Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java, Indonesia

Abstract

In Java, Indonesia, many nutrient-poor soils are intensively reforested with Pinus merkusii (pine). Information on nutrient cycles and microorganisms involved in these cycles will benefit the management of these important forests. Here, seasonal effects on the stratification of bacterial community structure in the soil profile of a tropical pine forest are described, and differences in bacterial communities are related to chemical and physical soil parameters. Culture-independent community profiles of litter, fragmented litter and mineral soil layers were made by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA-specific polymerase chain reaction (PCR) fragments. The community profiles of the different soil layers clustered separately, correlating with significant differences in organic matter content between the three layers. The bacterial communities appeared to be stable during the wet season of 1998. The drought in 1997, caused by the El Niño climatic effect, did not influence the bacterial communities in fragmentation and mineral soil, although moisture content and other soil parameters were markedly lower than in the wet season. However, communities in litter were influenced by drought. In the litter layer, the moisture content was significantly lower than in the fragmentation and mineral layers during the dry season. A clone library was made from a litter sample taken during the wet season. Partial sequencing of 74 clones and linking the DGGE banding positions of these clones to bands in the DGGE profile of the sample from which the clone library was derived showed considerable bacterial diversity. Alpha-proteobacteria (40.5% of the clones, of which 57% belonged to the Rhizobium-Agrobacterium group) and high-G+C content, Gram-positive bacteria (36.5%) dominated the clone library.

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

“…Also Shen et al (2008) and Tourna et al (2008) have found temporal shifts in archaeal abundance, and Stres et al (2008) and Tourna et al (2008) evidenced responsiveness of soil archaea to variations in soil temperature and soil moisture. Seasonal changes in soil climate were further closely linked to short-and medium-term variations in resource availability, which further correlated with the quantity and quality of organic matter entering the soil, as it was also previously suggested (Bell et al, 2009;Cookson et al, 2006;Krave et al, 2002). Consequently, total bacterial communities and individual phyla studied were clearly shaped by supply of DOC, DON and mineral N (that is, ammonia, nitrate), which is in agreement with previously published data (Drenovsky et al, 2004;Zak et al, 2003;Alden et al, 2001).…”

Positive correlation between soil bacterial metabolic and plant species diversity and bacterial and fungal diversity in a vegetation succession on Karst

“…As it appears from unchanged bacterial metabolic diversities in T, S and SF, litter leaching (Qiu et al 2005) and organic matter decomposition (Schmidt et al 2007;Zogg et al 1997) during the plant growth season (summer) were no determinant factors of bacterial activities in our study sites. Similarly, changes in soil moisture content that may have occurred were previously found not to explain the activity of microbial communities Krave et al 2002). Irrespective of the season, differences in plant community composition appeared to explain differences in bacterial metabolic diversity in the present and a previous field study (Rogers and Tate 2001).…”

Microbial dynamics in Mediterranean Moder humus

“…(2000), Krave et al (2002) and Griffiths et al (2003); they were attributed to decrease of either soil moisture or organic C down the soil cores.…”

“…Microbial diversity in soil has been analysed by cultureindependent techniques such as PLFA (phospholipid fatty acid) (Fritze et al 2000;Certini et al 2004) or microbial cell DNA (Krave et al 2002;Landeweert et al 2003;Agnelli et al 2004;Hansel et al 2008;Carletti et al 2009). These techniques can overcome problems associated with selective cultivation and isolation of microorganisms from natural samples, by-passing the so called 'great plate count anomaly' (Staley and Konopka 1985;Connon and Giovannoni 2002).…”