Microbial Diversity and Heterogeneity in Sandy Subsurface Soils

Zhou, Jizhong; Xia, Beicheng; Huang, Hsing Hua; Palumbo, Anthony V.; Tiedje, James M.

doi:10.1128/aem.70.3.1723-1734.2004

Cited by 143 publications

(91 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The spatial structure in other groups may be detectable beyond the scale of our study. For example, spatial structure in nematode populations can be detected at the scale of more than tens of metres (Liang et al, 2005), whereas bacterial communities shift within a few millimetres because of differences in soil microhabitats (Zhou et al, 2004). Soil animals comprise organisms of very different size and mobility, which may blur their distribution patterns because of multiple conflicting signals.…”

Section: Discussionmentioning

confidence: 99%

“…Such a sampling scheme enables to account for soil patchiness on a millimetre scale (Zhou et al, 2004) and provides sufficient replication for distance classes from 0.01 to 32 m. The central sampling spot was randomly selected with the constraint that it had to comprise a uniform 40.25-m 2 patch of microtopography and ground vegetation and lie 41 m from any surrounding tree (41 cm diameter at the base). Around each sample, a 0.5 × 0.5 m 2 quadrat was established, and the cover of understorey plant species was recorded.…”

Section: Sampling and Site Characteristicsmentioning

confidence: 99%

“…The remaining soil was used for chemical analysis of pH KCl and concentrations of P total , K, Ca, Mg, C, N, 15 N and 13 C (Supplementary Table S1) as described in Tedersoo et al, (2012). In each soil sample, the proportion of O, A and E horizons were measured because of differences in functional composition of soil microbes (Zhou et al, 2004;Lindahl et al, 2007). There were only minor differences in the thickness of soil layers within each plot (mean ± s.d.…”

Section: Sampling and Site Characteristicsmentioning

confidence: 99%

See 2 more Smart Citations

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment

et al. 2015

View full text Add to dashboard Cite

A central challenge in ecology is to understand the relative importance of processes that shape diversity patterns. Compared with aboveground biota, little is known about spatial patterns and processes in soil organisms. Here we examine the spatial structure of communities of small soil eukaryotes to elucidate the underlying stochastic and deterministic processes in the absence of environmental gradients at a local scale. Specifically, we focus on the fine-scale spatial autocorrelation of prominent taxonomic and functional groups of eukaryotic microbes. We collected 123 soil samples in a nested design at distances ranging from 0.01 to 64 m from three boreal forest sites and used 454 pyrosequencing analysis of Internal Transcribed Spacer for detecting Operational Taxonomic Units of major eukaryotic groups simultaneously. Among the main taxonomic groups, we found significant but weak spatial variability only in the communities of Fungi and Rhizaria. Within Fungi, ectomycorrhizas and pathogens exhibited stronger spatial structure compared with saprotrophs and corresponded to vegetation. For the groups with significant spatial structure, autocorrelation occurred at a very fine scale (o2 m). Both dispersal limitation and environmental selection had a weak effect on communities as reflected in negative or null deviation of communities, which was also supported by multivariate analysis, that is, environment, spatial processes and their shared effects explained on average o10% of variance. Taken together, these results indicate a random distribution of soil eukaryotes with respect to space and environment in the absence of environmental gradients at the local scale, reflecting the dominant role of drift and homogenizing dispersal.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Sampling and Site Characteristicsmentioning

confidence: 99%

Section: Sampling and Site Characteristicsmentioning

confidence: 99%

See 1 more Smart Citation

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Of the microbial groups that are abundant in the soil, bacteria have been the most extensively studied. Nevertheless, our understanding of the spatial distribution patterns of bacterial diversity is limited, mainly because most studies are limited to local scales (Navarro-Gonzalez et al, 2003;Zhou et al, 2004). Recent large-scale surveys have revealed that different ecosystems support unique microbial populations (Zhou et al, 2002;Fierer and Jackson, 2006;Green and Bohannan, 2006;Vishniac, 2006;Adler and Levine, 2007), giving rise to the notion that microbial populations can exhibit geographic distribution.…”

Section: Introductionmentioning

confidence: 99%

Biogeography of soil archaea and bacteria along a steep precipitation gradient

et al. 2009

View full text Add to dashboard Cite

For centuries, biodiversity has spellbound biologists focusing mainly on macroorganism's diversity and almost neglecting the geographic mediated dynamics of microbial communities. We surveyed the diversity of soil bacteria and archaea along a steep precipitation gradient ranging from the Negev Desert in the south of Israel (o100 mm annual rain) to the Mediterranean forests in the north (4900 mm annual rain). Soil samples were retrieved from triplicate plots at five long-term ecological research stations, collected from two types of patches: plant interspaces and underneath the predominant perennial at each site. The molecular fingerprint of each soil sample was taken using terminal restriction length polymorphism of the 16S rRNA gene to evaluate the bacterial and archaeal community composition and diversity within and across sites. The difference in community compositions was not statistically significant within sites (P ¼ 0.33 and 0.77 for bacteria and archaea, respectively), but it differed profoundly by ecosystem type. These differences could largely be explained by the precipitation gradient combined with the vegetation cover: the archaeal and bacterial operational taxonomic units were unique to each climatic region, that is, arid, semiarid and Mediterranean (P ¼ 0.0001, for both domains), as well as patch type (P ¼ 0.009 and 0.02 for bacteria and archaea, respectively). Our results suggest that unlike macroorganisms that are more diverse in the Mediterranean ecosystems compared with the desert sites, archaeal and bacterial diversities are not constrained by precipitation. However, the community composition is unique to the climate and vegetation cover that delineates each ecosystem.

show abstract

“…In addition, soil characteristics of both P and NP areas resulted to be similar. Notwithstanding the heterogeneity of microbial distribution in the soil (Zhou et al 2004 Zhou, J, Xia, B, Huang, H, Palumbo, AV and Tiedje, JM. 2004.…”

Section: Discussionmentioning

confidence: 99%

Bacterial and fungal communities associated withTuber magnatum‐productive niches

Mello

Miozzi

Vizzini

et al. 2010

Plant Biosystems - An International Journal Dealing with all As

View full text Add to dashboard Cite

Truffles are hypogeous ectomycorrhizal fungi of ecological interest for forestry in soils of the northern hemisphere, and of economical relevance for food markets worldwide. The molecular mechanisms that control truffle body formation are largely unknown, as well as the environmental factors that are likely involved. Among the latter, it has been hypothesized that soil-borne communities may have an impact on truffle production. To address this question, we investigated bacterial and fungal communities resident in productive versus adjacent non-productive grounds of the white truffle Tuber magnatum by using PCR-DGGE. Although bacterial communities were generally highly similar across all samples within the grounds, profiles did cluster according to the productivity of circumscribed niches, and a Moraxella osloensis population appeared to be associated with productive sites. Fungal communities revealed several populations, yet showed no obvious patterns in relation to productivity, although Mortierella and Fusarium oxysporum appeared to be more abundant in the productive area. Our results offer a first glimpse into microbial communities thriving in truffle productive niches, and open the question as to whether microbemediated mechanisms may facilitate/inhibit truffle fruiting-body production or, vice versa, i.e. whether truffle sporocarps have an impact on the microbes living in the rhizosphere.

show abstract

Microbial Diversity and Heterogeneity in Sandy Subsurface Soils

Cited by 143 publications

References 52 publications

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment

Biogeography of soil archaea and bacteria along a steep precipitation gradient

Bacterial and fungal communities associated withTuber magnatum‐productive niches

Contact Info

Product

Resources

About