Bacterial Community Diversity in the Brazilian Atlantic Forest Soils

The aim of this study was to characterize the bacterial community diversity of the Brazilian Atlantic forest soil by means of both cultivation and 16S rRNA clone libraries. A collection of 86 representative isolates, obtained from six samples of Atlantic forest soils from the National Park of Serra dos Órgãos (PARNASO), belonged to the genera Arthrobacter, Bacillus, Burkholderia, Leifsonia, Paenibacillus, Pseudomonas, Ralstonia, Serratia, and Streptomyces according to the 16S rRNA sequences. Representative isolates from the different genera degraded cellulose and lignin. The culture-independent analysis based on 894 partial 16S rRNA gene sequences revealed that the most frequently retrieved groups belonged to the phyla Acidobacteria (29–54%), Proteobacteria (16–38%), and Verrucomicrobia (0.6–14%). The majority of the sequences (82.6%) were unidentified singletons and doubletons, indicating a high diversity of rare unique sequences. Chao1 estimator disclosed a high number of phyla (41–152) and species (263–446). This is the first survey on the Atlantic Forest soils using a combination of cultivation and culture-independent approaches. We conclude that the Brazilian Atlantic Forest soil represents a vast source of novel bacteria.     

Microbial Community Structure at Different Depths in Disturbed and Undisturbed Semiarid Mediterranean Forest Soils

Metabolic abilities and micrfiobial community structure were investigated through three semiarid Mediterranean soils of SE Spain. The soils were (1) a Typic Calcixerept under an adult pine plantation (PP), growing on abandoned agricultural terraces; (2) a Typic Calcixeroll under a native pinewood (NP); and (3) a Typic Haploxerept covered with a grass steppe (GS). PP and NP were similar as regards their genesis, but the former used to be tilled. NP and GS were undisturbed and supported natural and seminatural vegetation, respectively. Seven samples in 10-cm depth increments were taken in triplicate along each soil profile. Community-level physiological profiles based on sole-C-source use were determined to characterize the metabolic abilities. A 16S rDNA polymerase chain reaction-denaturing gradient gel electrophoresis analysis was performed to investigate the microbial genetic structure. Plant cover and land-use history were major determinants of microbial community structure. Microbial communities residing in soils under a native pinewood, the most diverse and stable plant cover, were the most complex both metabolically and genetically. The microbial community structure distinctly changed with depth, related to the quantity and quality of total organic carbon. Both undisturbed soils showed falling gradients of metabolic and genetic complexity, which were invariably of a greater magnitude in the mature woodland than in the grass steppe. In the planted pinewood, however, the substrate-use diversity increased with depth, apparently a response to the depleted metabolic abilities within its upper layer (0–30 cm). Tilling and plant cover removal might be responsible for such a perturbation. In the same profile, molecular fingerprint patterns of the topsoil layer (0–10 cm) indicated a disturbed genetic structure that might underlie the loss of metabolic abilities. However, the genetic structure of the deeper layers of the planted and native pinewoods was not dissimilar, revealing that equivalent genetic resources perform different environmental functions under changing soil scenarios.     

Change in Bacterial Community Structure in Response to Disturbance of Natural Hardwood and Secondary Coniferous Forest Soils in Central Taiwan

Forest management often results in changes in the soil and its microbial communities. In the present study, differences in the soil bacterial community caused by forest management practices were characterized using small subunit (SSU) ribosomal RNA (rRNA) gene clone libraries. The communities were from a native hardwood forest (HWD) and two adjacent conifer plantations in a low-elevation montane, subtropical experimental forest at the Lienhuachi Experimental Forest (LHCEF) in central Taiwan. At this locality, the elevation ranges from 600 to 950 m, the mean annual precipitation is 2,200 mm, the mean annual temperature is 20.8°C, and the soil pH is 4. The conifer forests included a Cunninghamia konishii Hay (CNH) plantation of 40 years and an old growth Calocedrus formosana (Florin) Florin (CLC) forest of 80 years. A total of 476 clones were sequenced and assigned into 12 phylogenetic groups. Proteobacteria-affiliated clones (53%) predominated in the library from HWD soils. In contrast, Acidobacteria was the most abundant phylum and comprised 39% and 57% in the CLC and CNH libraries, respectively. Similarly, the most abundant OTUs in HWD soils were greatly reduced or absent in the CLC and CNH soils. Based on several diversity indices, the numbers of abundant OTUs and singletons, and rarefaction curves, the diversity of the HWD community (0.95 in evenness and Shannon diversity indices) was somewhat less than that in the CNH soils (0.97 in evenness and Shannon diversity indices). The diversity of the community in CLC soils was intermediate. The differences in diversity among the three communities may also reflect changes in abundances of a few OTUs. The CNH forest soil community may be still in a successional phase that is only partially stabilized after 40 years. Analysis of molecular variance also revealed that the bacterial community composition of HWD soils was significantly different from CLC and CNH soils (p = 0.001). These results suggest that the disturbance of forest conversion and tree species composition are important factors influencing the soil bacterial community among three forest ecosystems in the same climate.     

Diversity and Structure of Bacterial Chemolithotrophic Communities in Pine Forest and Agroecosystem Soils

Obligate lithotrophs (e.g., ammonia oxidizers) and facultative lithotrophs (e.g., CO and hydrogen oxidizers) collectively comprise a phylogenetically diverse functional group that contributes significantly to carbon and nitrogen cycles in soils and plays important roles in trace gas dynamics (e.g., carbon monoxide and nitrous and nitric oxides) that affect tropospheric chemistry and radiative forcing. In spite of their diverse physiologies, facultative and obligate lithotrophs typically possess the Calvin-Benson-Bassham cycle enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisCO). In an effort designed to understand the structure of lithotrophic communities in soil, genomic DNA extracts from surface (0 to 2 cm) and subsurface (5 to 7 cm) soils have been obtained from two sites in a Georgia agroecosystem (peanut and cotton plots) and an unmanaged pine stand (>50 years old). The extracts have been used in PCR amplifications of the cbbL gene for the rubisCO large subunit protein. cbbL PCR products were cloned, sequenced, and subjected to phylogenetic and statistical analyses. Numerous novel lineages affiliated with the form IC clade (one of four form I rubisCO clades), which is typified by facultative lithotrophs, comprised lithotrophic communities from all soils. One of the form IC clone sequences clustered with a form IC clade of ammonia-oxidizing Nitrosospira. Distinct assemblages were obtained from each of the sites and from surface and subsurface soils. The results suggest that lithotrophic populations respond differentially to plant type and land use, perhaps forming characteristic associations. The paucity of clone sequences attributed to ammonia-oxidizing bacteria indicates that even though ammonia oxidation occurs in the various soils, the relevant populations are small compared to those of facultative lithotrophs.     

Bacterial Diversity in Agricultural Soils during Litter Decomposition

Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.     

Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach

Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions.     

秸秆覆盖免耕对土壤细菌群落区系的影响

多年连续秸秆覆盖免耕对土壤细菌群落影响很大,免耕可提高０－１０ｃｍ土层土壤细菌总数、放线菌数、棒状细菌数和贫营养细菌数量,特别是免耕土壤能使芽孢杆菌数量增多几倍。     

Microbial Diversity and Community Structure of Postdisturbance Forest Soils as Determined by Sole-Carbon-Source Utilization Patterns

Abstract The impact of clear-cutting, scarification, and prescribed burning on forest soil microbial community structure was assessed using sole-carbon-source utilization (SCSU). Organic and mineral soil samples were collected on two dates from Pinus banksiana plots that had been clear-cut, clear-cut followed by prescribed burning, clear-cut followed by scarification, or had not been harvested. Microorganisms were extracted from the soil samples and used to inoculate Gram-negative Biolog? plates. Patterns of substrate metabolism were used to calculate Shannon, Simpson, McIntosh, and related evenness indices. Principal component analysis (PCA) resolved organic and mineral soils. Organic soil exhibited higher metabolic diversity than mineral soil. Scarified plots showed lower diversity on one date, when diversity indices were calculated using all carbon sources, and on both dates when calculated using carboxylic acids, only. The results suggest that SCSU may be used to assess the impact of forestry practices on microbial diversity and community structure by using a subset of carbon substrates. Received: 30 July 1996; Accepted 18 November 1996     

Structure of the Epiphyte Community in a Tropical Montane Forest in SW China

Vascular epiphytes are an understudied and particularly important component of tropical forest ecosystems. However, owing to the difficulties of access, little is known about the properties of epiphyte-host tree communities and the factors structuring them, especially in Asia. We investigated factors structuring the vascular epiphyte-host community and its network properties in a tropical montane forest in Xishuangbanna, SW China. Vascular epiphytes were surveyed in six plots located in mature forests. Six host and four micro-site environmental factors were investigated. Epiphyte diversity was strongly correlated with host size (DBH, diameter at breast height), while within hosts the highest epiphyte diversity was in the middle canopy and epiphyte diversity was significantly higher in sites with canopy soil or a moss mat than on bare bark. DBH, elevation and stem height explained 22% of the total variation in the epiphyte species assemblage among hosts, and DBH was the most important factor which alone explained 6% of the variation. Within hosts, 51% of the variation in epiphyte assemblage composition was explained by canopy position and substrate, and the most important single factor was substrate which accounted for 16% of the variation. Analysis of network properties indicated that the epiphyte host community was highly nested, with a low level of epiphyte specialization, and an almost even interaction strength between epiphytes and host trees. Together, these results indicate that large trees harbor a substantial proportion of the epiphyte community in this forest.     

Bacterial Diversity in Three Different Antarctic Cold Desert Mineral Soils

A bacterial phylogenetic survey of three environmentally distinct Antarctic Dry Valley soil biotopes showed a high proportion of so-called “uncultured” phylotypes, with a relatively low diversity of identifiable phylotypes. Cyanobacterial phylotypic signals were restricted to the high-altitude sample, whereas many of the identifiable phylotypes, such as the members of the Actinobacteria, were found at all sample sites. Although the presence of Cyanobacteria and Actinobacteria is consistent with previous culture-dependent studies of microbial diversity in Antarctic Dry Valley mineral soils, many phylotypes identified by 16S rDNA analysis were of groups that have not hitherto been cultured from Antarctic soils. The general belief that such “extreme” environments harbor a relatively low species diversity was supported by the calculation of diversity indices. The detection of a substantial number of uncultured bacterial phylotypes showing low BLAST identities (<95%) suggests that Antarctic Dry Valley mineral soils harbor a pool of novel psychrotrophic taxa.     

土壤细菌遗传多样性及其与植被类型相关性研究

细菌是土壤生物的重要类群,由于其形态简单,绝大多数无法人工培养,用传统分类法极难进行土壤细菌遗传多样性分析。选择土壤细菌１６Ｓ核糖体ＲＮＡ基因内一段２６碱基变异区为基因标签,连接成标签串测序,用标签类型、频率和多样性指数等在分子水平上描述土壤细菌遗传多样性,并分析了土壤细菌遗传多样性与植被类型的相关性。土壤细菌遗传多样性与土壤有机质、全氮含量等理化性质高度相关,不同植被土壤理化性质差异决定细菌遗传     

The Hummingbird Plant Community of a Tropical Montane Rain Forest in Southern Ecuador

Abstract: The diversity of a hummingbird plant community in the eastern Andes of southern Ecuador was studied on the equivalent of a hectare (two 500 ' 10 m transects) at 1920 - 2100 m a.s.l. over the course of a year. A total of 3186 flowering individuals, representing 12 plant families, 29 genera and 72 species, were found to be visited by hummingbirds. Bromeliaceae had the most species visited, followed by Orchidaceae and Ericaceae. The majority of visited plant species were represented by a very few individuals, and only a few species of the Bromeliaceae and Orchidaceae appeared in large numbers of visited individuals. With regard to life forms visited by hummingbirds, epiphytes predominated (59 %), followed by trees and shrubs (29 %), vines (8 %) and herbs (4 %). Visited flowers usually had short- to medium-long floral tubes which were either functionally or morphologically tubiform or campanulate. Fifty percent of the species had red-coloured flowers, and a considerable number of the blossoms (43 %) displayed contrasting colours. The 72 plant species received visits from 26 species of Trochilidae (hummingbirds) and two species of Coerebidae (honeycreepers). A mere eight species of hummingbirds were seen frequently at the study area; the remaining species were only occasionally sighted. The eight frequently sighted species of hummingbirds made use of a total of 74 % of all hummingbird-visited plant species growing in the study area.     

Forest Productivity and Efficiency of Resource Use Across a Chronosequence of Tropical Montane Soils

We tested the hypothesis that plants adjust to nutrient availability by altering carbon allocation patterns and nutrient-use efficiency (NUE = net primary production [NPP] per unit nutrient uptake), but are constrained by a trade-off between NUE and light-use efficiency () = NPP per unit intercepted light). NPP, NUE and ) were measured in montane Metrosideros polymorpha forest across a 4.1 x 10⁶ yr space for time substitution chronosequence in which available soil N and P pools change with site age. Although the range of N and P availability across sites was broad, there was little difference in NPP between sites, and in contrast to theories of carbon allocation relative to limiting resources, we found no consistent relationships in production allocation to leaves, fine roots or wood. However, canopy nutrient pools and fluxes were correlated with the mass of fine roots per unit soil volume and there was a weak but positive correlation of NPP with LAI. Patterns of ) and NUE across the soil developmental sequence were opposite to each other. ) increased as nutrient availability and nutrient turnover increased, while NUE decreased in response to the same influences but reached its highest values where either N or P availability and turnover of both N and P were low. A negative correlation between ) and NUE supports the hypothesis that a trade-off exists between ) and leaf characteristics affecting NUE.     

Species Asynchrony and Large Trees Jointly Drive Community Stability in a Montane Subtropical Forest

Ecosystems - The relationships between biodiversity and community stability have been well-documented in grassland ecosystems, yet the diversity–stability relationship and the mechanisms...     

Stability and Change in Estuarine Biofilm Bacterial Community Diversity

Biofouling communities contribute significantly to aquatic ecosystem productivity and biogeochemical cycling. Our knowledge of the distribution, composition, and activities of these microbially dominated communities is limited compared to other components of estuarine ecosystems. This study investigated the temporal stability and change of the dominant phylogenetic groups of the domain Bacteria in estuarine biofilm communities. Glass slides were deployed monthly over 1 year for 7-day incubations during peak tidal periods in East Sabine Bay, Fla. Community profiling was achieved by using 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes in combination with ribotyping, cloning, and sequencing to evaluate diversity and to identify dominant microorganisms. Bacterial community profiles from biofilms grown near the benthos showed distinct periods of constancy within winter and summer sampling periods. Similar periods of stability were also seen in T-RFLP patterns from floating biofilms. Alternating dominance of phylogenetic groups between seasons appeared to be associated with seasonal changes in temperature, nutrient availability, and light. The community structure appeared to be stable during these periods despite changes in salinity and in dissolved oxygen.     

Tree Diversity,Forest Structure and Productivity along Altitudinal and Topographical Gradients in a Species-Rich Ecuadorian Montane Rain Forest

We studied the spatial heterogeneity of tree diversity, and of forest structure and productivity in a highly diverse tropical mountain area in southern Ecuador with the aim of understanding the causes of the large variation in these parameters. Two major environmental gradients, elevation and topography, representing a broad range of climatic and edaphic site conditions, were analyzed. We found the highest species richness of trees in valleys <2100 m. Valleys showed highest values of basal area, leaf area index and tree basal area increment as well. Tree diversity also increased from ridges to valleys, while canopy openness decreased. Significant relationships existed between tree diversity and soil parameters (pH, total contents of Mg, K, Ca, N and P), and between diversity and the spatial variability of pH and Ca and Mg contents suggesting a dependence of tree diversity on both absolute levels and on the small-scale heterogeneity of soil nutrient availability. Tree diversity and basal area increment were positively correlated, partly because both are similarly affected by soil conditions. We conclude that the extraordinarily high tree species richness in the area is primarily caused by three factors: (1) the existence of steep altitudinal and topographic gradients in a rather limited area creating a small-scale mosaic of edaphically different habitats; (2) the intermingling of Amazonian lowland plant species, that reach their upper distribution limits, and of montane forest species; and (3) the geographical position of the study area between the humid eastern Andean slope and the dry interandean forests of South Ecuador.     

Evolution of Bacterial Diversity during Enrichment of PCP-Degrading Activated Soils

The microbiota of completely mixed soil slurry was acclimated with pentachlorophenol (PCP) or with a wood preservative mixture (WPM) containing several pollutants such as PCP and petroleum hydrocarbons. The impact of these compounds on the bacterial diversity was studied by using molecular tools. PCR amplifications of the 16S ribosomal RNA gene sequences (rDNA) were carried out with total DNA extracted from soil slurry samples taken at different time points during the enrichment process of the PCP and WPM reactors. The composition of these PCR products, reflecting the bacterial diversity, was monitored by the single-strand-conformation polymorphism (SSCP) method. Our results showed that the complexity of the SSCP profiles in the PCP reactor decreased significantly during the enrichment process, whereas they remained complex in the WPM reactor. PCR-amplified 16 rDNA libraries were generated from each reactor. The SSCP method was used to rapidly screen several clones of these libraries to find specific single-strand DNA migration profiles. In the PCP-activated soil, 96% of examined clones had the same SSCP profile, and sequences of representative clones were related to the genusSphingomonas, suggesting that the enrichment with PCP resulted in a selection of little phylogenetic diversity. Four different SSCP profiles were observed with the 68 examined clones from the WPM reactor. Representative clones of these profiles were related to Methylocystaceae or Rhizobiaceae, to sulfur-oxidizing symbionts, to the genusAcinetobacter, and to the genusSphingomonas. We also cloned and sequenced PCR-amplified DNA related to thepcpB gene, coding for theSphingomonas PCP-4-monooxygenase and detected in both reactors after two weeks of enrichment. Of the 16 examined clones, deduced amino acid sequences of 13 clones were highly related to theSphingomonas sp. strain UG30pcpB. The three remainingpcpB clones were not closely related to the three knownSphingomonas pcpB.