Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords

SummarySystems with strong horizontal and vertical gradients, such as fjords, are useful models for studying environmental forcing. Here we examine microbial (prokaryotic and eukaryotic) community changes associated with the surface low salinity layer (LSL) and underlying seawater in multiple fjords in Fiordland National Park (New Zealand). High rainfall (1200-8000 mm annually) and linked runoff from native forested catchments results in surface LSLs with high tannin concentrations within each fjord. These gradients are expected to drive changes in microbial communities. We used amplicon sequencing (16S and 18S) to assess the impact of these gradients on microbial communities and identified depth linked changes in diversity and community structure. With increasing depth we observed significant increases in Proteobacteria (15%) and SAR (37%), decreases in Opisthokonta (35%), and transiently increased Bacteroidetes (3% increase from 0 to 40 m, decreasing by 8% at 200 m). Community structure differences were observed along a transect from inner to outer regions, specifically 25% mean relative abundance decreases in Opisthokonta and Bacteroidetes, and increases in SAR (25%) and Proteobacteria (>5%) at the surface, indicating changes based on distance from the ocean. This provides the first in-depth view into the ecological drivers of microbial communities within New Zealand fjords.

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High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

10.21203/rs.3.rs-34433/v1 ◽

2020 ◽

Author(s):

Wu Qu ◽

Boliang Gao ◽

Jie Wu ◽

Min Jin ◽

Jianxin Wang ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Fungal Community ◽

Amplicon Sequencing ◽

Biotic Factors ◽

Community Structures ◽

Mangrove Sediments ◽

Element Cycling ◽

Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

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Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

Frontiers in Microbiology ◽

10.3389/fmicb.2021.668240 ◽

2021 ◽

Vol 12 ◽

Author(s):

Charles S. Cockell ◽

Bettina Schaefer ◽

Cornelia Wuchter ◽

Marco J. L. Coolen ◽

Kliti Grice ◽

...

Keyword(s):

Microbial Communities ◽

Amplicon Sequencing ◽

Granitic Rocks ◽

Rrna Gene ◽

Deep Biosphere ◽

Deep Subsurface ◽

Cell Biomass ◽

Colonization Potential ◽

The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

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Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins

Foods ◽

10.3390/foods9091247 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1247

Author(s):

Emiel Van Reckem ◽

Christina Charmpi ◽

David Van der Veken ◽

Wim Borremans ◽

Luc De Vuyst ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput ◽

Bacterial Communities ◽

Geographical Origin ◽

Salt Content ◽

Amplicon Sequencing ◽

Taxonomic Resolution ◽

Future Application ◽

Processing Conditions ◽

The Impact

Insight into the microbial species diversity of fermented meats is not only paramount to gain control over quality development, but also to better understand the link with processing technology and geographical origin. To study the composition of the microbial communities, the use of culture-independent methods is increasingly popular but often still suffers from drawbacks, such as a limited taxonomic resolution. This study aimed to apply a previously developed high-throughput amplicon sequencing (HTS) method targeting the 16S rRNA and tuf genes to characterize the bacterial communities in European fermented meats in greater detail. The data obtained broadened the view on the microbial communities that were associated with the various products examined, revealing the presence of previously underreported subdominant species. Moreover, the composition of these communities could be linked to the specificities of individual products, in particular pH, salt content, and geographical origin. In contrast, no clear links were found between the volatile organic compound profiles of the different products and the country of origin, distinct processing conditions, or microbial communities. Future application of the HTS method offers the potential to further unravel complex microbial communities in fermented meats, as well as to assess the impact of different processing conditions on microbial consortia.

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Large seasonal and spatial variation in nano- and microphytoplankton diversity along a Baltic Sea—North Sea salinity gradient

Scientific Reports ◽

10.1038/s41598-020-74428-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Malin Olofsson ◽

James G. Hagan ◽

Bengt Karlson ◽

Lars Gamfeldt

Keyword(s):

Community Structure ◽

Temporal Variation ◽

High Salinity ◽

Salinity Gradient ◽

Seasonal Succession ◽

Phytoplankton Diversity ◽

Cell Abundance ◽

Low Salinity ◽

Spatio Temporal ◽

The Impact

Abstract Aquatic phytoplankton experience large fluctuations in environmental conditions during seasonal succession and across salinity gradients, but the impact of this variation on their diversity is poorly understood. We examined spatio-temporal variation in nano- and microphytoplankton (> 2 µm) community structure using almost two decades of light-microscope based monitoring data. The dataset encompasses 19 stations that span a salinity gradient from 2.8 to 35 along the Swedish coastline. Spatially, both regional and local phytoplankton diversity increased with broad-scale salinity variation. Diatoms dominated at high salinity and the proportion of cyanobacteria increased with decreasing salinity. Temporally, cell abundance peaked in winter-spring at high salinity but in summer at low salinity. This was likely due to large filamentous cyanobacteria blooms that occur in summer in low salinity areas, but which are absent in higher salinities. In contrast, phytoplankton local diversity peaked in spring at low salinity but in fall and winter at high salinity. Whilst differences in seasonal variation in cell abundance were reasonably well-explained by variation in salinity and nutrient availability, variation in local-scale phytoplankton diversity was poorly predicted by environmental variables. Overall, we provide insights into the causes of spatio-temporal variation in coastal phytoplankton community structure while also identifying knowledge gaps.

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Community structure of micro- and macroflocs in pin-point sludge and the influence of sludge age and potassium addition on microfloc formation

Water Science & Technology ◽

10.2166/wst.2002.0508 ◽

2002 ◽

Vol 46 (1-2) ◽

pp. 405-412 ◽

Cited By ~ 9

Author(s):

E. Müller ◽

K. Kriebitzsch ◽

P.A. Wilderer ◽

S. Wuertz

Keyword(s):

Community Structure ◽

Microbial Communities ◽

Extracellular Polymeric Substances ◽

Point Of View ◽

Sludge Formation ◽

Industrial Plants ◽

Noticeable Improvement ◽

Lower Protein ◽

Utilization Patterns ◽

The Impact

Settling problems caused by pin-point sludge constitute a serious problem in biological wastewater treatment, particularly in many industrial plants. Until now, most studies focused on the relationship between pin-point sludge formation and either shearing forces or the impact of toxicants. This study deals with the community structure in both the micro- and macrofloc fraction which was analyzed by fluorescent in situ hybridization (FISH) and BIOLOG substrate utilization patterns. It was shown that each fraction consisted of different microbial communities with unique metabolic profiles suggesting that pin-point sludge formation is not due to dispersal of intact flocs but to microcolonies growing separately. Alternatively, macroflocs may have an architecture leading to segregation of microbial communities after floc dispersal. Further it could be shown that the formation of microflocs was influenced by sludge age. The best sludge sedimentation was obtained for a sludge age of 5 and 10 days. Additional analysis of extracellular polymeric substances (EPS) suggested that the lower protein to carbohydrate ratio of 10-day-old sludge led to better flocculation compared to 20-day-old sludge containing similar total amounts of EPS. From a practical point of view, addition of potassium (0.1 g/l) effected a noticeable improvement of sludge settleability.

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Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly

10.21203/rs.3.rs-33130/v1 ◽

2020 ◽

Author(s):

Oskar Modin ◽

Raquel Liebana ◽

Soroush Saheb-Alam ◽

Britt-Marie Wilén ◽

Carolina Suarez ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Null Model ◽

Amplicon Sequencing ◽

Null Models ◽

Marker Genes ◽

Experimental Systems ◽

Microbial Community Assembly ◽

The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.

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Deciphering the Influence of Multiple Anthropogenic Inputs on Taxonomic and Functional Profiles of the Microbial Communities in Yitong River, Northeast China

10.21203/rs.3.rs-729563/v1 ◽

2021 ◽

Author(s):

Ying Zhang ◽

Yang Huo ◽

Zhiruo Zhang ◽

Suiyi Zhu ◽

Wei Fan ◽

...

Keyword(s):

Microbial Communities ◽

Northeast China ◽

Environmental Changes ◽

Quantitative Polymerase Chain Reaction ◽

Amplicon Sequencing ◽

Fecal Indicator ◽

16S Rrna Amplicon Sequencing ◽

Anthropogenic Inputs ◽

Wwtp Effluent ◽

The Impact

Abstract We conducted physicochemical parameters analysis, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nutrients were significantly declined at the reservoir outlet, and WWTP effluent discharge caused changes in the river microbial community. NH3-N and NO3--N were the main environmental factors that drive the shift of the bacteria community, and rare taxa played a more important role in the response to environmental changes compared with the abundant ones. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.

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Copper affects composition and functions of microbial communities in marine biofilms at environmentally relevant concentrations

10.7287/peerj.preprints.27129 ◽

2018 ◽

Author(s):

Natàlia Corcoll ◽

Jianghua Yang ◽

Thomas Backhaus ◽

Xiaowei Zhang ◽

Martin Karl Eriksson ◽

...

Keyword(s):

Community Structure ◽

Primary Production ◽

Microbial Communities ◽

Algal Biomass ◽

Amplicon Sequencing ◽

Quality Standard ◽

Aquatic Communities ◽

Static Test ◽

Community Function ◽

Eukaryotic Organisms

Cu pollution in coastal areas is a worldwide threat for aquatic communities. This study assesses the effects of Cu exposure on microbial diversity, community structure and functions of microbial communities in marine periphyton biofilms at environmental relevant concentrations. Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and primary production. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9504 and 1242 OTUs for 16S and 18S, respectively, reflecting the huge biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 10 nM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (60 nM), which is still in the range of the Cu concentrations observed in the area (80 nM).The current environmental quality standard for Cu of 70 nM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of primary production. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including species within Proteobacteria, Bacteroidetes, Stramenopiles and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic species, and therefore to identify particularly sensitive, non-cultivable species and taxa.

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Simulated mining-related sedimentation impacts on the deep-sea macrofauna of the Chatham Rise, New Zealand

10.26686/wgtn.15020097.v1 ◽

2021 ◽

Author(s):

Campbell Murray

Keyword(s):

Community Structure ◽

New Zealand ◽

Deep Sea ◽

Benthic Communities ◽

Sampling Period ◽

Mining Area ◽

Warning Sign ◽

Disturbed Areas ◽

One Year ◽

The Impact

<p>With the possibility of deep-sea mining of marine mineral resources occurring in the near future, it is necessary to understand the potential impacts that mining may have on benthic communities. Previous simulated mining experiments have observed direct impacts of deep-sea mining (e.g., faunal mortality); however, indirect impacts of sedimentation were not understood. In New Zealand, there has been interest in mining the seabed of the Chatham Rise, but mining consents have been refused, partly due to the uncertainties of sedimentation impacts on benthic communities. A disturbance experiment conducted in 2019 on the Rise used a modified agricultural plough designed to create a sediment cloud that could result from mining. This disturbance was used to assess the resilience of benthic communities to sedimentation in a proposed future mining area. Macrofaunal and sediment samples were collected with a multicorer before, immediately after and one year after disturbance to assess the impact on the community and its ability to recover. Samplingevents took place in disturbed (physically run over by the plough and subjected to sedimentation) and undisturbed areas (subjected to sedimentation only) at each sampling period. Macrofaunal abundance significantly decreased in disturbed areas after disturbancebut not in undisturbed areas. However, community structure changed in both areas after disturbance; in disturbed areas this was mostly driven by changes in numerically dominant fauna, but in undisturbed areas by the more sensitive fauna which may provide an early warning sign for further changes under increased sedimentation. One year after disturbance, community structure had recovered in both areas. Abundance-based community structure correlated most strongly with C:N molar ratios in the sediment which increased after disturbance. Ecosystem function was measured by sediment community oxygen consumption (SCOC) which increased similarly in both disturbed and undisturbed areas after disturbance; SCOC may be a more sensitive measure than community structure in assessing sedimentation impacts. No correlations were found between SCOC and macrofaunal abundance, biomass, diversity or bacterial abundance. The results of this research are useful for managing the impacts of industries where sedimentation is an issue, such as for bottom trawl fisheries and deep-sea mining. The results highlight the importance of leaving unmined patches of seabed adjacent to or within mined areas, to aid the recovery of macrofaunal communities subjected to mining disturbance.</p>

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Is the poor establishment and performance of heather beetle in Tongariro National Park due to the impact of parasitoids predators or disease

New Zealand Plant Protection ◽

10.30843/nzpp.2004.57.6977 ◽

2004 ◽

Vol 57 ◽

pp. 89-93 ◽

Cited By ~ 5

Author(s):

P.G. Peterson ◽

S.V. Fowler ◽

P. Barrett

Keyword(s):

New Zealand ◽

Natural Enemies ◽

National Park ◽

Calluna Vulgaris ◽

The United Kingdom ◽

Adverse Weather ◽

And Performance ◽

The Impact ◽

Cermatulus Nasalis ◽

Heather Beetle

Heather beetle (Lochmaea suturalis) introduced in 1996 into Tongariro National Park New Zealand to control heather (Calluna vulgaris) has established poorly and only damaged heather at one site This work investigated whether natural enemies could be reducing heather beetle establishment and impact No egg larval or adult parasitism was found Possible egg predation by a carabid beetle larvae and occasional attacks on larvae by the native pentatomid (Cermatulus nasalis) were observed in the field Neither the microsporidian pathogen discovered in some beetles imported from the United Kingdom nor any other pathogenic diseases were detected in fieldcollected beetles in New Zealand It is suggested that adverse weather was responsible for a collapse in heather beetle numbers at Te Piripiri during 2002 Further efforts to redistribute heather beetle and continued monitoring of beetle numbers impact natural enemies and climate at release sites are recommended

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