Acidobacterial community responses to agricultural management of soybean in Amazon forest soils

RESEARCH ARTICLE Acidobacterial community responses to agricultural management of soybean in Amazon forest soils Acácio A. Navarrete1,2, Eiko E. Kuramae2,3, Mattias de Hollander2, Agata S. Pijl2, Johannes A. van Veen2,4 & Siu M. Tsai1 1 Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil; Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands; 3Department of Ecological Science, Free University Amsterdam, Amsterdam, The Netherlands; and 4Institute of Biology, Leiden University, Leiden, The Netherlands 2 Received 3 June 2012; revised 1 August 2012; accepted 23 September 2012. Final version published online 19 October 2012. MICROBIOLOGY ECOLOGY DOI: 10.1111/1574-6941.12018 Editor: Angela Sessitsch Keywords soil microbiology; soil factors; land-use changes; tropical rainforest; 16S rRNA gene. Abstract This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1–8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as earlywarning bioindicators of agricultural soil management effects in the Amazon area. Introduction Soil bacterial communities in the Amazon area have been analyzed in different types of soils (Borneman & Triplett, 1997; Kim et al., 2007; Cenciani et al., 2009; Jesus et al., 2009; O’Neill et al., 2009; Navarrete et al., 2010). Based on these studies, the bacterial community composition was revealed in soils from different Amazon regions. The Acidobacteria phylum has been described as dominant in soils from Western Amazon (Kim et al., 2007; Jesus et al., 2009) and Central Amazon (Navarrete et al., 2010). However, the role of this dominant group in the bacterial community of Amazon soils is largely unknown. Acidobacteria have consistently been detected in many different habitats around the globe by 16S rRNA gene– based molecular surveys, including soil and rhizosphere niches (Chow et al., 2002; Kuske et al., 2002; Gremion FEMS Microbiol Ecol 83 (2013) 607–621 et al., 2003; Quaiser et al., 2003; Fierer et al., 2005; Stafford et al., 2005; Janssen, 2006; Sanguin et al., 2006; De Cárcer et al., 2007; Singh et al., 2007; DeAngelis et al., 2009; Kielak et al., 2009). These observations have revealed that Acidobacteria are ubiquitous and among the most abundant bacteria phylum in soil. In spite of their high abundance, little information is available on their ecology, which is mainly due to the lack of culturable representatives in bacterial collections (Kishimoto et al., 1991; Liesack et al., 1994; Coates et al., 1999; Bryant et al., 2007; Eichorst et al., 2007, 2011; Fukunaga et al., 2008; Koch et al., 2008; Lee et al., 2008; Nunes da Rocha et al., 2009; Ward et al., 2009; Kulichevskaya et al., 2010; Pankratov & Dedysh, 2010; Männistö et al., 2011; Pankratov et al., 2011). Land-use changes is one of the greatest threats to biodiversity worldwide, and one of the most devastating ª 2012 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved Correspondence: Eiko E. Kuramae, Department of Microbial Ecology, Netherlands Institute of Ecology NIOOKNAW. Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands. Tel.: +31 317 473502; fax: +31 317 473675; e-mail: 608 Materials and methods Site description and soil sampling Bulk soil samples were collected in two different field locations in the Southeastern Brazilian Amazon, in the state of Mato Grosso, Brazil, in the Porto dos Gaúchos municipality ( 15°13′39″ S and 54°04′31″ W) and the Ipiranga do Norte municipality ( 13°21′57″ S and 54°54′24″ W) (Fig. 1). Oxisol is the predominant soil order in the sampling sites (Secretaria de Estado de Planejamento e Coordenação Geral, 2001), and the climate in the region is classified as Am (Koppen’s classification), with annual average temperature of 28 °C and average precipitation of 2000 mm. ª 2012 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved The field locations were considered replicates and the sampling sites were selected according to the vegetation cover, soil use, and management practices. In the Porto dos Gaúchos municipality, areas covered with native tropical rainforest were cleared in 2008 and subsequently converted into agricultural land. Since 2004, forest conversion to agricultural use occurred in areas located in Ipiranga do Norte municipality. In both field locations, forest conversion to agricultural use followed annually the rotational production order: millet, soybean, maize, under no-tillage. After deforestation, fertilizers, pesticides, and a liming treatment were applied to the cropland fields of both locations. The cropland fields received different amounts of lime to increase soil pH to 5 and 6. Bulk soil samples were collected from soybean production fields before sowing the seeds (October 2009) and after soybean (Glycine max [L.] Merrill cultivar M-SOY 8866) harvest (April 2010) in order to consider an expected variation in soil characteristics during the soybean cultivation (Fig. 1). Soil samples were also collected at the same time from adjacent forests to represent the native soil–plant conditions (Fig. 1). At each sampling site, the soil samples were collected from five points. One central sampling point and other four sampling points (at least 50 m apart from the central point) directed toward the north, south, east, and west of the central point. Soil samples were taken from the 0- to 20-cm topsoil layer (tilled zone). First, the litter layer was removed, and then, the soil sample was collected using a 5-cm-diameter aseptic cylindrical core. A total of 40 bulk soil samples were collected in field (2 field locations 9 2 sampling sites pe (...truncated)