Diversity and abundance of ammonia oxidizing archaea in tropical compost systems

Vidya De Gannes,Gaius Eudoxie,William J Hickey,David H Dyer

doi:10.3389/fmicb.2012.00244

Abstract

Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems.

Highlights

Composting is a self-heating process wherein microbes are employed to transform organic wastes into humus-like materials
Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium
It will be important to determine the association of ammonia oxidizing archaea (AOA) with nitrification in these systems

Summary

Introduction

Composting is a self-heating process wherein microbes are employed to transform organic wastes into humus-like materials. The composition and dynamics of microbial communities in compost have been examined extensively, but largely with a focus on heterotrophic microbes and their activities related to carbon transformations (Tuomela et al, 2000; Takaku et al, 2006). Nitrification rates and nitrate levels play significant roles in affecting the fate and behavior of N in composts These roles include assimilation into microbial biomass/humus, leaching by saturated flow and gaseous N oxide emissions which are produced via nitrification and denitrification (Rudolf and Kroneck, 2005; Maeda et al, 2011). There is little information concerning the diversity and community dynamics of nitrifying microbes in composts

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