the functional groups may increase the acidity or basicity of the soil. depending upon the soil initial condition it may be helpful to its habitat or may be harmful.

They can complex (depending upon their chemistry) with the micro-nutrients like Na, K, Mg, Ca..... which are essential for the plant materials..

The functional group varies with PH of the soil depending upon the soil conditions.Soil organisms are responsible, to a varying degree depending on the system, for performing vital functions in the soil. Soil organisms make up the diversity of life in the soil (attached Figure ). This soil biodiversity is an important but poorly understood component of terrestrial ecosystems. Soil biodiversity is comprised of the organisms that spend all or a portion of their life cycles within the soil or on its immediate surface (including surface litter and decaying logs) (attached Table)

Soil organisms represent a large fraction of global terrestrial biodiversity. They carry out a range of processes important for soil health and fertility in soils of both natural ecosystems and agricultural systems. This annex provides brief descriptions of organisms that are commonly found in the soil and their main biological and ecological attributes.

https://www.google.co.in/url?sa=t&rct=j&q=&esrc=s&source=web&cd=8&cad=rja&uact=8&ved=0ahUKEwi_hKDQ4InQAhWJsI8KHXq1B8kQFghKMAc&url=http%3A%2F%2Fwww.humates.com%2Fpdf%2FORGANICMATTERPettit.pdf&usg=AFQjCNHqnGcaEFOrksXWmHz38T8hEX1GmQ&sig2=2tnAN_2GEZ5Idk3CtqtYgw

Article Soil Organic Matter Functional Group Composition in Relation...

Soil fertility is related to the chemical composition of soil organic carbon. Direct relationship between functional group and mineralization had been reported in various works. The proportions of alkyl carbon to O-alkyl carbon of soil organic matter was related to mineralization of carbon, nitrogen etc, thus influencing the nutrient availability. Another important correlation of functional groups was established with stability of soil organic matter. Following few of many reported works, additional to ones mentioned by Prem Baboo Sir, may be worth reading:

http://ac.els-cdn.com/S0016706102003397/1-s2.0-S0016706102003397-main.pdf?_tid=7058e8f6-a0ce-11e6-a999-00000aacb35d&acdnat=1478072099_db9146b1fe2b3b130e68c9f638f5565d

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401563/pdf/pone.0124359.pdf

http://download.springer.com/static/pdf/426/art%253A10.1134%252FS1064229315100063.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Farticle%2F10.1134%2FS1064229315100063&token2=exp=1478072668~acl=%2Fstatic%2Fpdf%2F426%2Fart%25253A10.1134%25252FS1064229315100063.pdf%3ForiginUrl%3Dhttp%253A%252F%252Flink.springer.com%252Farticle%252F10.1134%252FS1064229315100063*~hmac=70c1e47011bdd1866fd9e878176430c37138f05226b3397edcea2f9984932d80

Very intelligently placed question ...

Soil organic matter plays key roles in crop sustainability, primarily through its interactions with soil chemical and physical properties in relation to nutrient release, cation retention and soil structure. The value of soil organic matter (as distinct from the value of organic inputs described in the Synchrony Principle) is well recognized, but little is known about the processes that contribute to its three key roles. This is in sharp contrast with the well understood processes underlying the use of chemical fertilizers. As low-input systems regain importance in the tropics it is essential to better understand the functioning of soil organic matter. Soil organic matter can differ in both quantity and quality (composition) resulting in differing patters of nutrient release and availability. The quality of organic inputs may affect both the composition, and long-term and the short-term nutrient release rates from soil organic matter. It is , therefore, proposed to identify the quantitative parameters that define the size of SOM fractions in relation to their functional significance and to determine the response of these pools to climate, soil type and management practice.

The presence of organic functional groups greatly influences the reactivity of soil organic matter. the functional groups are responsible for: 1. Cation exchange capacity (CEC), 2. Chelating effects, 3. Stabilization of soil aggregates, 4. Soil profile development. However, the functional groups can affect the pH as well as nutrient holding capacity and nutrient availability.

 Ms.Kataki,it is the humus formed in the manure during composting it  or the humus formed in the soil when the applied manure further decomposes (humus especially humic acid and fulvic acid) that really plays role through the functional groups mentioned by you..The functional groups mentioned are part of humic acd structure.One way it is a mixture of different acids as the functional groups ionize and release protons at different pHs..The humus  functional groups contribute to soil pH at diiferent pHs of soil so the functional group role is pH dependent-varying from around 3 to 10 pH(you may refer to pH titration curves of humic acids in literature).The functional groups contribution to cation exchange capacty of soil increases with increase in soil pH.Manure contribution to soil pH buffering is especially conspicuous in acid soils.The contribution of manure or manure derived humus is also predominantly seen in coarse textured sandy or sandy loam soils compared to clay or clay loam soils.Throuh CEC it contributes to cationic nutrient holding and release in soil.Through clay-metal cation- organic complex formation the functional groups contribute to soil aggregation and structure build up.These groups also react with pesticides applied to soil and can make them less active or release with time.Phosphate is also bound to humus through humus-metal-phosphate linkage.