Microbial Population Structures in Soil Particle Size Fractions of a Long-Term Fertilizer Field Experiment

Abstract

Soil structure depends on the association between mineral soil particles (sand, silt, and clay) and organic matter, in which aggregates of different size and stability are formed. Although the chemistry of organic materials, total microbial biomass, and different enzyme activities in different soil particle size fractions have been well studied, little information is available on the structure of microbial populations in microhabitats. In this study, topsoil samples of different fertilizer treatments of a long-term field experiment were analyzed. Size fractions of 200 to 63 m (fine sand fraction), 63 to 2 m (silt fraction), and 2 to 0.1 m (clay fraction) were obtained by a combination of low-energy sonication, wet sieving, and repeated centrifugation. Terminal restriction fragment length polymorphism analysis and cloning and sequencing of 16S rRNA genes were used to compare bacterial community structures in different particle size fractions. The microbial community structure was significantly affected by particle size, yielding higher diversity of microbes in small size fractions than in coarse size fractions. The higher biomass previously found in silt and clay fractions could be attributed to higher diversity rather than to better colonization of particular species. Low nutrient availability, protozoan grazing, and competition with fungal organisms may have been responsible for reduced diversities in larger size fractions. Furthermore, larger particle sizes were dominated by ␣-Proteobacteria, whereas high abundance and diversity of bacteria belonging to the Holophaga/Acidobacterium division were found in smaller size fractions. Although very contrasting organic amendments (green manure, animal manure, sewage sludge, and peat) were examined, our results demonstrated that the bacterial community structure was affected to a greater extent by the particle size fraction than by the kind of fertilizer applied. Therefore, our results demonstrate specific microbe-particle associations that are affected to only a small extent by external factors.

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

“…Girvan et al (2003) reported that soil type and its properties could be a dominant factor controlling the general microbial community composition. Soil total bacterial community composition could be more associated to the particle size fraction than the different organic amendments (Sessitsch et al 2001). Another possible reason for interpreting this surprising result could be that during long-term (16 years) applications of organic fertilizers, the soil bacterial population would have shifted so that those species capable of using such fertilizers would thrive while some other species would have died out, thus leading to a less diverse population.…”

Effect of pH on soil bacterial diversity

“…In terms of dominant bacterial groups related to particle size, bacteria belonging to the phylum Acidobacteria and the genus Prosthecobacter sp. (phylum Verrucomicrobia) were found to be more diverse in soils with small particles, whereas α-Proteobacteria dominated in large particle soils (Sessitsch et al 2001). In addition, the availabilities of nutrients and organic matter also strongly influence bacterial abundances and diversities (Smit et al 2001;Hartman et al 2008;Will et al 2001;Han et al 2008).…”

“…In addition, recent studies have shown relations between microbes and environmental factors, such as geographical location (Fierer and Jackson 2006;Lauber et al 2009), soil texture (Sessitsch et al 2001), land use (Smit et al 2001;Cookson et al 2007;Brons and van Elsas 2008;Hartman et al 2008;Will et al 2001), pH (Fierer and Jackson 2006;Lauber et al 2009;Hartman et al 2008), nutrients (Cookson et al 2007;Will et al 2001;Han et al 2008), contaminants like oil (Liang et al 2011), and heavy metals (Sandaa et al 2001;Kelly et al 1999;Roane and Pepper 2000;Lee et al 2008). Of the abovementioned factors, pH is regarded one of the most important in terms of shaping biogeographical patterns (Fierer and Jackson 2006;Lauber et al 2009).…”

Distantly sampled soils carry few species in common

“…In detailed studies community phyla structures also prove to be seasonally dynamic and highly heterogenous even in homogeneous landscapes (Axelrood et al, 2002;Franklin and Mills, 2003;Sliwinski and Goodman, 2004). A few studies have attempted to correlate community structure to ecological parameters (Sessitsch et al, 2001;Fierer and Jackson 2006;Fierer et al, 2007).…”