Differences of Gut Microbiota in the Freshwater Blackworm (Lumbriculus variegatus: Oligochaeta) in Two Different Habitat Conditions

The distribution of organisms is governed by their habitat condition. We analyzed bacterial communities in the gut of the blackworm Lumbriculus variegatus by pyrosequencing of the extracted intestinal metagenomic DNA. Blackworms were collected from two sampling sites with differences in irradiance and riparian vegetation, where site GP7 was covered by riparian vegetation and site GP8 was exposed to sunlight. We obtained the filtered 6414 reads from three samples of each site. At GP7, 271 OTUs were identified, including 32 OTUs unique to the site, whereas at GP8, 238 OTUs were identified, including 22 unique OTUs. Among them, 18 OTUs were shared between both sites. The phylum Proteobacteria was a major component contributing 67.84% and 64.05% of sequences at sites GP7 and GP8, respectively, while each remaining phylum contributed less than 10% at both sites. The two sites differed in microbial community composition and KEGG-indicated biochemical pathways. Community indices such as species richness and Shannon diversity were higher at site GP7 than at GP8. Meanwhile, the abundance of Cyanobacteria was significantly higher at site GP8, while site GP7 showed a greater proportion of genes for membrane transport and carbohydrate metabolism, reflecting differences in food resources.

Download Full-text

Comparative Analysis of the Gut Microbiota of Adult Mosquitoes From Eight Locations in Hainan, China

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2020.596750 ◽

2020 ◽

Vol 10 ◽

Author(s):

Xun Kang ◽

Yanhong Wang ◽

Siping Li ◽

Xiaomei Sun ◽

Xiangyang Lu ◽

...

Keyword(s):

Gut Microbiota ◽

Disease Control ◽

Bacterial Communities ◽

Mosquito Species ◽

Microbial Community Composition ◽

Variable Region ◽

Rrna Gene ◽

Microbial Composition ◽

Quality Filtering ◽

And Function

The midgut microbial community composition, structure, and function of field-collected mosquitoes may provide a way to exploit microbial function for mosquito-borne disease control. However, it is unclear how adult mosquitoes acquire their microbiome, how the microbiome affects life history traits and how the microbiome influences community structure. We analyzed the composition of 501 midgut bacterial communities from field-collected adult female mosquitoes, including Aedes albopictus, Aedes galloisi, Culex pallidothorax, Culex pipiens, Culex gelidus, and Armigeres subalbatus, across eight habitats using the HiSeq 4000 system and the V3−V4 hyper-variable region of 16S rRNA gene. After quality filtering and rarefaction, a total of 1421 operational taxonomic units, belonging to 29 phyla, 44 families, and 43 genera were identified. Proteobacteria (75.67%) were the most common phylum, followed by Firmicutes (10.38%), Bacteroidetes (6.87%), Thermi (4.60%), and Actinobacteria (1.58%). The genera Rickettsiaceae (33.00%), Enterobacteriaceae (20.27%), Enterococcaceae (7.49%), Aeromonadaceae (7.00%), Thermaceae (4.52%), and Moraxellaceae (4.31%) were dominant in the samples analyzed and accounted for 76.59% of the total genera. We characterized the midgut bacterial communities of six mosquito species in Hainan province, China. The gut bacterial communities were different in composition and abundance, among locations, for all mosquito species. There were significant differences in the gut microbial composition between some species and substantial variation in the gut microbiota between individuals of the same mosquito species. There was a marked variation in different mosquito gut microbiota within the same location. These results might be useful in the identification of microbial communities that could be exploited for disease control.

Download Full-text

Seasonal Dynamics and Persistency of Endophyte Communities in Kalidium schrenkianum Shifts Under Radiation Stress

Frontiers in Microbiology ◽

10.3389/fmicb.2021.778327 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jing Zhu ◽

Xiang Sun ◽

Qi-Yong Tang ◽

Zhi-Dong Zhang

Keyword(s):

Microbial Community ◽

Community Composition ◽

Bacterial Communities ◽

Community Dynamics ◽

Microbial Community Composition ◽

Northwest China ◽

Community Diversity ◽

Radiation Stress ◽

Core Microbiome ◽

Essential Components

Endophytes are essential components of plant microbiota. Studies have shown that environmental factors and seasonal alternation can change the microbial community composition of plants. However, most studies have mainly emphasized the transitive endophyte communities and seasonal alternation but paid less attention to their persistence through multiple seasons. Kalidium schrenkianum is a perennial halophyte growing in an arid habitat with radiation stress (137Cs) in northwest China. In this study, K. schrenkianum growing under different environmental stresses were selected to investigate the dynamics and persistency of endophytic microbial communities amid seasons in a year. The results showed that Gammaproteobacteria and unassigned Actinobacteria were the most dominant bacterial communities, while the most dominant fungal communities were Dothideomycetes, unassigned Fungi, and Sodariomycetes. The bacterial community diversity in roots was higher than that in aerial tissues, and root communities had higher diversity in summer and autumn. In contrast, the fungal community diversity was higher in aerial tissues comparing to roots, and the highest diversity was in spring. Season was a determinant factor in the microbial community composition in the roots but not in the aerial tissues. RaupCrick index suggested that the bacterial communities were mainly shaped by stochastic processes. Our research investigated the community traits and members with temporal persistency. For example, bacterial taxa Afipia, Delftia, Stenotrophomonas, Xanthomonadaceae_B_OTU_211, and fungal taxa Neocamarosporium F_OTU_388, F_OTU_404, F_OTU_445, and unassigned Fungi F_OTU_704, F_OTU_767 showed higher frequencies than predicted in all the four seasons tested with neutral community model. The networks of co-occurrence associations presented in two or more seasons were visualized which suggested potential time-continuous core modules in most communities. In addition, the community dynamics and persistency also showed different patterns by radiation levels. Our findings would enhance our understanding of the microbial community assembly under environmental stress, and be promising to improve the development of integrated concept of core microbiome in future.

Download Full-text

Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

Diversity ◽

10.3390/d13110525 ◽

2021 ◽

Vol 13 (11) ◽

pp. 525

Author(s):

Brianna L. Boss ◽

Bianca R. Charbonneau ◽

Javier A. Izquierdo

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Plant Species ◽

Bacterial Communities ◽

Environmental Gradients ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Spatial Diversity ◽

Microbial Composition

The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species.

Download Full-text

Leptospira spp. Prevalence in Small Mammal Populations in Cotonou, Benin

ISRN Epidemiology ◽

10.5402/2013/502638 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 9

Author(s):

G. Houemenou ◽

A. Ahmed ◽

R. Libois ◽

R. A. Hartskeerl

Keyword(s):

Health Care Workers ◽

Rattus Rattus ◽

Decision Makers ◽

Small Animals ◽

Pcr Assay ◽

As Species ◽

Three Samples ◽

Care Workers ◽

Taqman Pcr ◽

Clade 1

The aim of this study was to assess the Leptospira prevalence in small animals in Cotonou, the capital of Benin. Rodents and shrews were captured in urban and periurban settings and determined as species of the genera Rattus, Mastomys, and Crocidura. Kidney specimens of 90 animals were examined using a real-time PCR assay specific for leptospires that belong to pathogenic species. Leptospiral DNA was amplified from kidney tissues ranging from 13.3% (8/60) in Rattus rattus to 100.0% (1/1) in Crocidura spp. with an average of 18.9% (17/90) of the animals caught at 15 locations. Clade-specific Taqman PCR on 10 samples placed six of these within clade 1 comprising the species L. kirschneri, L. interrogans, L. meyeri, and L. noguchii and four within clade 2 consisting of species L. weilii, L. alexanderi, L. borgpetersenii, and L. santarosai. Phylogenetic analysis of partial sequences of the amplicons of seven samples of these 10 samples revealed that four of the clade 1 samples could equally be assigned to L. interrogans and L. kirschneri and three samples from clade 2 belonged to L. borgpetersenii. Results presented in the paper indicate that small mammals present a major public health risk for acquiring leptospirosis in Cotonou, Benin and will contribute to a raised awareness amongst health care workers and decision makers and hence promote appropriate clinical management of cases.

Download Full-text

Microbial Predation Accelerates Granulation and Modulates Microbial Community Composition

10.21203/rs.3.rs-146426/v1 ◽

2021 ◽

Author(s):

Siew Herng Chan ◽

Muhammad Hafiz Ismail ◽

Chuan Hao Tan ◽

Scott A. Rice ◽

Diane McDougald

Keyword(s):

Bacterial Communities ◽

Microbial Community Composition ◽

Extracellular Dna ◽

Biological Nutrient Removal ◽

Strong Positive Correlation ◽

Bacterial Cells ◽

Dominant Group ◽

Granule Formation ◽

Structural Formation ◽

Granulation Process

Abstract BackgroundBacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge.ResultsFour independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These protozoa had a strong, positive-correlation with the initial formation of compact aggregates prior to granule development. Furthermore, chemical inhibition of these ciliates in the floccular sludge delayed the initiation of granule formation. Analysis of the bacterial communities in the thiram treated sludge demonstrated that the recovery of ‘Candidatus Accmulibacter’ was positively correlated with the formation of compact aggregates and granules.ConclusionPredation by bacteriophage and protozoa were positively correlated with the formation of aerobic granules. Increases in Inoviridae abundance suggested that filamentous phages may promote the structural formation of granules. Initiation of granules formation was delayed due to an absence of protozoa after chemical treatment. The presence of Candidatus Accumulibacter was necessary for the formation of granules in the absence of protozoa.

Download Full-text

Impact of enzymatic digestion on bacterial community composition in CF airway samples

PeerJ ◽

10.7717/peerj.3362 ◽

2017 ◽

Vol 5 ◽

pp. e3362 ◽

Cited By ~ 1

Author(s):

Kayla M. Williamson ◽

Brandie D. Wagner ◽

Charles E. Robertson ◽

Emily J. Johnson ◽

Edith T. Zemanick ◽

...

Keyword(s):

Bacterial Community ◽

Dna Extraction ◽

Community Composition ◽

Bacterial Communities ◽

Beta Diversity ◽

Diversity Index ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Enzymatic Digestion ◽

Rrna Gene

BackgroundPrevious studies have demonstrated the importance of DNA extraction methods for molecular detection ofStaphylococcus,an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF.MethodsDNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD.ResultsShannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the generaGemella(p < 0.01),Streptococcus(p < 0.01), andRothia(p < 0.01).Staphylococcus(p < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD:Veillonella(p < 0.01),Granulicatella(p < 0.01),Prevotella(p < 0.01), andGemella(p = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition.DiscussionWe show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection ofStaphylococcusin CF OP samples. The enhanced identification ofStaphylococcus aureusis a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

Download Full-text

Negative Effects of Sample Pooling on PCR-Based Estimates of Soil Microbial Richness and Community Structure

Applied and Environmental Microbiology ◽

10.1128/aem.03017-09 ◽

2010 ◽

Vol 76 (7) ◽

pp. 2086-2090 ◽

Cited By ~ 35

Author(s):

Daniel K. Manter ◽

Tiffany L. Weir ◽

Jorge M. Vivanco

Keyword(s):

Microbial Community ◽

Soil Microbial Community ◽

Bacterial Communities ◽

Microbial Community Composition ◽

Pcr Amplification ◽

Intergenic Spacer ◽

Negative Effects ◽

Soil Microbial ◽

Sample Pooling ◽

The Impact

ABSTRACT In this study, we examined the effect of various pooling strategies on the characterization of soil microbial community composition and phylotype richness estimates. Automated ribosomal intergenic spacer analysis (ARISA) profiles were determined from soil samples that were (i) unpooled (extracted and amplified individually), (ii) pooled prior to PCR amplification, or (iii) pooled prior to DNA extraction. Regression analyses suggest that the less even the soil microbial community (i.e., low Shannon equitability, EH ), the greater was the impact of either pooling strategy on microbial detection (R 2 = 0.766). For example, at a tropical rainforest site, which had the most uneven fungal (EH of 0.597) and bacterial communities (EH of 0.822), the unpooled procedure detected an additional 67 fungal and 115 bacterial phylotypes relative to either of the pooled procedures. Phylotype rarity, resulting in missed detection upon pooling, differed between the fungal and bacterial communities. Fungi were typified by locally abundant but spatially rare phylotypes, and the bacteria were typified by locally rare but spatially ubiquitous phylotypes. As a result, pooling differentially influenced plot comparisons, leading to an increase in similarity for the bacterial community and a decrease in the fungal community. In conclusion, although pooling reduces sample numbers and variability, it could mask a significant portion of the detectable microbial community, particularly for fungi due to their higher spatial heterogeneity.

Download Full-text

Microbial predation accelerates granulation and modulates microbial community composition

BMC Microbiology ◽

10.1186/s12866-021-02156-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Siew Herng Chan ◽

Muhammad Hafiz Ismail ◽

Chuan Hao Tan ◽

Scott A. Rice ◽

Diane McDougald

Keyword(s):

Bacterial Communities ◽

Microbial Community Composition ◽

Extracellular Dna ◽

Biological Nutrient Removal ◽

Strong Positive Correlation ◽

Bacterial Cells ◽

Dominant Group ◽

Granule Formation ◽

Structural Formation ◽

Granulation Process

Abstract Background Bacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge. Results Four independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These protozoa had a strong, positive-correlation with the initial formation of compact aggregates prior to granule development. Furthermore, chemical inhibition of these ciliates in the floccular sludge delayed the initiation of granule formation. Analysis of the bacterial communities in the thiram treated sludge demonstrated that the recovery of ‘Candidatus Accumulibacter’ was positively correlated with the formation of compact aggregates and granules. Conclusion Predation by bacteriophage and protozoa were positively correlated with the formation of aerobic granules. Increases in Inoviridae abundance suggested that filamentous phages may promote the structural formation of granules. Initiation of granules formation was delayed due to an absence of protozoa after chemical treatment. The presence of ‘Candidatus Accumulibacter’ was necessary for the formation of granules in the absence of protozoa.

Download Full-text

The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore

Microorganisms ◽

10.3390/microorganisms9050898 ◽

2021 ◽

Vol 9 (5) ◽

pp. 898

Author(s):

Ren Min Oh ◽

Elena Bollati ◽

Prasha Maithani ◽

Danwei Huang ◽

Benjamin J. Wainwright

Keyword(s):

Coral Reef ◽

Microbial Communities ◽

Bacterial Communities ◽

Microbial Community Composition ◽

Pcr Amplification ◽

Rrna Gene ◽

Benthic Organisms ◽

Polymerase Chain ◽

Microbial Change ◽

The 16S Rrna Gene

The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.

Download Full-text

Structure of Riparian Vegetation and Its Implications for The Habitat Conditions of Arfak Rainbowfish, Melanotaenia Arfakensis at The Nimbai Stream, Manokwari, West Papua

Samakia : Jurnal Ilmu Perikanan ◽

10.35316/jsapi.v10i1.258 ◽

2019 ◽

Vol 10 (1) ◽

pp. 38-56

Author(s):

Paskalina Th. Lefaan ◽

Hans Fence Zakeus Peday ◽

Simon Petrus Oktovianus Leatemia ◽

Luky Sembel ◽

Emmanuel Manangkalangi

Keyword(s):

Vegetation Structure ◽

Riparian Vegetation ◽

Fish Larvae ◽

Riparian Forest ◽

Level Density ◽

Fish Habitat ◽

Canopy Cover ◽

Tree Level ◽

Habitat Conditions ◽

Sample Collection

Riparian vegetation has an important role in maintaining water stability, one of which is the river. This study aims to describe the structure of riparian vegetation so that its implications can be seen for the conditions of rainbow arfak habitat on the Nimbai River. The study was conducted in three forest types, namely primary riparia forest, secondary riparia forest and open riparia forest. Sample collection of riparian vegetation was carried out by purposive sampling using sample plots. Plots measuring 2 m x 2 m are used to sample seedling and understorey growth, plots measuring 5 m x 5 m for growth at the stake level, while plots measuring 10 m x 10 m and 20 m x 20 m, for growth of pole and tree levels respectively. The identification results obtained a total of 35 species of understorey and 51 tree-level plants in all three types of riparian forests. Based on the analysis of vegetation structure, it is known that the condition of primary riparia forest and secondary riparian forest still relatively supports the life of arfak rainbow fish compared to open riparian forest. Higher tree level density associated with canopy cover which has implications for the temperature of the water to be colder and less fluctuating, input larger litter into the food chain in the river, and hold suspended particles into the river. Also, the function of riparian vegetation in spawning activities, substrate attaching eggs and nursery habitat for arfak rainbow fish larvae. The results of this study indicate the importance of riparian vegetation structure on the condition of rainbow arfak fish habitat. An understanding of the structure of vegetation is also a basic information for efforts to rehabilitate this endemic fish habitat to maintain the existence of a natural population.

Download Full-text