scholarly journals Bacterial communities affected by experimental disturbances to canopy soils of a temperate rainforest

2016 ◽  
Author(s):  
Cody R. Dangerfield ◽  
Nalini M. Nadkarni ◽  
William J. Brazelton
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Forest Floor ◽  
Soil Bacteria ◽  
Host Tree ◽  
Temperate Rainforest ◽  
Living Tree ◽  
Canopy Soil ◽  
Unique Nature ◽  
Temperate Rainforests

ABSTRACTTrees of temperate rainforests host a large biomass of epiphytes, living plants associated with soils formed in the forest canopy. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different species-level operational taxonomic units. A field experiment was conducted to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, connection to the living tree is an important factor in the ecology of canopy soil bacteria. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.IMPORTANCETemperate rainforests host large accumulations of epiphytes, plants that live on the branches of trees. This study provides a first look at the unique nature of bacterial communities in soil that is formed by the decomposition of epiphytes in the canopy of a temperate rainforest. Falling of epiphytic material results in the transfer of significant amounts of carbon and nutrients from the canopy to the forest floor. This study also experimentally documented how soil bacterial communities are affected by their movement from the canopy to the forest floor. The bacterial composition of canopy soil was altered by the severing of the epiphytic material from the living tree, even when the epiphytes remained in the canopy. Therefore, the unique nature of canopy soil bacteria is determined in part by the living host tree and not only by the physical environmental conditions associated with the canopy.

scholarly journals Canopy soil bacterial communities altered by severing host tree limbs

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3773 ◽  
Author(s):  
Cody R. Dangerfield ◽  
Nalini M. Nadkarni ◽  
William J. Brazelton
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Forest Floor ◽  
Soil Bacteria ◽  
Forest Canopy ◽  
Evolutionary Dynamics ◽  
Host Tree ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Canopy Soil

Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.

scholarly journals Bacterial diversity and predicted enzymatic function in a multipurpose surface water system – from wastewater effluent discharges to drinking water production

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Ananda Tiwari ◽  
Anna-Maria Hokajärvi ◽  
Jorge Santo Domingo ◽  
Michael Elk ◽  
Balamuralikrishna Jayaprakash ◽  
...  
Keyword(s):  
Drinking Water ◽  
Surface Water ◽  
Bacterial Community ◽  
Human Health ◽  
Bacterial Diversity ◽  
Water Samples ◽  
Bacterial Communities ◽  
Treatment Process ◽  
Pollution Sources ◽  
Production Well

Abstract Background Rivers and lakes are used for multiple purposes such as for drinking water (DW) production, recreation, and as recipients of wastewater from various sources. The deterioration of surface water quality with wastewater is well-known, but less is known about the bacterial community dynamics in the affected surface waters. Understanding the bacterial community characteristics —from the source of contamination, through the watershed to the DW production process—may help safeguard human health and the environment. Results The spatial and seasonal dynamics of bacterial communities, their predicted functions, and potential health-related bacterial (PHRB) reads within the Kokemäenjoki River watershed in southwest Finland were analyzed with the 16S rRNA-gene amplicon sequencing method. Water samples were collected from various sampling points of the watershed, from its major pollution sources (sewage influent and effluent, industrial effluent, mine runoff) and different stages of the DW treatment process (pre-treatment, groundwater observation well, DW production well) by using the river water as raw water with an artificial groundwater recharge (AGR). The beta-diversity analysis revealed that bacterial communities were highly varied among sample groups (R = 0.92, p <  0.001, ANOSIM). The species richness and evenness indices were highest in surface water (Chao1; 920 ± 10) among sample groups and gradually decreased during the DW treatment process (DW production well; Chao1: 320 ± 20). Although the phylum Proteobacteria was omnipresent, its relative abundance was higher in sewage and industrial effluents (66–80%) than in surface water (55%). Phyla Firmicutes and Fusobacteria were only detected in sewage samples. Actinobacteria was more abundant in the surface water (≥13%) than in other groups (≤3%). Acidobacteria was more abundant in the DW treatment process (≥13%) than in others (≤2%). In total, the share of PHRB reads was higher in sewage and surface water than in the DW treatment samples. The seasonal effect in bacterial communities was observed only on surface water samples, with the lowest diversity during summer. Conclusions The low bacterial diversity and absence of PHRB read in the DW samples indicate AGR can produce biologically stable and microbiologically safe drinking water. Furthermore, the significantly different bacterial communities at the pollution sources compared to surface water and DW samples highlight the importance of effective wastewater treatment for protecting the environment and human health.

scholarly journals Effect of milk replacer allowance on calf faecal bacterial community profiles and fermentation

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sandeep Kumar ◽  
M. Ajmal Khan ◽  
Emma Beijer ◽  
Jinxin Liu ◽  
Katherine K. Lowe ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Body Weight ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Serum Protein ◽  
Bacterial Communities ◽  
Short Chain Fatty Acids ◽  
Short Chain ◽  
Milk Replacer ◽  
Protein Levels

Abstract Background The nutrition of calves from birth until weaning is predominantly from liquid (milk or milk-based) feeds. Liquid feed allowances are often restricted during artificial rearing to accelerate the development of the rumen by promoting solid feed intake. Liquid feeds bypass the rumen and are digested in the lower digestive tract, however, the influence of different types of milk feeds, and their allowances, on the calf hindgut microbiota is not well understood. In this study, faecal samples from 199 calves raised on three different allowances of milk replacer: 10% of initial bodyweight (LA), 20% of initial bodyweight (HA), and ad libitum (ADLIB), were collected just prior to weaning. Bacterial community structures and fermentation products were analysed, and their relationships with calf growth and health parameters were examined to identify potential interactions between diet, gut microbiota and calf performance. Results Differences in the total concentrations of short-chain fatty acids were not observed, but higher milk replacer allowances increased the concentrations of branched short-chain fatty acids and decreased acetate to propionate ratios. The bacterial communities were dominated by Ruminococcaceae, Lachnospiraceae and Bacteroides, and the bacterial diversity of the ADLIB diet group was greater than that of the other diet groups. Faecalibacterium was over three times more abundant in the ADLIB compared to the LA group, and its abundance correlated strongly with girth and body weight gains. Milk replacer intake correlated strongly with Peptococcus and Blautia, which also correlated with body weight gain. Bifidobacterium averaged less than 1% abundance, however its levels, and those of Clostridium sensu stricto 1, correlated strongly with initial serum protein levels, which are an indicator of colostrum intake and passive transfer of immunoglobulins in early life. Conclusions Higher milk replacer intakes in calves increased hindgut bacterial diversity and resulted in bacterial communities and short chain fatty acid profiles associated with greater protein fermentation. Increased abundances of beneficial bacteria such as Faecalibacterium, were also observed, which may contribute to development and growth. Moreover, correlations between microbial taxa and initial serum protein levels suggest that colostrum intake in the first days of life may influence microbiota composition at pre-weaning.

scholarly journals Spatio-Temporal Variation of the Bacterial Communities along a Salinity Gradient within a Thalassohaline Environment (Saline di Tarquinia Salterns, Italy)

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1338
Author(s):  
Susanna Gorrasi ◽  
Andrea Franzetti ◽  
Roberto Ambrosini ◽  
Francesca Pittino ◽  
Marcella Pasqualetti ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Generalized Linear Models ◽  
Bacterial Communities ◽  
Linear Models ◽  
Salinity Gradient ◽  
Sampling Site ◽  
Α Diversity ◽  
Spatio Temporal ◽  
Abundance Variation ◽  
Microbiological Aspects

The “Saline di Tarquinia” salterns have been scarcely investigated regarding their microbiological aspects. This work studied the structure and composition of their bacterial communities along the salinity gradient (from the nearby sea through different ponds). The communities showed increasing simplification of pond bacterial diversity along the gradient (particularly if compared to those of the sea). Among the 38 assigned phyla, the most represented were Proteobacteria, Actinobacteria and Bacteroidetes. Differently to other marine salterns, where at the highest salinities Bacteroidetes dominated, preponderance of Proteobacteria was observed. At the genus level the most abundant taxa were Pontimonas, Marivita, Spiribacter, Bordetella, GpVII and Lentibacter. The α-diversity analysis showed that the communities were highly uneven, and the Canonical Correspondence Analysis indicated that they were structured by various factors (sampling site, sampling year, salinity, and sampling month). Moreover, the taxa abundance variation in relation to these significant parameters were investigated by Generalized Linear Models. This work represents the first investigation of a marine saltern, carried out by a metabarcoding approach, which permitted a broad vision of the bacterial diversity, covering both a wide temporal span (two years with monthly sampling) and the entire salinity gradient (from the nearby sea up to the crystallisation ponds).

scholarly journals Ecological succession of fungal and bacterial communities in Antarctic mosses affected by a fairy ring disease

2021 ◽  
Author(s):  
Luiz Henrique Rosa ◽  
Otávio Henrique Bezerra Pinto ◽  
Lívia Costa Coelho ◽  
Peter Convey ◽  
Micheline Carvalho-Silva ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Pathogenic Fungi ◽  
Plant Pathogenic Fungi ◽  
King George Island ◽  
Fairy Rings ◽  
Fungal Assemblages ◽  
Antarctic Mosses

Abstract We evaluated fungal and bacterial diversity in an established moss carpet on King George Island, Antarctica, affected by ‘fairy ring’ disease using metabarcoding. These microbial communities were assessed through the main stages of the disease. A total of 127 fungal and 706 bacterial taxa were assigned. The phylum Ascomycota dominated the fungal assemblages, followed by Basidiomycota, Rozellomycota, Chytridiomycota, Mortierellomycota and Monoblepharomycota. The fungal community displayed high indices of diversity, richness and dominance, which increased from healthy through infected to dead moss samples. Bacterial diversity and richness were greatest in healthy moss and least within the infected fairy ring. Chalara sp. 1, Alpinaria sp., Helotiaceae sp. 2, Chaetothyriales sp. 1, Ascomycota sp. 1, Rozellomycota sp. and Fungi sp. were most abundant within the fairy ring samples. A range of fungal taxa were more abundant in dead rather than healthy or fairy ring moss samples. The dominant prokaryotic phyla were Actinobacteriota, Proteobacteria, Bacteroidota and Cyanobacteria. The taxon Cyanobacteriia sp., whilst consistently dominant, were less abundant in fairy ring samples. Microbacteriaceae sp. and Chloroflexi sp. were the most abundant taxa within the fairy rings. Our data confirmed the presence and abundance of a range of plant pathogenic fungi, supporting the hypothesis that the disease is linked with multiple fungal taxas. Further studies are required to characterise the interactions between plant pathogenic fungi and their host Antarctic mosses. Monitoring the dynamics of mutualist, phytopathogenic and decomposer microorganisms associated with moss carpets may provide bioindicators of moss health.

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