Dynamics of an experimental microbial invasion

The ecological dynamics underlying species invasions have been a major focus of research in macroorganisms for the last five decades. However, we still know little about the processes behind invasion by unicellular organisms. To expand our knowledge of microbial invasions, we studied the roles of propagule pressure, nutrient supply, and biotic resistance in the invasion success of a freshwater invasive alga, Prymnesium parvum, using microcosms containing natural freshwater microbial assemblages. Microcosms were subjected to a factorial design with two levels of nutrient-induced diversity and three levels of propagule pressure, and incubated for 7 d, during which P. parvum densities and microbial community composition were tracked. Successful invasion occurred in microcosms receiving high propagule pressure whereas nutrients or community diversity played no role in invasion success. Invaded communities experienced distinctive changes in composition compared with communities where the invasion was unsuccessful. Successfully invaded microbial communities had an increased abundance of fungi and ciliates, and decreased abundances of diatoms and cercozoans. Many of these changes mirrored the microbial community changes detected during a natural P. parvum bloom in the source system. This role of propagule pressure is particularly relevant for P. parvum in the reservoir-dominated southern United States because this species can form large, sustained blooms that can generate intense propagule pressures for downstream sites. Human impact and global climate change are currently causing widespread environmental changes in most southern US freshwater systems that may facilitate P. parvum establishment and, when coupled with strong propagule pressure, could put many more systems at risk for invasion.

Download Full-text

Competitive displacement or biotic resistance? Disentangling relationships between community diversity and invasion success of tall herbs and shrubs

Journal of Vegetation Science ◽

10.1111/j.1654-1103.2009.01139.x ◽

2010 ◽

Vol 21 (2) ◽

pp. 213-220 ◽

Cited By ~ 36

Author(s):

Jan Thiele ◽

Maike Isermann ◽

Annette Otte ◽

Johannes Kollmann

Keyword(s):

Biotic Resistance ◽

Invasion Success ◽

Community Diversity ◽

Competitive Displacement

Download Full-text

Spatial and Annual Variation in Microbial Abundance, Community Composition, and Diversity Associated With Alpine Surface Snow

Frontiers in Microbiology ◽

10.3389/fmicb.2021.781904 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lucas Fillinger ◽

Kerstin Hürkamp ◽

Christine Stumpp ◽

Nina Weber ◽

Dominik Forster ◽

...

Keyword(s):

Climate Change ◽

Microbial Community ◽

Community Composition ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Community Diversity ◽

Taxon Richness ◽

European Alps ◽

Prokaryotic Cell ◽

Surface Snow

Understanding microbial community dynamics in the alpine cryosphere is an important step toward assessing climate change impacts on these fragile ecosystems and meltwater-fed environments downstream. In this study, we analyzed microbial community composition, variation in community alpha and beta diversity, and the number of prokaryotic cells and virus-like particles (VLP) in seasonal snowpack from two consecutive years at three high altitude mountain summits along a longitudinal transect across the European Alps. Numbers of prokaryotic cells and VLP both ranged around 104 and 105 per mL of snow meltwater on average, with variation generally within one order of magnitude between sites and years. VLP-to-prokaryotic cell ratios spanned two orders of magnitude, with median values close to 1, and little variation between sites and years in the majority of cases. Estimates of microbial community alpha diversity inferred from Hill numbers revealed low contributions of common and abundant microbial taxa to the total taxon richness, and thus low community evenness. Similar to prokaryotic cell and VLP numbers, differences in alpha diversity between years and sites were generally relatively modest. In contrast, community composition displayed strong variation between sites and especially between years. Analyses of taxonomic and phylogenetic community composition showed that differences between sites within years were mainly characterized by changes in abundances of microbial taxa from similar phylogenetic clades, whereas shifts between years were due to significant phylogenetic turnover. Our findings on the spatiotemporal dynamics and magnitude of variation of microbial abundances, community diversity, and composition in surface snow may help define baseline levels to assess future impacts of climate change on the alpine cryosphere.

Download Full-text

Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range

Frontiers in Microbiology ◽

10.3389/fmicb.2020.626713 ◽

2021 ◽

Vol 11 ◽

Author(s):

Janneke Schreuder ◽

Francisca C. Velkers ◽

Alex Bossers ◽

Ruth J. Bouwstra ◽

Willem F. de Boer ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Intestinal Microbiota ◽

Environmental Changes ◽

Temporal Dynamics ◽

Microbial Community Composition ◽

Sudden Change ◽

Rrna Gene ◽

Poultry House ◽

Over Time

Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.

Download Full-text

Response of Soil Microbial Community Structure and Function to Different Altitudes in Arid Valley in Panzhihua, China

10.21203/rs.3.rs-1055315/v1 ◽

2021 ◽

Author(s):

Runji Zhang ◽

Xianrui Tian ◽

Quanju Xiang ◽

Petri Penttinen ◽

Yunfu Gu

Keyword(s):

Microbial Community ◽

Community Composition ◽

Environmental Changes ◽

Microbial Community Composition ◽

Chemical Properties ◽

Microbial Biomass C ◽

Chemical Characteristics ◽

Soil Microbial Community Structure ◽

Available N ◽

Different Altitudes

Abstract Background: Altitude affects biodiversity and physic-chemical properties of soil, providing natural sites for studying species distribution and the response of biota to environmental changes. We sampled soil at three altitudes in an arid valley, determined the physic-chemical characteristics and microbial community composition in the soils, identified differentially abundant taxa and the relationships between community composition and environmental factors. Results: The low, medium and high altitudes were roughly separated based on the physic-chemical characteristics and clearly separated based on the microbial community composition. The differences in community composition were associated with differences in all measured factors except pH. The contents of organic and microbial biomass C, total and available N and available P, and the richness and diversity of the microbial communities were lowest in the medium altitude. The relative abundances of phyla Proteobacteria, Gemmatimonadetes, Actinobacteria and Acidobacteria were high at all altitudes. The differentially abundant ASVs were mostly assigned to Proteobacteria and Acidobacteria. The highest number of ASVs characterizing altitude were detected in the high altitude. However, the predicted functions of the communities were overlapping, suggesting that the contribution of the communities to soil processes changed relatively little along the altitude gradient. Conclusions: The composition of microbial community at different altitudes was related to the differences of all measuring factors except pH in arid valley in Panzhihua, China.

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

Feed Types Driven Differentiation of Microbial Community and Functionality in Marine Integrated Multitrophic Aquaculture System

Water ◽

10.3390/w12010095 ◽

2019 ◽

Vol 12 (1) ◽

pp. 95

Author(s):

Yale Deng ◽

Fan Zhou ◽

Yunjie Ruan ◽

Bin Ma ◽

Xueyan Ding ◽

...

Keyword(s):

Microbial Community ◽

Metabolic Pathways ◽

Pathogenic Bacteria ◽

Microbial Community Composition ◽

Nutrient Utilization ◽

Community Diversity ◽

Antibiotic Biosynthesis ◽

Fish Diet ◽

Formulated Diet ◽

Frozen Fish

Integrated multi trophic aquaculture (IMTA) improves the production of aquatic animals by promoting nutrient utilization through different tropical levels. Microorganisms play an important role in elements cycling, energy flow and farmed-species health. The aim of this study was to evaluate how feed types, fresh frozen fish diet (FFD) or formulated diet (FD), influence the microbial community diversity and functionality in both water and sediment in a marine IMTA system. Preferable water quality, higher animal yields and higher cost efficiency were achieved in the FD pond. Feed types changed the pond bacterial community distribution, especially in the rearing water. The FFD pond was dominated with Cyanobacteria in the water, which played an important role in nitrogen fixation through photosynthesis due to the high nitrogen input of the frozen fish diet. The high carbohydrate composition in the formulated diet triggered higher metabolic pathways related to carbon and lipid metabolism in the water of the FD pond. Sediment had significantly higher microbial diversity than the rearing water. In sediment, the dominating genus, Sulfurovum and Desulfobulbus, were found to be positively correlated by network analysis, which had similar functionality in sulfur transformation. The relatively higher rates of antibiotic biosynthesis in the FFD sediment might be related to the pathogenic bacteria introduced by the trash fish diet. The difference in microbial community composition and metabolic pathways may be associated with the different pathways for nutrient cycling and animal growth performance. The formulated diet was determined to be more ecologically and economically sustainable than the frozen fish diet for marine IMTA pond systems.

Download Full-text

Elevated ozone concentration and nitrogen addition increase poplar rust severity by shifting the phyllosphere microbial community

10.1101/2021.12.23.474070 ◽

2021 ◽

Author(s):

Siqi Tao ◽

Yunxia Zhang ◽

Chengming Tian ◽

Sébastien Duplessis ◽

Naili Zhang

Keyword(s):

Microbial Community ◽

Environmental Changes ◽

Negative Impact ◽

Plant Immunity ◽

Microbial Community Composition ◽

Environmental Pollutants ◽

Soil N ◽

N Addition ◽

Α Diversity ◽

Rust Severity

The tropospheric ozone and nitrogen deposition are two major environmental pollutants. Numerous studies have focused on the negative impacts of elevated O3 and the complementary effect of soil N addition to tree physiological characteristics. However, it was notoriously ignored of how elevated O3 with N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host-pathogen-environment interplay. Here, we examined the effects of elevated O3 and soil N addition on poplar leaf rust (Melampsora larici-populina) severity of two susceptible hybrid poplars (clone ‘107’: Populus euramericana cv. ‘74/76’; clone ‘546’: P. deltoides × P. cathayana) in Free-Air-Controlled-Environment plots, besides, the link between Mlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone ‘107’ significantly increased under elevated O3 or N addition only, however, the negative impact of elevated O3 could be significantly alleviated when simultaneously conducting N addition, likewise, this trade-off was also found in its phyllosphere microbial α-diversity responding to elevated O3 and N addition. However, the rust severity of clone ‘546’ did not significantly differ in the cases of elevated O3 and N addition. Mlp-infection altered microbial community composition and increased its sensitivity to elevated O3 assessed by significantly different abundance of taxa. Elevated O3 and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings demonstrated that poplars need shifting phyllosphere microbial associations to optimize plant immunity in response to environmental changes.

Download Full-text

Biotic resistance shapes the influence of propagule pressure on invasion success in bacterial communities

Ecology ◽

10.1002/ecy.1852 ◽

2017 ◽

Vol 98 (7) ◽

pp. 1743-1749 ◽

Cited By ~ 15

Author(s):

Matt L. Jones ◽

Josep Ramoneda ◽

Damian W. Rivett ◽

Thomas Bell

Keyword(s):

Bacterial Communities ◽

Biotic Resistance ◽

Propagule Pressure ◽

Invasion Success

Download Full-text

Microbial assembly, interaction, functioning, activity and diversification: a review derived from community compositional data

Marine Life Science & Technology ◽

10.1007/s42995-019-00004-3 ◽

2019 ◽

Vol 1 (1) ◽

pp. 112-128 ◽

Cited By ~ 11

Author(s):

Jiwen Liu ◽

Zhe Meng ◽

Xiaoyue Liu ◽

Xiao-Hua Zhang

Keyword(s):

Microbial Community ◽

Ecosystem Functioning ◽

High Throughput Sequencing ◽

Environmental Changes ◽

Compositional Data ◽

Marker Gene ◽

Microbial Community Composition ◽

Gene Transcription Level ◽

Occurrence Patterns ◽

Phylogenetic Divergence

Abstract Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge in studies on marine microbial community composition using high-throughput sequencing methods. Extensive mining of the compositional data has provided exciting new insights into marine microbial ecology from a number of perspectives. Both deterministic and stochastic processes contribute to microbial community assembly but their relative importance in structuring subcommunities, that are categorized by traits such as abundance, functional type and activity, differs. Through correlation-based network analysis, significant progress has been made in unraveling microbial co-occurrence patterns and dynamics in response to environmental changes. Prediction of ecosystem functioning, based on microbial data, is receiving increasing attention, as closely related microbes often share similar ecological traits and microbial diversity often exhibits significant correlations to ecosystem functioning. The ecosystem functioning is likely executed not by the whole community, but rather by an active fraction of a community, which can be inferred from the marker gene transcription level of community members. Furthermore, the huge amount of microbial community data has significantly expanded the tree of life and illuminated microbial phylogenetic divergence and evolutionary history. This review summarizes important findings in microbial assembly, interaction, functioning, activity and diversification, highlighting the interacting roles of different aspects, derived from community compositional data.

Download Full-text