you monitoring the C respiration but If  I understand I see two possibilities :

-In paddy field : Anoxic conditions can decrease the respiration of the organic carbon (production of C02) of the manure. You should have a look on the fermentation and the methane production.

-In dry land : The soil organic carbon is often very low and if you add a new source of carbon very digestive  it's going to be quickly digested while with the inorganic fertilizer you can only consume the low amount of carbon which could be very difficult to reach by microorganisms (aggergate protection, complex organic chain, etc).

I'm not sure that you need to go through the functional diversity of microorganisms to answer this question but I may be wrong.

Thank you very much and you may not understand me. We simultaneously incubated soils from long-term manure and fertilizer application at the same water condition (60%WFPS) in the lab, both for paddy and upland soils .

Now I think I can answer my questions reasonably.

One reason could be that in the paddy soil, organic amendments (OA) can be binded with large amount of Fe/Al oxides and hydrous oxides (i.e., chemical protection) and thus not easily decomposed by microbes, which was considered as a prevailing mechanism of carbon sequestration in the paddy soils (Zhou et al., 2009). Accordingly, the paddy soils with OA (higher carbon concentration) had a lower relative soil respiration rates than the ones with inorganic fertilizer (IF). However, for the upland soils (low amount of Fe/Al oxides and hydrous oxides), organic amendment could be individually dispersed among the soil matrix and easily decomposed by microbes, and thus OA had higher relative soil respiration than IF.

An additional reason could be that different microbial activities contribute to that the paddy soil do not have significant priming effect of organic amendment on the mineralization of native organic carbon, while the positive priming effect was significant in the upland soil (Wu et al., 2012).

Anyhow, for whatever reason, our study indicated that paddy soils have a better outcome of carbon sequestration by organic amendment than upland soils, which is agree with Pan et al. (2004) and Ouyang et al. (2014), who found that paddy soils usually have higher carbon sequestration potential or faster sequestration rates than upland soils. 

Welcome for suggestions and comments!

indeed I didn't understand the experiment. Now I think I've got it. Can I ask a question ?  Do you want to compare the soil carbon sequestration rate under manure and inorganic fertilizer on both site (upland and paddy)?  And if it's correct , is the experiment with the same water content  representative of these field systems ?

Possibly there are other limiting factors after significant other biotic activities in a paddy field, whereas on dry land the constraining factor was water. Thus, carbon in manure would remain in place while providing other inputs for plants whereas biotic activity on dry land would eat up the carbon. I'm mostly thinking of the effect that Simon pointed to here, and ALSO that other biotic activities could also be a driving factor leading to additional chemical constraining factors which reduce microbial breakdown of carbon.

Possibly this means the same thing as "negative priming effect in the paddy field", but I am not familiar with this phrase.

I'm not sure I understand why the Fe/Al oxides would affect microbial decomposition of the carbon, but perhaps that simply communicates that I didn't go far in soil sciences.

Is it one cycle/season in the study? Perhaps the carbon in the manure could not break down while under water in a single season, but would break down in the dry season. Is it possible to compare, for example, in continuous cultivation where the paddy field is basically always under water, or otherwise where the paddy field is always at least wet or high water content, compared to a paddy field where one crop is possible and it is very dry in other seasons? Perhaps this would give a hint. In much of West Africa where rice is increasingly popular, only one harvest per year is possible because it is too dry the rest of the year. This is much different from irrigated areas which can easily access water for a full three crops a year, which to the best of my knowledge is the most common case in the east or south of China, for example (wheat being the preferred grain in other regions, no?)

Re: Phillip's comment on different microbial communities. I think to date the rhizosphere is easily the most understudied area of agricultural sciences. Much like we have studied perhaps a fraction of a percent of all the fungi out there, we know astonishingly little about the rhizosphere.

This was widely recognized as a problem when I was studying some botany at a very established research university in undergrad and also working in one of the labs there, but it is hard to get funding for things that research granting organizations don't even know exists. What's the rhizosphere? If scientists on boards of relevant granting organizations could more easily answer that question in at least a broad manner, some of the best kept secrets of nature w.r.t. farming could begin to be unlocked. From gene sequencing and species identification in the rhizosphere, to in situ and (ridiculously oversimplified) lab experiments on interactions between different microbial communities in different conditions ... it easily gets very complicated very quickly.

I really think you need to get deep into composition of the rhizosphere and/or broader microbial communities to provide meaningful answers here.

... But that's really about the limits for me in this direction. I wasn't so interested in the evaluation procedures for getting good grades in those kinds of classes and instead opted to get more into the political and economic factors involved in farm management decisions and policy frameworks which contribute to farmers' abilities to make profitable and ideally sustainable decisions ...

Perhaps this is already obvious to people on this board, but rice cultures have been identified as a main source of methane, one of the most potent greenhouse gases around. This is hugely relevant stuff.

Re to Simon：yes, your guess is correct. I want to compare the soil carbon sequestration rate under manure and inorganic fertilizer on both site (upland and paddy). I agree with you that soils  with the same water content may not represent paddy soils when immersed. But in the paddy soils in china, the soils was irrigated for only about four months and was not immersed for the rest in one year. Thus, we incubated with all the soil with the same water content for comparing  them with each other. 

Re to Nathan: Thank you for your  comments. The Fe/Al oxides can absorb organic matter, which make it difficult to be decomposed by microbes. yes, you are right,   a full three crops a year is the most common case in the east or south of China and wheat or maize are the preferred grain in the north of China.

Tthe carbon added through manure is in more stable form and is less exposed to decomposition under paddy soil which is mostly irrigated. The  mineralization of humic carbon is some what difficult

Yes， i am agree with you.

I echo the previous statements about species composition...  It would be interesting to measure CH4 evolution of both soils when saturated to determine if C loss is greater from the paddy soils. If it is, it may be due to a shift in species composition aligned to match the predominate soil O2 status. 

Interesting phenomenon, good luck!